From 30e631d9527060c45d07c1f41aebf7794bf1c8bc Mon Sep 17 00:00:00 2001 From: q2d2 Date: Mon, 3 Jun 2024 22:09:01 +0000 Subject: [PATCH] Update Galaxy Tools --- .../qiime2__alignment__mafft.xml | 8 +- .../qiime2__alignment__mafft_add.xml | 8 +- .../qiime2__alignment__mask.xml | 8 +- .../qiime2__composition__add_pseudocount.xml | 8 +- .../qiime2__composition__ancom.xml | 8 +- .../qiime2__composition__ancombc.xml | 8 +- .../qiime2__composition__da_barplot.xml | 8 +- .../qiime2__composition__tabulate.xml | 8 +- .../test-data/ancombc.test0.table.qza | Bin 54454 -> 54454 bytes .../test-data/ancombc.test1.table.qza | Bin 54454 -> 54454 bytes .../qiime2__cutadapt__demux_paired.xml | 8 +- .../qiime2__cutadapt__demux_single.xml | 8 +- .../qiime2__cutadapt__trim_paired.xml | 8 +- .../qiime2__cutadapt__trim_single.xml | 8 +- .../test-data/demux_paired.test0.seqs.qza | Bin 3098177 -> 3098177 bytes .../test-data/demux_single.test0.seqs.qza | Bin 336160 -> 336160 bytes 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.../qiime2__longitudinal__volatility.xml | 8 +- .../qiime2__metadata__distance_matrix.xml | 8 +- .../qiime2__metadata__merge.xml | 8 +- .../qiime2__metadata__shuffle_groups.xml | 8 +- .../qiime2__metadata__tabulate.xml | 8 +- ...hylogeny__align_to_tree_mafft_fasttree.xml | 8 +- ..._phylogeny__align_to_tree_mafft_iqtree.xml | 8 +- ...__phylogeny__align_to_tree_mafft_raxml.xml | 8 +- .../qiime2__phylogeny__fasttree.xml | 8 +- .../qiime2__phylogeny__filter_table.xml | 12 +- .../qiime2__phylogeny__filter_tree.xml | 14 +- .../qiime2__phylogeny__iqtree.xml | 8 +- ..._phylogeny__iqtree_ultrafast_bootstrap.xml | 8 +- .../qiime2__phylogeny__midpoint_root.xml | 8 +- .../qiime2__phylogeny__raxml.xml | 8 +- ...ime2__phylogeny__raxml_rapid_bootstrap.xml | 8 +- .../qiime2__phylogeny__robinson_foulds.xml | 10 +- ..._to_tree_mafft_fasttree.test0.rep-seqs.qza | Bin 58051 -> 58051 bytes ...qiime2__quality_control__bowtie2_build.xml | 8 +- ...e2__quality_control__decontam_identify.xml | 12 +- 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+- ...me2__sample_classifier__fit_classifier.xml | 12 +- ...ime2__sample_classifier__fit_regressor.xml | 12 +- .../qiime2__sample_classifier__heatmap.xml | 12 +- .../qiime2__sample_classifier__metatable.xml | 12 +- ...ple_classifier__predict_classification.xml | 12 +- ..._sample_classifier__predict_regression.xml | 12 +- ...e2__sample_classifier__regress_samples.xml | 12 +- ...sample_classifier__regress_samples_ncv.xml | 12 +- ...qiime2__sample_classifier__scatterplot.xml | 8 +- ...qiime2__sample_classifier__split_table.xml | 18 +- .../qiime2__sample_classifier__summarize.xml | 10 +- .../qiime2__taxa__barplot.xml | 10 +- .../qiime2__taxa__collapse.xml | 8 +- .../qiime2__taxa__filter_seqs.xml | 8 +- .../qiime2__taxa__filter_table.xml | 13 +- .../test-data/barplot.test0.table.qza | Bin 43996 -> 43996 bytes .../test-data/barplot.test0.taxonomy.qza | Bin 105087 -> 105087 bytes .../test-data/collapse.test0.table.qza | Bin 43996 -> 43996 bytes .../test-data/collapse.test0.taxonomy.qza | Bin 105087 -> 105087 bytes ...rch__cluster_features_closed_reference.xml | 8 +- ...me2__vsearch__cluster_features_de_novo.xml | 8 +- ...earch__cluster_features_open_reference.xml | 8 +- ...qiime2__vsearch__dereplicate_sequences.xml | 8 +- .../qiime2__vsearch__fastq_stats.xml | 8 +- .../qiime2__vsearch__merge_pairs.xml | 8 +- .../qiime2__vsearch__uchime_denovo.xml | 8 +- .../qiime2__vsearch__uchime_ref.xml | 8 +- .../qiime2_core__tools__export.xml | 409 +++++++-- .../qiime2_core__tools__import.xml | 841 ++++++++++++++++-- .../qiime2_core__tools__import_fastq.xml | 8 +- 304 files changed, 2056 insertions(+), 1018 deletions(-) create mode 100644 tools/suite_qiime2__diversity/qiime2__diversity__filter_alpha_diversity.xml diff --git a/tools/suite_qiime2__alignment/qiime2__alignment__mafft.xml b/tools/suite_qiime2__alignment/qiime2__alignment__mafft.xml index 05ac56f..b16fc44 100644 --- a/tools/suite_qiime2__alignment/qiime2__alignment__mafft.xml +++ b/tools/suite_qiime2__alignment/qiime2__alignment__mafft.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + De novo multiple sequence alignment with MAFFT - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version alignment q2galaxy run alignment mafft '$inputs' diff --git a/tools/suite_qiime2__alignment/qiime2__alignment__mafft_add.xml b/tools/suite_qiime2__alignment/qiime2__alignment__mafft_add.xml index 66dc446..7010372 100644 --- a/tools/suite_qiime2__alignment/qiime2__alignment__mafft_add.xml +++ b/tools/suite_qiime2__alignment/qiime2__alignment__mafft_add.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Add sequences to multiple sequence alignment with MAFFT. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version alignment q2galaxy run alignment mafft_add '$inputs' diff --git a/tools/suite_qiime2__alignment/qiime2__alignment__mask.xml b/tools/suite_qiime2__alignment/qiime2__alignment__mask.xml index a83b098..91816ce 100644 --- a/tools/suite_qiime2__alignment/qiime2__alignment__mask.xml +++ b/tools/suite_qiime2__alignment/qiime2__alignment__mask.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Positional conservation and gap filtering. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version alignment q2galaxy run alignment mask '$inputs' diff --git a/tools/suite_qiime2__composition/qiime2__composition__add_pseudocount.xml b/tools/suite_qiime2__composition/qiime2__composition__add_pseudocount.xml index a204ec9..9f1c8b1 100644 --- a/tools/suite_qiime2__composition/qiime2__composition__add_pseudocount.xml +++ b/tools/suite_qiime2__composition/qiime2__composition__add_pseudocount.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Add pseudocount to table. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version composition q2galaxy run composition add_pseudocount '$inputs' diff --git a/tools/suite_qiime2__composition/qiime2__composition__ancom.xml b/tools/suite_qiime2__composition/qiime2__composition__ancom.xml index 46634bc..b0eff91 100644 --- a/tools/suite_qiime2__composition/qiime2__composition__ancom.xml +++ b/tools/suite_qiime2__composition/qiime2__composition__ancom.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Apply ANCOM to identify features that differ in abundance. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version composition q2galaxy run composition ancom '$inputs' diff --git a/tools/suite_qiime2__composition/qiime2__composition__ancombc.xml b/tools/suite_qiime2__composition/qiime2__composition__ancombc.xml index fcfa401..2100ac0 100644 --- a/tools/suite_qiime2__composition/qiime2__composition__ancombc.xml +++ b/tools/suite_qiime2__composition/qiime2__composition__ancombc.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Analysis of Composition of Microbiomes with Bias Correction - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version composition q2galaxy run composition ancombc '$inputs' diff --git a/tools/suite_qiime2__composition/qiime2__composition__da_barplot.xml b/tools/suite_qiime2__composition/qiime2__composition__da_barplot.xml index a1c832b..bcf9e31 100644 --- a/tools/suite_qiime2__composition/qiime2__composition__da_barplot.xml +++ b/tools/suite_qiime2__composition/qiime2__composition__da_barplot.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Differential abundance bar plots - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version composition q2galaxy run composition da_barplot '$inputs' diff --git a/tools/suite_qiime2__composition/qiime2__composition__tabulate.xml b/tools/suite_qiime2__composition/qiime2__composition__tabulate.xml index 45e08e0..85e05b5 100644 --- a/tools/suite_qiime2__composition/qiime2__composition__tabulate.xml +++ b/tools/suite_qiime2__composition/qiime2__composition__tabulate.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + View tabular output from ANCOM-BC. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version composition q2galaxy run composition tabulate '$inputs' diff --git a/tools/suite_qiime2__composition/test-data/ancombc.test0.table.qza b/tools/suite_qiime2__composition/test-data/ancombc.test0.table.qza index 67ddd33983d7995a5100432b2a1c68e63984c04c..b8feafcc5d1d860ef5b56c84511a62a564644ead 100644 GIT binary patch delta 603 zcmdnCl6l)oX5IjAW)=|!1_lm>V`~pjKE_nQ45TOWt^-jU_pvg8=*^bQe^@kccin9cFe7J22E>d9YrQ9* zKcG6<{eTr%W%l-eU_J~MJ7xoUIEfo4u=MkWzvxI-hZ?kW_~1Ug$Ch;=3_oH3g$ zc2-y(=(32diyux(1d1jAu@Ml%z>>z|$qJ`5CWoDoQ~;?f?{O^I!N|a1%Zjc}g>kat zDfP+Q&PaltrE@kNOf#O7p1kp_$>e}@5b>OI(o9!p1C<(0zCVXuC%_xkg~;x(g*gI9 zFKG;(1J+bEg?I9q^E_a)FP_T<)3?t{PmVdCJeh9=@8sBX5V<>-q?tah0cx?CeC~n; zSefH_X~ubzCtgUJy#GAJF`O6Y@PT}l{`2gmhinWC3wS4QzF0i@z$J(@$c&TwfMz64 zj=C%i_J8l=psnRV_cQ@<4vPEA_JbAP-i~k|{}t)U-Iuc_cb?+mNAu|9g3HoOrH6o8 OGA92%z&&}v6)^zvL-<7i delta 619 zcmdnCl6l)oX5IjAW)=|!1_lm>sk3KJY*@z(q&6EevNC}f6L|~3d`srP6F`i~33GNr z1g0!w7X%7KT-{YDq6yTl4#eh@C+;_%9B__(veq19urissb2-8KReOH7wvm9pRrRRY80g=bwRZ#@Sw zXMViSXFqlZhKm9W47M;sfb^2a7gK=d7)`F4!aMoQc^W4{0q{PW6mc}etQApa>w&PEz2iQJY+L@)_FUylG{L`%WI)Rs+059vQJL90I`7c z;vBGJdmjgFEeE=yiDB~Qi^Y>eE<+rf{`2gmhinWC3wRkAa!?!_zXNDq;^f=g5sn2} xb80_W_`oGdSO{E^p4@#oYx2)S+>>WsgjiW{S(=IU6i`{lV`~pjKE_nQ45TOWt^-jU_pvg8=*^bQe^@kccin9cFe7J22E>d9YrQ9* zKcG6<{eTr%W%l-eU_J~MJ7xoUIEfo4u=MkWzvxI-hZ?kW_~1Ug$Ch;=3_oH3g$ zc2-y(=(32diyux(1d1jAu@Ml%z>>z|$qJ`5CWoDoQ~;?f?{O^I!N|a1%Zjc}g>kat zDfP+Q&PaltrE@kNOf#O7p1kp_$>e}@5b>OI(o9!p1C<(0zCVXuC%_xkg~;x(g*gI9 zFKG;(1J+bEg?I9q^E_a)FP_T<)3?t{PmVdCJeh9=@8sBX5V<>-q?tah0cx?CeC~n; zSefH_X~ubzCtgUJy#GAJF`O6Y@PT}l{`2gmhinWC3wS4QzF0i@z$J(@$c&TwfMz64 zj=C%i_J8l=psnRV_cQ@<4vPEA_JbAP-i~k|{}t)U-Iuc_cb?+mNAu|9g3HoOrH6o8 OGA92%z&&}v6)^zvL-<7i delta 619 zcmdnCl6l)oX5IjAW)=|!1_lm>sk3KJY*@z(q&6EevNC}f6L|~3d`srP6F`i~33GNr z1g0!w7X%7KT-{YDq6yTl4#eh@C+;_%9B__(veq19urissb2-8KReOH7wvm9pRrRRY80g=bwRZ#@Sw zXMViSXFqlZhKm9W47M;sfb^2a7gK=d7)`F4!aMoQc^W4{0q{PW6mc}etQApa>w&PEz2iQJY+L@)_FUylG{L`%WI)Rs+059vQJL90I`7c z;vBGJdmjgFEeE=yiDB~Qi^Y>eE<+rf{`2gmhinWC3wRkAa!?!_zXNDq;^f=g5sn2} xb80_W_`oGdSO{E^p4@#oYx2)S+>>WsgjiW{S(=IU6i`{l - + Demultiplex paired-end sequence data with barcodes in-sequence. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version cutadapt q2galaxy run cutadapt demux_paired '$inputs' diff --git a/tools/suite_qiime2__cutadapt/qiime2__cutadapt__demux_single.xml b/tools/suite_qiime2__cutadapt/qiime2__cutadapt__demux_single.xml index 45b80c5..e5397b1 100644 --- a/tools/suite_qiime2__cutadapt/qiime2__cutadapt__demux_single.xml +++ b/tools/suite_qiime2__cutadapt/qiime2__cutadapt__demux_single.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Demultiplex single-end sequence data with barcodes in-sequence. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version cutadapt q2galaxy run cutadapt demux_single '$inputs' diff --git a/tools/suite_qiime2__cutadapt/qiime2__cutadapt__trim_paired.xml b/tools/suite_qiime2__cutadapt/qiime2__cutadapt__trim_paired.xml index 453f800..ec2f1ba 100644 --- a/tools/suite_qiime2__cutadapt/qiime2__cutadapt__trim_paired.xml +++ b/tools/suite_qiime2__cutadapt/qiime2__cutadapt__trim_paired.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Find and remove adapters in demultiplexed paired-end sequences. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version cutadapt q2galaxy run cutadapt trim_paired '$inputs' diff --git a/tools/suite_qiime2__cutadapt/qiime2__cutadapt__trim_single.xml b/tools/suite_qiime2__cutadapt/qiime2__cutadapt__trim_single.xml index 507b219..e858770 100644 --- a/tools/suite_qiime2__cutadapt/qiime2__cutadapt__trim_single.xml +++ b/tools/suite_qiime2__cutadapt/qiime2__cutadapt__trim_single.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Find and remove adapters in demultiplexed single-end sequences. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version cutadapt q2galaxy run cutadapt trim_single '$inputs' diff --git a/tools/suite_qiime2__cutadapt/test-data/demux_paired.test0.seqs.qza b/tools/suite_qiime2__cutadapt/test-data/demux_paired.test0.seqs.qza index 1247df5a4603df68d6fcd8b18ff29b43a00a1d85..81f07d2ce9fd686a93c1a278c4359db94a3bf5f2 100644 GIT binary patch delta 550 zcmZ9}J4ga?90%}wm}z>Y`6#opx96)LT3{9g<~f9cy0u45F2X_c(I8Y1w*1EkToM|h zhf{^PwY3ICR9iGP)ztTn4D8^;@5lXrkNb1Y{cFAnQXwar+#JVQxYyIxp->hPs?xb0 z&RUDS9(Posq6$3dQ3Mloff>5N0#@h&8`wdDUg!e{IH4b0;08}a6}%5?`hrR^?}Y&v z1Ro56ABJHBMj-%WFb)$i2~#i)GY|wBLJ)=sL?PBF=4W?b^i7SU1Ubx3Wa}ZRejLWd zWk^=7F6sqeekg%9WOJ#f$E_D&vH4|sW7^+ps$@hhFHOS{=sQMv`T z#oWf`b+;TfJgtU@fm>DZ!T|VS5d08;AsB`ra2SD62*DVPLl`13;WRwa*By63t5S-> zBuqgJra^-ln1wlrLjvYu0Ty8imSF{wkb*R1U=^~k=2S}S$M5bYv9Hsk+ckK|I1zGq% zH_dNmpC!eIL1B5rQ;~LMlQjEH&BCU(NgJYLQB2NGP14l!JPD>#PQ>%X#i!YS!jC(< P)#XeVWvd^*Sak3QFB_ZU diff --git a/tools/suite_qiime2__cutadapt/test-data/demux_single.test0.seqs.qza b/tools/suite_qiime2__cutadapt/test-data/demux_single.test0.seqs.qza index f2769d658340b79ecebd52fe2dfdda659ecb4f9c..97f8f1f4b60827f798b5d522b5363c6c135a7cc0 100644 GIT binary patch delta 269 zcmZ2*NMykw5#9iAW)=|!1_lm>M{5sHe$Lp$45TOWZUs>rkIFNG=;j=z_8cZgAO_LQ zK+Li|hly368zi|sk&jiL4aAz>EW+9gX3XPdJph&y7G=H00Tx;#$0|LYU5-_A`Ug2y zVX)8}SypMr*69;PST&{_$gxU-1$}_(m~0uR7x1yFPoDr2Ws_%31xw$Q2O85U&uTJV zLxELN0cdMP_nMa-)<7Rv0wXAec9l3<}cc~)uW p5I)xF7lc_2r{CuV`uCJPD-T%iCP=PK1T1GUU0(qzyi$R+8~|y - + Denoise and dereplicate single-end Pacbio CCS - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version dada2 q2galaxy run dada2 denoise_ccs '$inputs' diff --git a/tools/suite_qiime2__dada2/qiime2__dada2__denoise_paired.xml b/tools/suite_qiime2__dada2/qiime2__dada2__denoise_paired.xml index 80de97c..d430b85 100644 --- a/tools/suite_qiime2__dada2/qiime2__dada2__denoise_paired.xml +++ b/tools/suite_qiime2__dada2/qiime2__dada2__denoise_paired.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Denoise and dereplicate paired-end sequences - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version dada2 q2galaxy run dada2 denoise_paired '$inputs' diff --git a/tools/suite_qiime2__dada2/qiime2__dada2__denoise_pyro.xml b/tools/suite_qiime2__dada2/qiime2__dada2__denoise_pyro.xml index 2b2469c..0a72d90 100644 --- a/tools/suite_qiime2__dada2/qiime2__dada2__denoise_pyro.xml +++ b/tools/suite_qiime2__dada2/qiime2__dada2__denoise_pyro.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Denoise and dereplicate single-end pyrosequences - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version dada2 q2galaxy run dada2 denoise_pyro '$inputs' diff --git a/tools/suite_qiime2__dada2/qiime2__dada2__denoise_single.xml b/tools/suite_qiime2__dada2/qiime2__dada2__denoise_single.xml index 3ad9d72..a7786f5 100644 --- a/tools/suite_qiime2__dada2/qiime2__dada2__denoise_single.xml +++ b/tools/suite_qiime2__dada2/qiime2__dada2__denoise_single.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. 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(SPDX: BSD-3-Clause) --> - + Deblur sequences using a 16S positive filter. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version deblur q2galaxy run deblur denoise_16S '$inputs' @@ -23,9 +23,9 @@ for: - - + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[JoinedSequencesWithQuality]', 'SampleData[PairedEndSequencesWithQuality]', 'SampleData[SequencesWithQuality]'] diff --git a/tools/suite_qiime2__deblur/qiime2__deblur__denoise_other.xml b/tools/suite_qiime2__deblur/qiime2__deblur__denoise_other.xml index 7780b61..bb05c30 100644 --- a/tools/suite_qiime2__deblur/qiime2__deblur__denoise_other.xml +++ b/tools/suite_qiime2__deblur/qiime2__deblur__denoise_other.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Deblur sequences using a user-specified positive filter. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version deblur q2galaxy run deblur denoise_other '$inputs' @@ -23,9 +23,9 @@ for: - - + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[JoinedSequencesWithQuality]', 'SampleData[PairedEndSequencesWithQuality]', 'SampleData[SequencesWithQuality]'] diff --git a/tools/suite_qiime2__deblur/qiime2__deblur__visualize_stats.xml b/tools/suite_qiime2__deblur/qiime2__deblur__visualize_stats.xml index 3949820..4f4532d 100644 --- a/tools/suite_qiime2__deblur/qiime2__deblur__visualize_stats.xml +++ b/tools/suite_qiime2__deblur/qiime2__deblur__visualize_stats.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Visualize Deblur stats per sample. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version deblur q2galaxy run deblur visualize_stats '$inputs' diff --git a/tools/suite_qiime2__deblur/test-data/denoise_16S.test0.demux-filtered.qza b/tools/suite_qiime2__deblur/test-data/denoise_16S.test0.demux-filtered.qza index e7409b23c4635e1b95ca4b18cd68735ac88b4308..037ac0d636aa9f2115ff2a609922fd9ae2ad0fea 100644 GIT binary patch delta 2710 zcmZWq2~3nn6rP{G*o$3uVLTSXT7$cC7tmUGO4bSOhzLs3ID?Y3K~h`~iq)@*(t%~>zVTDlb29{znjx^ofzl|);{z(^ z;{)ot3=V86QluuKMd}q^65R)EHdvY54q+DQ299nRQ|6lKAe5~ zkhZ5c%!K@6W{U!)?>luyLzfvXCLfl5I)ZCW=f_@1L~yQVeEx?CghVEAa4b8&jP`f7 zs1=C`Xwfg)zorc}$7Aok`%z0s(RRK84SgOxrI~8ORMi8? z$eT8SoV1ClR$i@hUab?n!~|yrO6Si;s+}hczc+Ht(b_6FTU)(K=HjpYGxg5>Gkx{` z{1;n!#5fb-B@2x5Wb~Y_ex@^r5n>8+Wm_d39flZvtYKX>Vw@${Z3o*3VQm}}!y*f* zX_I-Jk_CRRR5(wLld->-o(-W#JGUG0ljn$ zr(L-BO(OlwDvdLtCg7mQ6}Q zt4mMyaLjyGP!qG*X(U@_^9f*Q3aJL8Z7HHAulAeVFq}PVmx@~hxTB`knh4+`#UP{J zMg!m7rC=9L4_fjd&s$JAK8=mUA&Mgd9o;E6WM zL>?FpfjvQK>_8^WlZ$&9b~+e+)D^>WTBBU_(N;_cA^q69q2y%*Ax}U&=@;Hc>_miZ zHK&wpyhq4#kR*>Ne%33*vb{d1?2A#LLH+5Q7djshav#Jq{WC9J2D4<|Zna#o65=!8 z_7=%5uB3x7?8_Cf9H>ytarAM(mW%p!;(Y z37G=oi9I~qg}wN;O2x~-U1cVoiKI}&yO46@MkLCtIfn;jKX@<=vKxK-a&s& z#J%L6TNwq{&&$V$Wv`_cmTspq_WBa^f3Jy_`QXcq%4V2@zo}TkDr#d+J-ipgYh2lX z>;RI3{+uM5)jBAScQ$VoH3=c?tb@kz_oW{m%^nBMMWu8d%*d!}8qXhCp^3c z2vt^2ID+pF!vkDIp6iO>G%7$Ac$|u}2O7+@lYlC3oh!C6wLo=za5q&j`>~e#Ydr_{ z!Sw)Y4s`>COs58xyP9gyvp(tb5WAd^W18NcJL0)fHd{F2o%lPFTw94$@y-)bvKl;Y z8zmz0;#?7qj>bvRs&w9<#ewGv(HvjKR+4Nf{Id%WNt_lb*Q*iH_0SsqD-ASiJOWJiOaH)O&BuAg4ucZJ!nhG$vb@KJKsI`ynD|Z zYF;_iyi%HJ75D`sgaXjL#)iF)ivoCbr1MNd#@Q>~%skw(e4#a!dY$XUJqsAmskF-6 zN~_#Vac5Jj!rj!Wv~Q3>EXQsC(Q>R0A<{>>9{IiIe)4kgtv(v*_*I({unwW;AFz=+ zm)x|DDj&3|D~!}zA0=Ksm+?COy(jOdkWPl3JnF4#7ly<$o-?SE=ML)Rj|5V@woTlW zLcOP1n((vKyEZC%_jl@jc_paz2rVE|RyMAWMkqX*DIkHkw_>gPoo;@7G$sC|5DhY}O<(p9sytUjP#R!unTWCq_O`N2np4<=l)=_oOo% z5*wjjODS>lC7C@d5W28}Qpko%9O8b7r@6g?;W=aa1KctFfn$+W*)S-s>7)5c7++oDb26yqKI!!>L4J#1SOHfL%1JEfnXA7>_`fl?}$!U=gX)?~{9wW4sV5nQSVyFV*g#x`cp4Qt4iN7WQFQb5^*u<~J@k~gR-TX*0s}QS|3^gh1liJ_lygUF~NVG+G?!FRipwfAzSjYc5gGq=X z$4aq*Y6pd*I7RjAq>wJhttJUmsn*XWc79|p(^+w!WGkAt6-QF8O|o>$>nRACz}6=QNxeFEFtKm=PAEdRzku(r$f&(u&#+qsLnqzqt5 zyoQBI83)gC!Z56?!U?3t$qmDNxYGO$3c}lsEv#j;qFIa(_1raMK=cu=e&^I^6yU^@T)5FeVu#Pf(Y9ZSje8ZI<_CxnLI zU_-WK2+8WW5M6wDJ{L-ZFU%Xeu!J6Mz20G3qe5uuY=k!ZY@vAp!!P&xgk|o+8on!= zf#R>q~24GbcQuBu@+a hY9REuU^2@{%u!f^Gp+uxK0>qM@0k{%fh`#R`yT`3bIJe! diff --git a/tools/suite_qiime2__deblur/test-data/visualize_stats.test0.deblur-stats.qza b/tools/suite_qiime2__deblur/test-data/visualize_stats.test0.deblur-stats.qza index 94e76afcfb2d515a729061c2b100cee26aa71f06..ca1cc925f3a3a6735b2b9daeb4fcc5864d203120 100644 GIT binary patch delta 827 zcmX@z!gRWYi8sKTnMH(wfq{cTeBI&6g3JZXKzbtYY!J0^butr(-rT~xff>wrz@Ewu zVodhnuLjfR?90Fs$M`LT!Hn;bSr8RruHKUk8dN90Z(yH%JJFaAs4Jp?;R}By(6T0m z$%%FjVCmiUypszfo56ZLOFuJmBROZYV3H}s)G)ihY+(DsTvvfjI#6kOy&Psz>g1!g zeP9!q-QEd-<*#0K*}R>Vf#E6_*ro|Js*~HRc{eAh9At%><2@N9I7Q0}%x6@-4>sVU zR;3UxBa;X-B1||dq$j78Yfkp90J~+fXSp@gby!+hS!RaJh#5VQkJ7dA*UC2CDR*q8_mZ-_H(>!q3a zw828V>m|W9bw(WU$zx<-_{zkYpkt>B57@k@%FchLF z=hp)&&zRiRC=Ry0pjMj6-4Q5cGkJln>g0E|5Wj*PgB+~oYm4y&tkyBkf=r2sGbZLR;+;pMShhu(-nm9+bT$K oFs=FO_*IaBq09{3f7?=^W>|`_0t1_YK@Dsm*eX$xI-|MBV~0zlC`NGl(%+mVX&o zz??mm9V{@PuNo|HjNd{SEbuV-J|9qJ#MP@Vo42zvFkI!D9Pj8b`9g#0}Us zS;6Y^w7h|WI+Ir?8-oovoKh*ojpUTcjGq6%5+RO%+2A_nd&CQZOxMt8)K3y(VDPhG zU?`l-7;8IuzN6~oJ@rDHTfB0FK*|?OYcqoNGb(36oSLV#3M?R_X9{-eW;vbDjM9uu zBFu3AM@&%I`pyp+8sR`}G&#K7Z1VGRNqLZsLCYC~#h4fvZnFVpfU+>Kq;Ve5evQfQ z6_Q|AdX`Hwu`o{-^irSPTMh}5Np778G5GOhXQ_*IaBq09^zuqX~W0#m3uS-DAM z@`ZXXu!aMbmeatSCMexw^ax;!xQ1c z_q5n2_f_+N-8E|wU*t+)GI|P1MktPFNdjvysC5P_?2I_zlgG%w@D-Q>icl2VltN9m W5@7}UkbyxI2!C@iFj#>?g#iG4l_zrm diff --git a/tools/suite_qiime2__demux/qiime2__demux__emp_paired.xml b/tools/suite_qiime2__demux/qiime2__demux__emp_paired.xml index c025575..426cfa0 100644 --- a/tools/suite_qiime2__demux/qiime2__demux__emp_paired.xml +++ b/tools/suite_qiime2__demux/qiime2__demux__emp_paired.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Demultiplex paired-end sequence data generated with the EMP protocol. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version demux q2galaxy run demux emp_paired '$inputs' diff --git a/tools/suite_qiime2__demux/qiime2__demux__emp_single.xml b/tools/suite_qiime2__demux/qiime2__demux__emp_single.xml index 25738ff..94dd33d 100644 --- a/tools/suite_qiime2__demux/qiime2__demux__emp_single.xml +++ b/tools/suite_qiime2__demux/qiime2__demux__emp_single.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Demultiplex sequence data generated with the EMP protocol. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version demux q2galaxy run demux emp_single '$inputs' diff --git a/tools/suite_qiime2__demux/qiime2__demux__filter_samples.xml b/tools/suite_qiime2__demux/qiime2__demux__filter_samples.xml index b185b9d..eaf1e67 100644 --- a/tools/suite_qiime2__demux/qiime2__demux__filter_samples.xml +++ b/tools/suite_qiime2__demux/qiime2__demux__filter_samples.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Filter samples out of demultiplexed data. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version demux q2galaxy run demux filter_samples '$inputs' @@ -23,8 +23,8 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[JoinedSequencesWithQuality]', 'SampleData[PairedEndSequencesWithQuality]', 'SampleData[SequencesWithQuality]'] diff --git a/tools/suite_qiime2__demux/qiime2__demux__partition_samples_paired.xml b/tools/suite_qiime2__demux/qiime2__demux__partition_samples_paired.xml index ea96520..d44939b 100644 --- a/tools/suite_qiime2__demux/qiime2__demux__partition_samples_paired.xml +++ b/tools/suite_qiime2__demux/qiime2__demux__partition_samples_paired.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Split demultiplexed sequence data into partitions. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version demux q2galaxy run demux partition_samples_paired '$inputs' diff --git a/tools/suite_qiime2__demux/qiime2__demux__partition_samples_single.xml b/tools/suite_qiime2__demux/qiime2__demux__partition_samples_single.xml index 4e70fab..3691fa9 100644 --- a/tools/suite_qiime2__demux/qiime2__demux__partition_samples_single.xml +++ b/tools/suite_qiime2__demux/qiime2__demux__partition_samples_single.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Split demultiplexed sequence data into partitions. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version demux q2galaxy run demux partition_samples_single '$inputs' diff --git a/tools/suite_qiime2__demux/qiime2__demux__subsample_paired.xml b/tools/suite_qiime2__demux/qiime2__demux__subsample_paired.xml index 40be768..512a9e8 100644 --- a/tools/suite_qiime2__demux/qiime2__demux__subsample_paired.xml +++ b/tools/suite_qiime2__demux/qiime2__demux__subsample_paired.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Subsample paired-end sequences without replacement. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version demux q2galaxy run demux subsample_paired '$inputs' diff --git a/tools/suite_qiime2__demux/qiime2__demux__subsample_single.xml b/tools/suite_qiime2__demux/qiime2__demux__subsample_single.xml index 464b8f3..f909954 100644 --- a/tools/suite_qiime2__demux/qiime2__demux__subsample_single.xml +++ b/tools/suite_qiime2__demux/qiime2__demux__subsample_single.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Subsample single-end sequences without replacement. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version demux q2galaxy run demux subsample_single '$inputs' @@ -23,8 +23,8 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[PairedEndSequencesWithQuality]', 'SampleData[SequencesWithQuality]'] diff --git a/tools/suite_qiime2__demux/qiime2__demux__summarize.xml b/tools/suite_qiime2__demux/qiime2__demux__summarize.xml index a25c4bb..e2a69c9 100644 --- a/tools/suite_qiime2__demux/qiime2__demux__summarize.xml +++ b/tools/suite_qiime2__demux/qiime2__demux__summarize.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Summarize counts per sample. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version demux q2galaxy run demux summarize '$inputs' @@ -23,8 +23,8 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[JoinedSequencesWithQuality]', 'SampleData[PairedEndSequencesWithQuality]', 'SampleData[SequencesWithQuality]'] diff --git a/tools/suite_qiime2__demux/qiime2__demux__tabulate_read_counts.xml b/tools/suite_qiime2__demux/qiime2__demux__tabulate_read_counts.xml index 7130f66..d4b88f1 100644 --- a/tools/suite_qiime2__demux/qiime2__demux__tabulate_read_counts.xml +++ b/tools/suite_qiime2__demux/qiime2__demux__tabulate_read_counts.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Tabulate counts per sample - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version demux q2galaxy run demux tabulate_read_counts '$inputs' @@ -23,8 +23,8 @@ for: - + diff --git a/tools/suite_qiime2__demux/test-data/emp_single.test0.sequences.qza b/tools/suite_qiime2__demux/test-data/emp_single.test0.sequences.qza index 06b40b855be20a633d6d004319d13322f7b2c4a1..ac8c541c1b87e7f2a926584c6b3a87aaa1031e1f 100644 GIT binary patch delta 378 zcmaFyL*>N}73lzPW)=|!1_llWgLQ`^G1QoD*(d8WnJ@$8 zC-N=@Q5&~fF@os!;D_wngCBC7b_4O6)0o=Rm>7W=L^A_13lOscG28YuCiYkNK#I0s z(clzd1F@z**W;`KGZZyAH-P2R^f?na!9tyuoYK>uSa52BtQQ6gowVSTW-NiYiPw@- z5-g|*RL3O4IGK@2eR?iT(ANs6`JW}H-t@kQ?1H)h-i%Bl%m_cKY6jh#e2<;s^IdiZ z8=ya7U`eC8C*yQRD^5?a(TdhUQ!ZL@noKXShT7Hx6k=A_N}72W`EW)=|!1_lm>53^@ZY+T9=q&90ZS}}qc6L||kRJ(~MBM>tIF*6Xe z05K~NvjH*tb`wvISNA}wn$wuJr!g^}b^~#yZ`R}70Ag%c)Zi3g0}Gkxan^u^()2kK zI0b={5e4rrxDMhd&8DYYa!SgB4qAdb{MWywC0p%zNH72HJn~x4Rz>8YtC{2xH)>> diff --git a/tools/suite_qiime2__demux/test-data/summarize.test0.demux.qza b/tools/suite_qiime2__demux/test-data/summarize.test0.demux.qza index c47e640904336afe070afb4c2ebd4b1beec2302c..60144548f4b82a12c00ebabab771cacc82239fad 100644 GIT binary patch delta 2472 zcmZ8i3s6*57(RCwc3Ie6mdm1W7uZ7?xMI+T@yrKgra{PK)GcJ%F~LMdQD-7oW?BK4 z1>_xvM*=big^Y$X%{5DL%f=aeB$cm9RLloyP5f7gLQzlaVU-&;tOxzzYYzX>3*$$?;gP`BoSPE*$q1Mu&1DkXKFwIo=U8zOE~z z`7yEE#tpn}JXn`U>=~<=f&yZX?d15_PD9Faq9qRd@`=N`eg)CSF6sEOOMYVsM1!0U z4>@&JmZ0&u$;yFET0FC4Ke9b)NdcfH1zq=J&Ac|=YcPeZ@jIkEUO{5@P7hx1^gQ(} z(S~}|{7{ePdyZ&nHh)K&P0y#<0@TFMU+`li(+Re~%FTj_1ZwDYc#W)T z%YyH-21cfr|9>nkCQaYIIrxyy#xfV#OJOW}uMGMdF}0;J_@Sm4+jn7k5zFLnzkNIM zv$C@hUkZbuuyXN_;q^tH0Ca1ouY8$7H{!e^8hsdzZ$_$w8(pn~2J}f8G$T_zoE0Vj ztxn7PC+0B#Ml4Gw`S7^k?kHeTaps+*AD73wk6S153VD?+3 zp43;e2Zj@zW3n^RyAv3&35yh`sZv4LMqJj3a2{7egY1KoDA@_0N2@uX;Hd%+R$vP4 zOcl+yHCajXCB?TnvG40L720RzqR}1aB>lR<%$y1U(y&PBPn=Q-^vkB;(;XPXp5aa5 zGn^ijnv`+5Q##x-n;iE*Y}JJlwf&HvU{*rO&Ka|{-WZ7 zYcPBCVJ-FL*FX~?p1MYuX*jvSm#$rCWkom{^%$qepc5LgbZS4Vmwvo#OC|vMSf&;5 z7FipGOm~fKg7&&^^5XS%+7HNkfmvBNr6dD;-i7MM!i@^?*7$_L(2oUAA zw-Nh7zX}n2k?3|K3?xUR>hp`irn3M9V3Af`j@RO|9gP;&xtqGD3`6KELn-x@GWX}P zv6Zd6{{{e~SfmgaKQbcwZg=AbgqvmdJtIx-Ndq*I=4=*vHYXm^ypB{sJ$d=Yni^C` z@C|s;8$D`*i&4*qFo+~9zF^}d-^8hf5Dh2b+t05Vl4~5@7aG505iu`7&Q|vw7tsvq z)4lbt^4OaS06I0OyBVe`a*XSBf}lG$k_WR?YyIUiclXKilKr!ClgY0_Mi2Q>tl zBFlXLgK75H;aAvs!QN XS6iT7?}?iRz&!kK2n1klDa6`;mMA6W delta 2416 zcmZWr3rv$&6uv)&R{DTaiWExeWjdgPwltuCP6XZDl*bBgNOV&dtxSfBi&=C68&Xy% zltNK1;6yP*7J~1XpD~q?X*5JOb+4E?pEGVlP0XfQn2Wpj{FPFLoc#Bm^PTTJ?!5<^ z26u2xR20@+QJ@+jGz~r6-Pu}mRzyF?7jvhB*rHXjnSC5_&R9OqsUKFc9Y3*7RWlD( z*`uPeGC-IHl)PymO#eX$MU<3xs#@;lBXldDWRL4Dync^9yZ~?oay4HdkGP?PU9(ln zH(O=rX28y(i{LG~>HlT09skvzQI#uTrHu?ex&c;W=Ymhy!|FSG@V^V#%2C~`;;VbZ z$4X(Bu_&6)Sfs5=hn?$;gm;~p)>s5S=^5C;!RmrdV!p>I`6Cl(Up*F*1ZCEh zg`Ox=F46+V=$1Q-ZUt|2hscFO2dlJ>!KxU3uu4~v1r2LF@l%Xp455fIXc&3w!8(5Y zq%L&~h^=Z>AJkAQmGDvt=U4;k<67nZEQoP1Es#H$7PR0kA)+mSH`+u>8=z*5>!0R9 zly~!NPf{lk(oYD-a7;HgxUTHh@GHBcO7g(9WV!PDLI5ny#uq^~l8Kd2 zJNaQgt^`$l4(fDaSAR#EtbHH0iguX69BAx#_@W;*zVQCWCi1P%247 zpg=WhmBvh(qTSSVX&{K?=pq(RY9F>R?H#e;Ft-&aLfjDD_VI!Z2)#z-O~1I-9EpHk z78&fz^Hk|@;fi{M@~HUZ0}o4BL^F|}5BBx%P(2NMHhr2vC94ytpc^U8)b!0KU^0=) zW*iS^CcZZGyEdIe0aW}u(RPdEG+-k+@+^7FAu?nr;*gArKQugA#+vpv1Zvtz1ND^4 zSq@3$$DLRWrGG8mTAiGMPy!YIQj#_THknvkumLDSos{C#0Z^OB3MWngbqi~?XGB4A zil;-Xfq2R!c`hyErBIfHiKN(rd_Br{P?oDdE1Ai6U=u9l`7o8xxvj@SeAla@k(wT_ z@|uPky=U3C=XP}eO97~gihn!iZx3fFn#hN4xi9W7t(2yqJA#?aB+-N8A${M3dcH3s zS0jZZ4rudYZ^pZaUN1suE*1Zf)_#qUx!Z*kp;<2aN<|Y-G{U2}V#hNf-2L#7K@=myfb_{=8$%QUTf2^JI4DY7%cY6h%GE2KVX`sEi zUgysUmI^4>dWvFkAsq{$s2hbZpuXKiXZb0L(zBr!Fz_hnQ5ZrW&qipoUv@5Xli+!b zIg>csu@s7_K!1mBqp%%R%KhMBHeVz&S=fQ2z~Q6Eb+d1a5!$PG-a)-?s>7Vz7jm!J y-~+&a7vyONEy=Xer#6$SP8F$44@m5j* diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__adonis.xml b/tools/suite_qiime2__diversity/qiime2__diversity__adonis.xml index 2165ab6..65a6469 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__adonis.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__adonis.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + adonis PERMANOVA test for beta group significance - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version diversity q2galaxy run diversity adonis '$inputs' diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__alpha.xml b/tools/suite_qiime2__diversity/qiime2__diversity__alpha.xml index dc9b0cd..810c3b2 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__alpha.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__alpha.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Alpha diversity - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version diversity q2galaxy run diversity alpha '$inputs' @@ -23,9 +23,9 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__alpha_correlation.xml b/tools/suite_qiime2__diversity/qiime2__diversity__alpha_correlation.xml index 662cdf5..0680929 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__alpha_correlation.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__alpha_correlation.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Alpha diversity correlation - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version diversity q2galaxy run diversity alpha_correlation '$inputs' diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__alpha_group_significance.xml b/tools/suite_qiime2__diversity/qiime2__diversity__alpha_group_significance.xml index b5b82ef..bbd7c2e 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__alpha_group_significance.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__alpha_group_significance.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Alpha diversity comparisons - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version diversity q2galaxy run diversity alpha_group_significance '$inputs' diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__alpha_phylogenetic.xml b/tools/suite_qiime2__diversity/qiime2__diversity__alpha_phylogenetic.xml index bf85d4a..1d18f29 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__alpha_phylogenetic.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__alpha_phylogenetic.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Alpha diversity (phylogenetic) - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version diversity q2galaxy run diversity alpha_phylogenetic '$inputs' @@ -23,9 +23,9 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__alpha_rarefaction.xml b/tools/suite_qiime2__diversity/qiime2__diversity__alpha_rarefaction.xml index 53affa2..b03e8bc 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__alpha_rarefaction.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__alpha_rarefaction.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Alpha rarefaction curves - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version diversity q2galaxy run diversity alpha_rarefaction '$inputs' diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__beta.xml b/tools/suite_qiime2__diversity/qiime2__diversity__beta.xml index 65fc824..16afc14 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__beta.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__beta.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Beta diversity - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version diversity q2galaxy run diversity beta '$inputs' @@ -23,13 +23,13 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] - + @@ -44,7 +44,6 @@ for: - diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__beta_correlation.xml b/tools/suite_qiime2__diversity/qiime2__diversity__beta_correlation.xml index e67c754..3bfcedb 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__beta_correlation.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__beta_correlation.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Beta diversity correlation - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version diversity q2galaxy run diversity beta_correlation '$inputs' @@ -52,12 +52,12 @@ for: - + - + diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__beta_group_significance.xml b/tools/suite_qiime2__diversity/qiime2__diversity__beta_group_significance.xml index 0637d78..0dd55ca 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__beta_group_significance.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__beta_group_significance.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Beta diversity group significance - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version diversity q2galaxy run diversity beta_group_significance '$inputs' diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__beta_phylogenetic.xml b/tools/suite_qiime2__diversity/qiime2__diversity__beta_phylogenetic.xml index 9795671..577823a 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__beta_phylogenetic.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__beta_phylogenetic.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Beta diversity (phylogenetic) - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version diversity q2galaxy run diversity beta_phylogenetic '$inputs' @@ -23,9 +23,9 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__beta_rarefaction.xml b/tools/suite_qiime2__diversity/qiime2__diversity__beta_rarefaction.xml index ccf1287..068889e 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__beta_rarefaction.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__beta_rarefaction.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Beta diversity rarefaction - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version diversity q2galaxy run diversity beta_rarefaction '$inputs' @@ -27,7 +27,7 @@ for: hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]'] - + @@ -43,7 +43,6 @@ for: - diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__bioenv.xml b/tools/suite_qiime2__diversity/qiime2__diversity__bioenv.xml index d333e9d..9043e47 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__bioenv.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__bioenv.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + bioenv - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version diversity q2galaxy run diversity bioenv '$inputs' diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__core_metrics.xml b/tools/suite_qiime2__diversity/qiime2__diversity__core_metrics.xml index 30c214a..3fc1e27 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__core_metrics.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__core_metrics.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Core diversity metrics (non-phylogenetic) - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version diversity q2galaxy run diversity core_metrics '$inputs' diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__core_metrics_phylogenetic.xml b/tools/suite_qiime2__diversity/qiime2__diversity__core_metrics_phylogenetic.xml index 0641a4f..8cfa229 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__core_metrics_phylogenetic.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__core_metrics_phylogenetic.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Core diversity metrics (phylogenetic and non-phylogenetic) - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version diversity q2galaxy run diversity core_metrics_phylogenetic '$inputs' diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__filter_alpha_diversity.xml b/tools/suite_qiime2__diversity/qiime2__diversity__filter_alpha_diversity.xml new file mode 100644 index 0000000..3d6659c --- /dev/null +++ b/tools/suite_qiime2__diversity/qiime2__diversity__filter_alpha_diversity.xml @@ -0,0 +1,91 @@ + + + + + Filter samples from an alpha diversity metric. + + quay.io/qiime2/amplicon:2024.5 + + q2galaxy version diversity + q2galaxy run diversity filter_alpha_diversity '$inputs' + + + + + + + + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[AlphaDiversity]'] + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + +
+ + + + + + +QIIME 2: diversity filter-alpha-diversity +========================================= +Filter samples from an alpha diversity metric. + + +Outputs: +-------- +:filtered_alpha_diversity.qza: <no description> + +| + +Description: +------------ +Filter samples from an alpha diversity metric, retaining samples with corresponding `metadata` (or retaining samples without metadata, if `exclude_ids` is True). See the filtering tutorial on https://docs.qiime2.org for additional details. + + +| + + + + 10.1038/s41587-019-0209-9 + + diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__filter_distance_matrix.xml b/tools/suite_qiime2__diversity/qiime2__diversity__filter_distance_matrix.xml index 0539864..43b61a8 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__filter_distance_matrix.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__filter_distance_matrix.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Filter samples from a distance matrix. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version diversity q2galaxy run diversity filter_distance_matrix '$inputs' diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__mantel.xml b/tools/suite_qiime2__diversity/qiime2__diversity__mantel.xml index e99c144..b94e89f 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__mantel.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__mantel.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Apply the Mantel test to two distance matrices - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version diversity q2galaxy run diversity mantel '$inputs' diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__partial_procrustes.xml b/tools/suite_qiime2__diversity/qiime2__diversity__partial_procrustes.xml index 6e3a45e..ff3289d 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__partial_procrustes.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__partial_procrustes.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Partial Procrustes - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version diversity q2galaxy run diversity partial_procrustes '$inputs' diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__pcoa.xml b/tools/suite_qiime2__diversity/qiime2__diversity__pcoa.xml index 02108b2..ba116af 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__pcoa.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__pcoa.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Principal Coordinate Analysis - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version diversity q2galaxy run diversity pcoa '$inputs' diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__pcoa_biplot.xml b/tools/suite_qiime2__diversity/qiime2__diversity__pcoa_biplot.xml index 3230732..d5e4215 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__pcoa_biplot.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__pcoa_biplot.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Principal Coordinate Analysis Biplot - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version diversity q2galaxy run diversity pcoa_biplot '$inputs' diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__procrustes_analysis.xml b/tools/suite_qiime2__diversity/qiime2__diversity__procrustes_analysis.xml index 92977eb..d768576 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__procrustes_analysis.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__procrustes_analysis.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Procrustes Analysis - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version diversity q2galaxy run diversity procrustes_analysis '$inputs' diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__tsne.xml b/tools/suite_qiime2__diversity/qiime2__diversity__tsne.xml index 28fd50d..5791e30 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__tsne.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__tsne.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + t-distributed stochastic neighbor embedding - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version diversity q2galaxy run diversity tsne '$inputs' diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__umap.xml b/tools/suite_qiime2__diversity/qiime2__diversity__umap.xml index 543068b..13fe94b 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__umap.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__umap.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Uniform Manifold Approximation and Projection - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version diversity q2galaxy run diversity umap '$inputs' diff --git a/tools/suite_qiime2__diversity/test-data/alpha_correlation.test0.alpha-div-faith-pd.qza b/tools/suite_qiime2__diversity/test-data/alpha_correlation.test0.alpha-div-faith-pd.qza index e305a13a512db427840dfcea2457168528c157fb..fc2d002d337f3752d1b2ef7aa9d8c9212fe22970 100644 GIT binary patch delta 1898 zcmZWpZA_b06uy^I+S2cjQJ_%3?B&CeC4kwKjR|bi5~5=&g1CfLoST6uU&c*GfT_P^ zlX9^)!;P7U(Wx`AMx~1*7=LJ{BNA7mon*l*2Hc#%bvpM0Jomi)geJ{rTa5H}{q#)#ZBO#@1ezK64tEt|n zq{|9H^Bq>2<;5c!V~U8dX5*{)J*K{ZjCb#ml5sI-oVMWN_p^VbB1OBgmO1^+xW4nr zbp-qTW-Bg^ElN?=P^j4;+zgoW|Je&x-GnWjtsDwT%)0opULgAy>^I)C5aMNYqzV9j z(@8D9YoYfo+PLa`YImNTw7B(Slr7r(E2;%sTU5B{zjRfuLzuhzy~KXJT#nkqmcY3d z&~8O-fKDUd6d1H3zTvwj^MHzwezWlAwNr_|nFg(z@OUvZgM<(*X2Hv4C|xtSfEoTh zu`KsxLw7LB9O{wyl#Qxb?-7|@*|mU$-kw-0S6T^q8w#!V+URFu|B@(U~p~J&9TV(SW3${i2_7RGIo4TV2;-E=3 zMRdj*J2mrlMbOFu_!sjr72U)~)YO_Id{%wcq}m7ZPWYF?Kk^&v@51p5s%S>8ASO&^ zgazNR{zB@Rz0X)zn;^=^)${2xh72sP zrj%EvQfw@Dh@itQPy#(BI6B^{q252Iuc~Jm&w%JOzK4H)-&0!jA{sRts|r@f!gp8>j=5|bauRf z-Z~66IjI%5$1daQ?Zvy1nIGBS?gXc4k3p~tE5@Q8G(*s}4_dL6FPq@DTrh{#ei2C9 zi!r3Z5|;eyM(A!mI2HFW(Q#&bguV^4AGAP@|Dr*OU$;;vB3Cj2X+9+A;(qg|9Pvd~ z^+thPj&P%^#EzR0pcIcEQ)#jQxY8Hd!TJK0Sbh350ACp9OEy};`aC7E8N=gz{bU4L z&m}vxs>Mtf4cyzs%~qP0RB|c`GykAGa;UjQoO;%16y<(<_&Dp%56nFd56};$)y>JC z5Og_&p@I0`3u!hbHdN10W)x!S#8EA={ ze{P8DEZxsN4(Pk delta 1848 zcmZuxZA@EL7(R!#w1wW5+m;n5En?^@!WJoW2!UmwnM`ymWGv{+3SsyWhyo)K#Du~h zP1KEYHcmi3Tx5xJ8o)*!iv#@ON8-R}zz+gZ|2W2Qj=+96$nd@Iy)9po-1PE1&w0-K zKIgrsb5z|qsusLODz%jmq9ZXqT><~6D)rlsUJE=L?d3RZi-c&V9p1%2i#$!`1o|Hg^ z;Lzk(8}4IMvU@^xoiW2q$d~9I9Gt0_8xVdzhP^X)?JRawT9q7ywKctZ8G*>UN-ehN zJF_-d0WFqei|Zr3NIyJ0qeXq7=jo2CDeSe89K`#t1}uml=$%KP`J6?k2tPs~weP+e zjeptezi|qT>m}n3kBj}}kz@XD_kvstBnl|lxU@YHO{ zBC#CR?^n4Puayr7S3L5TxZVw;b|iNDiq+5x4{wiAHtvssjgzWFR@@;fc}$2vOl%NE zX6i)$@W;5LqRi8L$wn*qUvWwfIX3WcHXzEnhvi|xDZ+$Sn`P zXiJ|Tz9GB%npq%fCrFk0# z1^Tw!jTYz};Ixn`;3Rdmk^l8?ZfoYhKnc2qe zI~<>qnb8(4f7_x|dZ5?3riR>)?#Nv=Ey-Ijt?Nc`?wp5Wa;5urTa5H}{q#)#ZBO#@1ezK64tEt|n zq{|9H^Bq>2<;5c!V~U8dX5*{)J*K{ZjCb#ml5sI-oVMWN_p^VbB1OBgmO1^+xW4nr zbp-qTW-Bg^ElN?=P^j4;+zgoW|Je&x-GnWjtsDwT%)0opULgAy>^I)C5aMNYqzV9j z(@8D9YoYfo+PLa`YImNTw7B(Slr7r(E2;%sTU5B{zjRfuLzuhzy~KXJT#nkqmcY3d z&~8O-fKDUd6d1H3zTvwj^MHzwezWlAwNr_|nFg(z@OUvZgM<(*X2Hv4C|xtSfEoTh zu`KsxLw7LB9O{wyl#Qxb?-7|@*|mU$-kw-0S6T^q8w#!V+URFu|B@(U~p~J&9TV(SW3${i2_7RGIo4TV2;-E=3 zMRdj*J2mrlMbOFu_!sjr72U)~)YO_Id{%wcq}m7ZPWYF?Kk^&v@51p5s%S>8ASO&^ zgazNR{zB@Rz0X)zn;^=^)${2xh72sP zrj%EvQfw@Dh@itQPy#(BI6B^{q252Iuc~Jm&w%JOzK4H)-&0!jA{sRts|r@f!gp8>j=5|bauRf z-Z~66IjI%5$1daQ?Zvy1nIGBS?gXc4k3p~tE5@Q8G(*s}4_dL6FPq@DTrh{#ei2C9 zi!r3Z5|;eyM(A!mI2HFW(Q#&bguV^4AGAP@|Dr*OU$;;vB3Cj2X+9+A;(qg|9Pvd~ z^+thPj&P%^#EzR0pcIcEQ)#jQxY8Hd!TJK0Sbh350ACp9OEy};`aC7E8N=gz{bU4L z&m}vxs>Mtf4cyzs%~qP0RB|c`GykAGa;UjQoO;%16y<(<_&Dp%56nFd56};$)y>JC z5Og_&p@I0`3u!hbHdN10W)x!S#8EA={ ze{P8DEZxsN4(Pk delta 1848 zcmZuxZA@EL7(R!#w1wW5+m;n5En?^@!WJoW2!UmwnM`ymWGv{+3SsyWhyo)K#Du~h zP1KEYHcmi3Tx5xJ8o)*!iv#@ON8-R}zz+gZ|2W2Qj=+96$nd@Iy)9po-1PE1&w0-K zKIgrsb5z|qsusLODz%jmq9ZXqT><~6D)rlsUJE=L?d3RZi-c&V9p1%2i#$!`1o|Hg^ z;Lzk(8}4IMvU@^xoiW2q$d~9I9Gt0_8xVdzhP^X)?JRawT9q7ywKctZ8G*>UN-ehN zJF_-d0WFqei|Zr3NIyJ0qeXq7=jo2CDeSe89K`#t1}uml=$%KP`J6?k2tPs~weP+e zjeptezi|qT>m}n3kBj}}kz@XD_kvstBnl|lxU@YHO{ zBC#CR?^n4Puayr7S3L5TxZVw;b|iNDiq+5x4{wiAHtvssjgzWFR@@;fc}$2vOl%NE zX6i)$@W;5LqRi8L$wn*qUvWwfIX3WcHXzEnhvi|xDZ+$Sn`P zXiJ|Tz9GB%npq%fCrFk0# z1^Tw!jTYz};Ixn`;3Rdmk^l8?ZfoYhKnc2qe zI~<>qnb8(4f7_x|dZ5?3riR>)?#Nv=Ey-Ijt?Nc`?wp5Wa;5u - + Alpha Passthrough (non-phylogenetic) - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version diversity_lib q2galaxy run diversity_lib alpha_passthrough '$inputs' diff --git a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__beta_passthrough.xml b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__beta_passthrough.xml index 5c86faf..19798e4 100644 --- a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__beta_passthrough.xml +++ b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__beta_passthrough.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Beta Passthrough (non-phylogenetic) - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version diversity_lib q2galaxy run diversity_lib beta_passthrough '$inputs' @@ -27,7 +27,7 @@ for: hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]'] - + @@ -40,7 +40,6 @@ for: - @@ -73,7 +72,7 @@ for: - + @@ -148,7 +147,7 @@ to run on n cores, replace 1 here with your preferred integer ************************************************************* Using the ``qiime2 diversity-lib beta-passthrough`` tool: #. Set *"table"* to ``#: feature-table.qza`` - #. Set *"metric"* to ``kulsinski`` + #. Set *"metric"* to ``euclidean`` #. Press the ``Execute`` button. Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: @@ -161,7 +160,7 @@ Once completed, for the new entry in your history, use the ``Edit`` button to se * - History Name - *"Name"* to set (be sure to press ``Save``) * - ``#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza`` - - ``kulsinski-dm.qza`` + - ``euclidean-dm.qza`` use 'auto' to run on all of host system's available CPU cores ************************************************************* diff --git a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__beta_phylogenetic_meta_passthrough.xml b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__beta_phylogenetic_meta_passthrough.xml index 80a97aa..d02503c 100644 --- a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__beta_phylogenetic_meta_passthrough.xml +++ b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__beta_phylogenetic_meta_passthrough.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Beta Phylogenetic Meta Passthrough - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version diversity_lib q2galaxy run diversity_lib beta_phylogenetic_meta_passthrough '$inputs' diff --git a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__beta_phylogenetic_passthrough.xml b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__beta_phylogenetic_passthrough.xml index 944298c..5e997af 100644 --- a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__beta_phylogenetic_passthrough.xml +++ b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__beta_phylogenetic_passthrough.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Beta Phylogenetic Passthrough - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version diversity_lib q2galaxy run diversity_lib beta_phylogenetic_passthrough '$inputs' diff --git a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__bray_curtis.xml b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__bray_curtis.xml index ab98912..c2263e7 100644 --- a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__bray_curtis.xml +++ b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__bray_curtis.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Bray-Curtis Dissimilarity - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version diversity_lib q2galaxy run diversity_lib bray_curtis '$inputs' diff --git a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__faith_pd.xml b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__faith_pd.xml index 8f044d8..7ed8997 100644 --- a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__faith_pd.xml +++ b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__faith_pd.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Faith's Phylogenetic Diversity - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version diversity_lib q2galaxy run diversity_lib faith_pd '$inputs' @@ -24,8 +24,8 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__jaccard.xml b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__jaccard.xml index 752bc6f..1612a95 100644 --- a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__jaccard.xml +++ b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__jaccard.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Jaccard Distance - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version diversity_lib q2galaxy run diversity_lib jaccard '$inputs' @@ -24,8 +24,8 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__observed_features.xml b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__observed_features.xml index bd6df05..bdea044 100644 --- a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__observed_features.xml +++ b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__observed_features.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Observed Features - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version diversity_lib q2galaxy run diversity_lib observed_features '$inputs' @@ -24,8 +24,8 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__pielou_evenness.xml b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__pielou_evenness.xml index 5f750eb..310ba7d 100644 --- a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__pielou_evenness.xml +++ b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__pielou_evenness.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Pielou's Evenness - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version diversity_lib q2galaxy run diversity_lib pielou_evenness '$inputs' diff --git a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__shannon_entropy.xml b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__shannon_entropy.xml index fcc5e06..de8973c 100644 --- a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__shannon_entropy.xml +++ b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__shannon_entropy.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Shannon's Entropy - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version diversity_lib q2galaxy run diversity_lib shannon_entropy '$inputs' diff --git a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__unweighted_unifrac.xml b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__unweighted_unifrac.xml index 925e3c6..422ca0a 100644 --- a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__unweighted_unifrac.xml +++ b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__unweighted_unifrac.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Unweighted Unifrac - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version diversity_lib q2galaxy run diversity_lib unweighted_unifrac '$inputs' @@ -24,8 +24,8 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__weighted_unifrac.xml b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__weighted_unifrac.xml index ec1eac6..1ce3800 100644 --- a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__weighted_unifrac.xml +++ b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__weighted_unifrac.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Weighted Unifrac - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version diversity_lib q2galaxy run diversity_lib weighted_unifrac '$inputs' diff --git a/tools/suite_qiime2__diversity_lib/test-data/alpha_passthrough.test0.feature-table.qza b/tools/suite_qiime2__diversity_lib/test-data/alpha_passthrough.test0.feature-table.qza index ab7975841a5daeda73e34161877aa2539c20387c..8bfad11c1f16f764f375f320530faea2a0a9cb97 100644 GIT binary patch literal 7712 zcmc(E1x#IEw*JN4X=$Nc+}(;pap&Stw79!optuxoak;n_xwva_*W&K9Sn=YI&b-O| ze|?#MI+K^Yo$Q>PoORZ>_S!31@+rx|!Q%q}0AxTsv`dR^IMj^p>5b-TGd^t-R(3;E zGahy(4sKo}CQf5xUM3?BUK1u(HeS}(tfm}nCR|)B8WJk1G9X2?^Ye38b=D18M%mGR zM!8xQ)=gOk*E+U$P{X>00YXkzGM z$P6~LwL$pOjOs^<4;WuA|A7=#ayiK+YVje_A`Fp)8`(1)^ZxzrRtu5>9CCyXMRI9^ zaqv|*?`K#zXcla|Ks=SqYG5j14V@IEl;433XEieEQKM@4q()|{jwJN0!``LEsJPEx z4Gsog`A$6<>I?I47;J1|YHaQ7YU|8wYr+*3BdFN*20Pd*(}?8_d-ckECY;hZJPPH_ 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a/tools/suite_qiime2__emperor/qiime2__emperor__biplot.xml +++ b/tools/suite_qiime2__emperor/qiime2__emperor__biplot.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Visualize and Interact with Principal Coordinates Analysis Biplot - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version emperor q2galaxy run emperor biplot '$inputs' diff --git a/tools/suite_qiime2__emperor/qiime2__emperor__plot.xml b/tools/suite_qiime2__emperor/qiime2__emperor__plot.xml index 3d2bcfd..b205021 100644 --- a/tools/suite_qiime2__emperor/qiime2__emperor__plot.xml +++ b/tools/suite_qiime2__emperor/qiime2__emperor__plot.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Visualize and Interact with Principal Coordinates Analysis Plots - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version emperor q2galaxy run emperor plot '$inputs' diff --git a/tools/suite_qiime2__emperor/qiime2__emperor__procrustes_plot.xml b/tools/suite_qiime2__emperor/qiime2__emperor__procrustes_plot.xml index b9a2728..dbec522 100644 --- a/tools/suite_qiime2__emperor/qiime2__emperor__procrustes_plot.xml +++ b/tools/suite_qiime2__emperor/qiime2__emperor__procrustes_plot.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. 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b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__blast.xml index a29e0da..345355e 100644 --- a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__blast.xml +++ b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__blast.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + BLAST+ local alignment search. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version feature_classifier q2galaxy run feature_classifier blast '$inputs' diff --git a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_consensus_blast.xml b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_consensus_blast.xml index fde3d90..da94003 100644 --- a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_consensus_blast.xml +++ b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_consensus_blast.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + BLAST+ consensus taxonomy classifier - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version feature_classifier q2galaxy run feature_classifier classify_consensus_blast '$inputs' diff --git a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_consensus_vsearch.xml b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_consensus_vsearch.xml index c8bcec5..eb3df71 100644 --- a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_consensus_vsearch.xml +++ b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_consensus_vsearch.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + VSEARCH-based consensus taxonomy classifier - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version feature_classifier q2galaxy run feature_classifier classify_consensus_vsearch '$inputs' diff --git a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_hybrid_vsearch_sklearn.xml b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_hybrid_vsearch_sklearn.xml index fb554cb..de721ae 100644 --- a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_hybrid_vsearch_sklearn.xml +++ b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_hybrid_vsearch_sklearn.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + ALPHA Hybrid classifier: VSEARCH exact match + sklearn classifier - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version feature_classifier q2galaxy run feature_classifier classify_hybrid_vsearch_sklearn '$inputs' diff --git a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_sklearn.xml b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_sklearn.xml index fc27dd1..0be630c 100644 --- a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_sklearn.xml +++ b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_sklearn.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Pre-fitted sklearn-based taxonomy classifier - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version feature_classifier q2galaxy run feature_classifier classify_sklearn '$inputs' diff --git a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__extract_reads.xml b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__extract_reads.xml index 339c574..3b42829 100644 --- a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__extract_reads.xml +++ b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__extract_reads.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Extract reads from reference sequences. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version feature_classifier q2galaxy run feature_classifier extract_reads '$inputs' diff --git a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__find_consensus_annotation.xml b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__find_consensus_annotation.xml index 68ad12d..f7ba608 100644 --- a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__find_consensus_annotation.xml +++ b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__find_consensus_annotation.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Find consensus among multiple annotations. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version feature_classifier q2galaxy run feature_classifier find_consensus_annotation '$inputs' diff --git a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__fit_classifier_naive_bayes.xml b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__fit_classifier_naive_bayes.xml index 485c4d4..512fdd3 100644 --- a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__fit_classifier_naive_bayes.xml +++ b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__fit_classifier_naive_bayes.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Train the naive_bayes classifier - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version feature_classifier q2galaxy run feature_classifier fit_classifier_naive_bayes '$inputs' diff --git a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__fit_classifier_sklearn.xml b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__fit_classifier_sklearn.xml index 33d778d..24bdd23 100644 --- a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__fit_classifier_sklearn.xml +++ b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__fit_classifier_sklearn.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Train an almost arbitrary scikit-learn classifier - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version feature_classifier q2galaxy run feature_classifier fit_classifier_sklearn '$inputs' diff --git a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__makeblastdb.xml b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__makeblastdb.xml index f0edba3..6baad1b 100644 --- a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__makeblastdb.xml +++ b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__makeblastdb.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Make BLAST database. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version feature_classifier q2galaxy run feature_classifier makeblastdb '$inputs' diff --git a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__vsearch_global.xml b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__vsearch_global.xml index f0d769a..b389d34 100644 --- a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__vsearch_global.xml +++ b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__vsearch_global.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + VSEARCH global alignment search - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version feature_classifier q2galaxy run feature_classifier vsearch_global '$inputs' diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__core_features.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__core_features.xml index 45e2577..200afcf 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__core_features.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__core_features.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Identify core features in table - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version feature_table q2galaxy run feature_table core_features '$inputs' diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_features.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_features.xml index 0246f86..30b1edf 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_features.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_features.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Filter features from table - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version feature_table q2galaxy run feature_table filter_features '$inputs' diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_features_conditionally.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_features_conditionally.xml index d4416f6..e5579b1 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_features_conditionally.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_features_conditionally.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Filter features from a table based on abundance and prevalence - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version feature_table q2galaxy run feature_table filter_features_conditionally '$inputs' @@ -24,9 +24,9 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_samples.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_samples.xml index f98844f..586f571 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_samples.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_samples.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Filter samples from table - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version feature_table q2galaxy run feature_table filter_samples '$inputs' @@ -24,9 +24,9 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_seqs.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_seqs.xml index 4bbbeb9..2395407 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_seqs.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_seqs.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Filter features from sequences - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version feature_table q2galaxy run feature_table filter_seqs '$inputs' @@ -23,8 +23,8 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[AlignedSequence]', 'FeatureData[Sequence]'] diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__group.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__group.xml index bdcf97e..e7db53c 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__group.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__group.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Group samples or features by a metadata column - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version feature_table q2galaxy run feature_table group '$inputs' diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__heatmap.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__heatmap.xml index 264b7f1..d991356 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__heatmap.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__heatmap.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Generate a heatmap representation of a feature table - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version feature_table q2galaxy run feature_table heatmap '$inputs' diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__merge.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__merge.xml index 054bb9a..37476b7 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__merge.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__merge.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Combine multiple tables - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version feature_table q2galaxy run feature_table merge '$inputs' diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__merge_seqs.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__merge_seqs.xml index 81514ca..0d2933b 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__merge_seqs.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__merge_seqs.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Combine collections of feature sequences - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version feature_table q2galaxy run feature_table merge_seqs '$inputs' diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__merge_taxa.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__merge_taxa.xml index a6e3609..6180bae 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__merge_taxa.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__merge_taxa.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Combine collections of feature taxonomies - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version feature_table q2galaxy run feature_table merge_taxa '$inputs' diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__presence_absence.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__presence_absence.xml index 81d7f09..033a85d 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__presence_absence.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__presence_absence.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Convert to presence/absence - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version feature_table q2galaxy run feature_table presence_absence '$inputs' diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__rarefy.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__rarefy.xml index 171217d..97cc068 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__rarefy.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__rarefy.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Rarefy table - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version feature_table q2galaxy run feature_table rarefy '$inputs' diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__relative_frequency.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__relative_frequency.xml index 3f3e65f..c5ae1af 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__relative_frequency.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__relative_frequency.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Convert to relative frequencies - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version feature_table q2galaxy run feature_table relative_frequency '$inputs' diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__rename_ids.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__rename_ids.xml index 8b92b51..c4492a1 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__rename_ids.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__rename_ids.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Renames sample or feature ids in a table - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version feature_table q2galaxy run feature_table rename_ids '$inputs' @@ -24,9 +24,9 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__split.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__split.xml index 6f1478c..237046b 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__split.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__split.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Split one feature table into many - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version feature_table q2galaxy run feature_table split '$inputs' @@ -24,9 +24,9 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__subsample_ids.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__subsample_ids.xml index be74b43..ebbc4a9 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__subsample_ids.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__subsample_ids.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Subsample table - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version feature_table q2galaxy run feature_table subsample_ids '$inputs' diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__summarize.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__summarize.xml index c3ead22..bbec807 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__summarize.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__summarize.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Summarize table - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version feature_table q2galaxy run feature_table summarize '$inputs' @@ -23,8 +23,8 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]'] diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__summarize_plus.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__summarize_plus.xml index 54f8ac2..ba84ae7 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__summarize_plus.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__summarize_plus.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Summarize table plus - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version feature_table q2galaxy run feature_table summarize_plus '$inputs' @@ -23,8 +23,8 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]'] diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__tabulate_feature_frequencies.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__tabulate_feature_frequencies.xml index 6e1b8ff..edd0a2d 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__tabulate_feature_frequencies.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__tabulate_feature_frequencies.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Tabulate feature frequencies - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version feature_table q2galaxy run feature_table tabulate_feature_frequencies '$inputs' @@ -23,9 +23,9 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__tabulate_sample_frequencies.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__tabulate_sample_frequencies.xml index e7fb6ad..6952847 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__tabulate_sample_frequencies.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__tabulate_sample_frequencies.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Tabulate sample frequencies - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version feature_table q2galaxy run feature_table tabulate_sample_frequencies '$inputs' @@ -23,9 +23,9 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__tabulate_seqs.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__tabulate_seqs.xml index 823158a..a9b200a 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__tabulate_seqs.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__tabulate_seqs.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + View sequence associated with each feature - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version feature_table q2galaxy run feature_table tabulate_seqs '$inputs' @@ -23,8 +23,8 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[AlignedSequence]', 'FeatureData[Sequence]'] diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__transpose.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__transpose.xml index 8fe3e43..af6a5d1 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__transpose.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__transpose.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Transpose a feature table. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version feature_table q2galaxy run feature_table transpose '$inputs' @@ -24,9 +24,9 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__feature_table/test-data/filter_features.test0.feature-table.qza b/tools/suite_qiime2__feature_table/test-data/filter_features.test0.feature-table.qza index b8f69089bb34e7328c30f349b6d30e01ef774bf8..fe7827ad3a56d5ceb8461c6f148e661b009f95c0 100644 GIT binary patch delta 433 zcmccefa%HuCf)#VW)=|!1_llW#`T9M?$2cgQM~Ix)MkA~y?zj5vh2hPFr6@A7g%D( z#4a|l!0iRg!Sv1f|G^Spm#<~yMlx`7>%v@^N}tJpXR1stpJ@)(p*rI}SjWbhvTVGJ zOd`y1M@;5lB|Z7nO3lf^tAxQy*RPajESS81rpDyYD<#1qnXA&lwB2gy$?sN~Opcq# 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100644 GIT binary patch delta 688 zcmX?nl=<*cX5IjAW)=|!1_llW#`T9MpJggw2GSFGH-M;(2e_C(^kxU<$4z`dM#L%~ z-;xM628JS@$%bualVk7jZZ>L9Vgo6fJiWIXOslo+25S=Sixmbl&g{uz2g_I8N0&Hgd4gJaK z4BTmV0<7J3Qb4n=SK5nyGaaRLY4zz#BCnY9C57 zHLrn61EcLI_hkFKJYX+ez3Q@gJ1YajRW5X^cJGI3-~z?KE=GDeg0Z$WHA#1{iYA&RHEkHa-gSZOX6;LQq5Vhjv|Ksb+sfr0-P Ghz9^frUY~V delta 706 zcmX?nl=<*cX5IjAW)=|!1_lm>#dBs(Y}mjIq&6EfaxsAz6L|~3dJa2{I)7MO9oQivPLuEqT;8To)_MihN( zHG9m)z%ZY8^1)*cn-46MX9t_adCYtAfrY9Qovpz7C#*3Q76hs9j5y$v$H>6&m5G6& zXtE=t#^eL{tR}5xpFI0M&t}op1&q>+Od`y1KSi)Dxuuf~^kFs-8%@@^Wj1-wElGKh zN$>mg^!5TxvSS6x0A*odN#kaqxu%mfZ}Wg%B6mxg=>XH@k1NzCC*6X0)8cjp*zpL% zC$GEhGI>TX@8t7$coaaUuk!INi2(Ymh=+l}7G^Y%Ueb8I4QQ6pf}RrB*9i(z3Q@gJJ9i0xfmF7 zP^|D;1T@PAsMrqdgZB@lnYvd%g;Xc!K7?2y`$(F}VkKO7_9GEql(3szb5ELS&u*ZC z#L53xg1rVd&hM@?)BZhR;WKw7;Wp?T0SaYI&bEWn!;7?2DMf - + Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version fragment_insertion q2galaxy run fragment_insertion classify_otus_experimental '$inputs' diff --git a/tools/suite_qiime2__fragment_insertion/qiime2__fragment_insertion__filter_features.xml b/tools/suite_qiime2__fragment_insertion/qiime2__fragment_insertion__filter_features.xml index 39552b1..fdd6c4f 100644 --- a/tools/suite_qiime2__fragment_insertion/qiime2__fragment_insertion__filter_features.xml +++ b/tools/suite_qiime2__fragment_insertion/qiime2__fragment_insertion__filter_features.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Filter fragments in tree from table. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version fragment_insertion q2galaxy run fragment_insertion filter_features '$inputs' diff --git a/tools/suite_qiime2__fragment_insertion/qiime2__fragment_insertion__sepp.xml b/tools/suite_qiime2__fragment_insertion/qiime2__fragment_insertion__sepp.xml index 157b9de..305b00c 100644 --- a/tools/suite_qiime2__fragment_insertion/qiime2__fragment_insertion__sepp.xml +++ b/tools/suite_qiime2__fragment_insertion/qiime2__fragment_insertion__sepp.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Insert fragment sequences using SEPP into reference phylogenies. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version fragment_insertion q2galaxy run fragment_insertion sepp '$inputs' diff --git a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__anova.xml b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__anova.xml index a0504ec..2eea975 100644 --- a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__anova.xml +++ b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__anova.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + ANOVA test - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version longitudinal q2galaxy run longitudinal anova '$inputs' diff --git a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__feature_volatility.xml b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__feature_volatility.xml index 1de1b20..df09824 100644 --- a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__feature_volatility.xml +++ b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__feature_volatility.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Feature volatility analysis - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version longitudinal q2galaxy run longitudinal feature_volatility '$inputs' diff --git a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__first_differences.xml b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__first_differences.xml index 704524b..9ad840e 100644 --- a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__first_differences.xml +++ b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__first_differences.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Compute first differences or difference from baseline between sequential states - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version longitudinal q2galaxy run longitudinal first_differences '$inputs' diff --git a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__first_distances.xml b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__first_distances.xml index a59ec3b..7355df3 100644 --- a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__first_distances.xml +++ b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__first_distances.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Compute first distances or distance from baseline between sequential states - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version longitudinal q2galaxy run longitudinal first_distances '$inputs' diff --git a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__linear_mixed_effects.xml b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__linear_mixed_effects.xml index 13f93d4..e477dce 100644 --- a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__linear_mixed_effects.xml +++ b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__linear_mixed_effects.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Linear mixed effects modeling - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version longitudinal q2galaxy run longitudinal linear_mixed_effects '$inputs' diff --git a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__maturity_index.xml b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__maturity_index.xml index 55722e8..021ada8 100644 --- a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__maturity_index.xml +++ b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__maturity_index.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Microbial maturity index prediction. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version longitudinal q2galaxy run longitudinal maturity_index '$inputs' diff --git a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__nmit.xml b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__nmit.xml index d720fa7..fb2e70a 100644 --- a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__nmit.xml +++ b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__nmit.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Nonparametric microbial interdependence test - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version longitudinal q2galaxy run longitudinal nmit '$inputs' diff --git a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__pairwise_differences.xml b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__pairwise_differences.xml index f19edce..75673f9 100644 --- a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__pairwise_differences.xml +++ b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__pairwise_differences.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Paired difference testing and boxplots - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version longitudinal q2galaxy run longitudinal pairwise_differences '$inputs' diff --git a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__pairwise_distances.xml b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__pairwise_distances.xml index 4176741..d5884c7 100644 --- a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__pairwise_distances.xml +++ b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__pairwise_distances.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Paired pairwise distance testing and boxplots - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version longitudinal q2galaxy run longitudinal pairwise_distances '$inputs' diff --git a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__plot_feature_volatility.xml b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__plot_feature_volatility.xml index a319108..39dd861 100644 --- a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__plot_feature_volatility.xml +++ b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__plot_feature_volatility.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Plot longitudinal feature volatility and importances - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version longitudinal q2galaxy run longitudinal plot_feature_volatility '$inputs' diff --git a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__volatility.xml b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__volatility.xml index fca18f9..8befde4 100644 --- a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__volatility.xml +++ b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__volatility.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Generate interactive volatility plot - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version longitudinal q2galaxy run longitudinal volatility '$inputs' diff --git a/tools/suite_qiime2__metadata/qiime2__metadata__distance_matrix.xml b/tools/suite_qiime2__metadata/qiime2__metadata__distance_matrix.xml index a69fcb2..589f86a 100644 --- a/tools/suite_qiime2__metadata/qiime2__metadata__distance_matrix.xml +++ b/tools/suite_qiime2__metadata/qiime2__metadata__distance_matrix.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Create a distance matrix from a numeric Metadata column - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version metadata q2galaxy run metadata distance_matrix '$inputs' diff --git a/tools/suite_qiime2__metadata/qiime2__metadata__merge.xml b/tools/suite_qiime2__metadata/qiime2__metadata__merge.xml index 1000c8b..9828c71 100644 --- a/tools/suite_qiime2__metadata/qiime2__metadata__merge.xml +++ b/tools/suite_qiime2__metadata/qiime2__metadata__merge.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Merge metadata - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version metadata q2galaxy run metadata merge '$inputs' diff --git a/tools/suite_qiime2__metadata/qiime2__metadata__shuffle_groups.xml b/tools/suite_qiime2__metadata/qiime2__metadata__shuffle_groups.xml index d35dc8f..520503d 100644 --- a/tools/suite_qiime2__metadata/qiime2__metadata__shuffle_groups.xml +++ b/tools/suite_qiime2__metadata/qiime2__metadata__shuffle_groups.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Shuffle values in a categorical sample metadata column. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version metadata q2galaxy run metadata shuffle_groups '$inputs' diff --git a/tools/suite_qiime2__metadata/qiime2__metadata__tabulate.xml b/tools/suite_qiime2__metadata/qiime2__metadata__tabulate.xml index 62ba15f..681011f 100644 --- a/tools/suite_qiime2__metadata/qiime2__metadata__tabulate.xml +++ b/tools/suite_qiime2__metadata/qiime2__metadata__tabulate.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Interactively explore Metadata in an HTML table - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version metadata q2galaxy run metadata tabulate '$inputs' diff --git a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__align_to_tree_mafft_fasttree.xml b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__align_to_tree_mafft_fasttree.xml index baa1ad1..6920f04 100644 --- a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__align_to_tree_mafft_fasttree.xml +++ b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__align_to_tree_mafft_fasttree.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Build a phylogenetic tree using fasttree and mafft alignment - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version phylogeny q2galaxy run phylogeny align_to_tree_mafft_fasttree '$inputs' diff --git a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__align_to_tree_mafft_iqtree.xml b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__align_to_tree_mafft_iqtree.xml index 5f19266..965ae0c 100644 --- a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__align_to_tree_mafft_iqtree.xml +++ b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__align_to_tree_mafft_iqtree.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Build a phylogenetic tree using iqtree and mafft alignment. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version phylogeny q2galaxy run phylogeny align_to_tree_mafft_iqtree '$inputs' diff --git a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__align_to_tree_mafft_raxml.xml b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__align_to_tree_mafft_raxml.xml index f510ea8..5e6430b 100644 --- a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__align_to_tree_mafft_raxml.xml +++ b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__align_to_tree_mafft_raxml.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Build a phylogenetic tree using raxml and mafft alignment. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version phylogeny q2galaxy run phylogeny align_to_tree_mafft_raxml '$inputs' diff --git a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__fasttree.xml b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__fasttree.xml index 5112b09..6975235 100644 --- a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__fasttree.xml +++ b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__fasttree.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Construct a phylogenetic tree with FastTree. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version phylogeny q2galaxy run phylogeny fasttree '$inputs' diff --git a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__filter_table.xml b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__filter_table.xml index 905b4b5..3fdebc8 100644 --- a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__filter_table.xml +++ b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__filter_table.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Remove features from table if they're not present in tree. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version phylogeny q2galaxy run phylogeny filter_table '$inputs' @@ -23,16 +23,16 @@ for: + - hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Phylogeny[Rooted]', 'Phylogeny[Unrooted]'] diff --git a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__filter_tree.xml b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__filter_tree.xml index 9518298..37c4ddb 100644 --- a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__filter_tree.xml +++ b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__filter_tree.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Remove features from tree based on metadata - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version phylogeny q2galaxy run phylogeny filter_tree '$inputs' @@ -23,18 +23,18 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Phylogeny[Rooted]', 'Phylogeny[Unrooted]']

+ - - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__iqtree.xml b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__iqtree.xml index 4486ab5..c7a471e 100644 --- a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__iqtree.xml +++ b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__iqtree.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Construct a phylogenetic tree with IQ-TREE. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version phylogeny q2galaxy run phylogeny iqtree '$inputs' diff --git a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__iqtree_ultrafast_bootstrap.xml b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__iqtree_ultrafast_bootstrap.xml index 228f980..87eaf54 100644 --- a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__iqtree_ultrafast_bootstrap.xml +++ b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__iqtree_ultrafast_bootstrap.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Construct a phylogenetic tree with IQ-TREE with bootstrap supports. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version phylogeny q2galaxy run phylogeny iqtree_ultrafast_bootstrap '$inputs' diff --git a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__midpoint_root.xml b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__midpoint_root.xml index 1fb7146..e0705f6 100644 --- a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__midpoint_root.xml +++ b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__midpoint_root.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Midpoint root an unrooted phylogenetic tree. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version phylogeny q2galaxy run phylogeny midpoint_root '$inputs' diff --git a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__raxml.xml b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__raxml.xml index 09f6157..1c74fc4 100644 --- a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__raxml.xml +++ b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__raxml.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Construct a phylogenetic tree with RAxML. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version phylogeny q2galaxy run phylogeny raxml '$inputs' diff --git a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__raxml_rapid_bootstrap.xml b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__raxml_rapid_bootstrap.xml index 3620f15..e754fe9 100644 --- a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__raxml_rapid_bootstrap.xml +++ b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__raxml_rapid_bootstrap.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Construct a phylogenetic tree with bootstrap supports using RAxML. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version phylogeny q2galaxy run phylogeny raxml_rapid_bootstrap '$inputs' diff --git a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__robinson_foulds.xml b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__robinson_foulds.xml index d9ea187..73e0e98 100644 --- a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__robinson_foulds.xml +++ b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__robinson_foulds.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Calculate Robinson-Foulds distance between phylogenetic trees. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version phylogeny q2galaxy run phylogeny robinson_foulds '$inputs' @@ -23,8 +23,8 @@ for: - +
diff --git a/tools/suite_qiime2__phylogeny/test-data/align_to_tree_mafft_fasttree.test0.rep-seqs.qza b/tools/suite_qiime2__phylogeny/test-data/align_to_tree_mafft_fasttree.test0.rep-seqs.qza index 25a7e76a6b09f7ceb43bd5280a2f4d649f22d60d..d7bf4be5310df52f432052880ed14118bf85c99f 100644 GIT binary patch delta 688 zcmX?nl=<*cX5IjAW)=|!1_lm>$PI@lpJggw2GSFGH-M;(2e_C(^kxU<$4z`dM#L%~ z-;xM628JS@$%bualVk7jZZ>L9Vgo6fJiWIXOslo+25S=Sixmbl&g{uz2g_I8N0&Hgd4gJaK z4BTmV0<7J3Qb4n=SK5nyGaaRLY4zz#BCnY9C57 zHLrn61EcLI_hkFKJYX+ez3Q@gJ1YajRW5X^cJGI3-~z?KE=GDeg0Z$WHA#1{iYA&RHEkHa-gSZOX6;LQq5Vhjv|Ksb+sfr0-P Ghz9_zIS@tw delta 706 zcmX?nl=<*cX5IjAW)=|!1_lm>=(#f|Hf&%9Qk#t#xtKtViM$11z60~)CJdBZ|JY znmuM?V3^N4`QR~!%?B3Bvx80IJmx+5z(UoD&Q@Uk6V{jt3xd>lMjY_TV`O0X%EZ7> zG})0+WAcG}R+HAUPo90BXS3+)0!C>@CJ|=1pCZ_n+|o$~`Y;=ajV9~dGMl{TmZUt$ zr1yP#dV7H;*|7p;fU+>Kq;WIQT+_*#w|T%Wk-H_$bbx8{#}(?6lWsx0X>mIP?0AIX zlh@sLnLMMHck=l=JPIJwSNZssL;(F&#KXW~3o{x>FKN8q1~kiPa(Wx@LaLKB57@k@%FchM=?&gun r3s+@KwtgTE_6ACfq9_!+0aREb7U0ba3`hnBK_HyR!N9 - + Build bowtie2 index from reference sequences. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version quality_control q2galaxy run quality_control bowtie2_build '$inputs' diff --git a/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_identify.xml b/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_identify.xml index c179508..ab01781 100644 --- a/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_identify.xml +++ b/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_identify.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Identify contaminants - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version quality_control q2galaxy run quality_control decontam_identify '$inputs' @@ -21,7 +21,7 @@ for: - + @@ -109,7 +109,7 @@ Identify contaminants Outputs: -------- -:decontam_scores.qza: The resulting table of scores from the decontam algorithm which scores each ASV or OTU on how likely they are to be a contaminant sequence +:decontam_scores.qza: The resulting table of scores from the decontam algorithm which scores each feature on how likely they are to be a contaminant sequence | diff --git a/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_identify_batches.xml b/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_identify_batches.xml index 8635960..c05c83b 100644 --- a/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_identify_batches.xml +++ b/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_identify_batches.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Identify contaminants in Batch Mode - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version quality_control q2galaxy run quality_control decontam_identify_batches '$inputs' @@ -21,7 +21,7 @@ for: - + @@ -55,6 +55,12 @@ for: value != '__q2galaxy__::literal::None'
+ + + + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]'] + @@ -132,7 +138,7 @@ Identify contaminants in Batch Mode Outputs: -------- :batch_subset_tables.qza: Directory where feature tables split based on metadata and parameter split_column values should be written. -:decontam_scores.qza: The resulting table of scores from the decontam algorithm which scores each ASV or OTU on how likely they are to be a contaminant sequence +:decontam_scores.qza: The resulting table of scores from the decontam algorithm which scores each feature on how likely they are to be a contaminant sequence :score_histograms.qzv: The vizulaizer histograms for all decontam score objects generated from the pipeline | diff --git a/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_remove.xml b/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_remove.xml index 3ba7074..02a62e2 100644 --- a/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_remove.xml +++ b/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_remove.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - - Removes contaminant + + Remove contaminants - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version quality_control q2galaxy run quality_control decontam_remove '$inputs' @@ -21,41 +21,49 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[DecontamScore]'] - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]'] + + + + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]'] +
- +
+ QIIME 2: quality-control decontam-remove ======================================== -Removes contaminant +Remove contaminants Outputs: -------- -:filtered_table.qza: The resulting feature table of scores once contaminants are removed +:filtered_table.qza: Feature table with contaminants removed. +:filtered_rep_seqs.qza: Feature representative sequences with contaminants removed. | Description: ------------ -This method removes contaminant sequences from an OTU or ASV table and returns the amended table to the user +Remove contaminant sequences from a feature table and the associated representative sequences. | diff --git a/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_score_viz.xml b/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_score_viz.xml index 72fe603..73ec91b 100644 --- a/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_score_viz.xml +++ b/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_score_viz.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Generate a histogram representation of the scores - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version quality_control q2galaxy run quality_control decontam_score_viz '$inputs' @@ -32,9 +32,15 @@ for:
- + + + + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]'] + + - +
diff --git a/tools/suite_qiime2__quality_control/qiime2__quality_control__evaluate_composition.xml b/tools/suite_qiime2__quality_control/qiime2__quality_control__evaluate_composition.xml index 0f163e0..411d05e 100644 --- a/tools/suite_qiime2__quality_control/qiime2__quality_control__evaluate_composition.xml +++ b/tools/suite_qiime2__quality_control/qiime2__quality_control__evaluate_composition.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Evaluate expected vs. observed taxonomic composition of samples - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version quality_control q2galaxy run quality_control evaluate_composition '$inputs' diff --git a/tools/suite_qiime2__quality_control/qiime2__quality_control__evaluate_seqs.xml b/tools/suite_qiime2__quality_control/qiime2__quality_control__evaluate_seqs.xml index 4631b8a..a1cb643 100644 --- a/tools/suite_qiime2__quality_control/qiime2__quality_control__evaluate_seqs.xml +++ b/tools/suite_qiime2__quality_control/qiime2__quality_control__evaluate_seqs.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Compare query (observed) vs. reference (expected) sequences. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version quality_control q2galaxy run quality_control evaluate_seqs '$inputs' diff --git a/tools/suite_qiime2__quality_control/qiime2__quality_control__evaluate_taxonomy.xml b/tools/suite_qiime2__quality_control/qiime2__quality_control__evaluate_taxonomy.xml index 77ccc90..dce7e7b 100644 --- a/tools/suite_qiime2__quality_control/qiime2__quality_control__evaluate_taxonomy.xml +++ b/tools/suite_qiime2__quality_control/qiime2__quality_control__evaluate_taxonomy.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Evaluate expected vs. observed taxonomic assignments - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version quality_control q2galaxy run quality_control evaluate_taxonomy '$inputs' diff --git a/tools/suite_qiime2__quality_control/qiime2__quality_control__exclude_seqs.xml b/tools/suite_qiime2__quality_control/qiime2__quality_control__exclude_seqs.xml index b54760d..2777a99 100644 --- a/tools/suite_qiime2__quality_control/qiime2__quality_control__exclude_seqs.xml +++ b/tools/suite_qiime2__quality_control/qiime2__quality_control__exclude_seqs.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Exclude sequences by alignment - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version quality_control q2galaxy run quality_control exclude_seqs '$inputs' diff --git a/tools/suite_qiime2__quality_control/qiime2__quality_control__filter_reads.xml b/tools/suite_qiime2__quality_control/qiime2__quality_control__filter_reads.xml index b0de43a..ec8f431 100644 --- a/tools/suite_qiime2__quality_control/qiime2__quality_control__filter_reads.xml +++ b/tools/suite_qiime2__quality_control/qiime2__quality_control__filter_reads.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Filter demultiplexed sequences by alignment to reference database. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version quality_control q2galaxy run quality_control filter_reads '$inputs' diff --git a/tools/suite_qiime2__quality_filter/qiime2__quality_filter__q_score.xml b/tools/suite_qiime2__quality_filter/qiime2__quality_filter__q_score.xml index e3ddf72..3a2fd72 100644 --- a/tools/suite_qiime2__quality_filter/qiime2__quality_filter__q_score.xml +++ b/tools/suite_qiime2__quality_filter/qiime2__quality_filter__q_score.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Quality filter based on sequence quality scores. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version quality_filter q2galaxy run quality_filter q_score '$inputs' diff --git a/tools/suite_qiime2__quality_filter/test-data/q_score.test0.demuxed-seqs.qza b/tools/suite_qiime2__quality_filter/test-data/q_score.test0.demuxed-seqs.qza index 24dc9e3dc0f737576a1a2665004613a0b4b46b18..9a7b159176737b78126e11a95026284dce8e7260 100644 GIT binary patch delta 2472 zcmZ8i3s6*57(RCwc3Ie6mdm1W7uZ7?xMDCH#xoy~nFb+`QMZt3#{?4kyO4aQ86E+ku#0iXjtc-v&6mZ&Ohh;|9}4P`~Ux( zdrtMykCS%SvrCMyRvY4OaG{n+-nB?W+*6m-LnHS^kdufY_u#_y2wLuZ+^FuwF?>VBS+58=8Ha(wa3s4h3f6_opHEg?*x|)r z*r7VNj%em$Id3lZxS=E3NWUjP(yy3^Ct9aVT|-Z)LY4W zE15x-n6I1U%hSoMCOhO`ihgjT+QAT8QzF!nT|&K!;7-AWTnX?3@r5VDy(%&b%ZCL@ z;;h*O`-DkvXda{p+wAa9#z%Cd_@qMkvOkIIPlXF8I*v<451Zi&C^rix5~!g!;B~U9 zEen3Y8W@>g{{OMGm^6KR=ioy+8_Qf|FNLw_{W9op#MG9?;76KbZ2t($OIRj<`|R71 zpOu}B_)-`Ig_Vnc46iTp1fW|xedQ|*x*6vc(dffyd^1ud+~`^zG@#GQpc$F!;jAzL zXmwiNKQT`LFk)Fc$%n^%c1Hn&l8fb0=zLd*0a>e{niQAR01a}OC!@YE#tqa*z_O2c znUw_qOst;{7BeIl0_LLXRZIv0BLRO~TDz~OGr)yK%HB241BD$@MxpJUoQU1L8?)ao z^`yR%-7uWs9G9Jq-j%?BO<1HjO_d6|HsXp-g!7~l8e|`yLdj0}B3jM)1Wy%sumV$P zXR2tvt;tH7FDbswiG5#}snA|47me;ZC+XJ>X694?kcLG{fAX|SpkFoxpYFgA_6%-Asf*#Jz;1@u9(yedfFvx^;$GFWG^y6UKvDbVY@0g} zIv;=_EK>I0^I5uO%gbRn*-0Hf0P>=JEbXe+=0%B#@9Hk>OIGUz4pDK#r#hf{@Mo7sbbh|8!oI=0Kp~kZWT=J_B!p?g=FE;j8gjNh zRMhDN;W+mH7DRpA9fhc1#mKRHhByYuut+-;xr7q}qR_~wN>tg-S`2oe#6ZDNM}R1| zJ&o8G`c;VFi$r%CVIVmgRi9r9Hk|_?0E@Kha=aFw?P#>H&fV1AWf($V8A_?ImbpKV zjje3mgEs*f#Uh2c^obGKcexukAlxjo?;B}yPaB|#G-tEWvpMmQ=5@3R>dDJD*3_Un zif_P6-so`?T#R}?hCw7@@dXsva<;nfxQJ#* zpYE-HmB-#v0MMyH-OVr^8QbwaKcfu>k<88@A+s!q%=yrY4!5~MpS57~wAc&l$I&Cd;N-n2Wpj{FPFLoc#Bm^PTTJ?!5<^ zhjwtyR1}sxQJ@+jG!5<9+tpTkPDDQ^7ISBU*rH9bnSJbWj#xg zIb)*oazGddmAr8HlT29slJYQB^BorHu?ewgFb2^TB5tVD+sn_}>L=Wv}T|@il$n zo-){FE{f(e7ip_AVCOt5;hkrvH5G$TMkcm%u)1i~xFCwXbc>8H-6Fpd4R~|Obi27E zk~f!VIzvNQCF60O?=2B?$Smf_h*p_uH`;=DqfJ~X28UjUnD2E+e$N8hSC5AzL7DaC zp(o3gi?o1Aamno|E(M?B3Xuzi4pnRIL)9_-P_?cy8yePh^2Zp12cZZLG>klTV;w(! zN|)vVVvAbU4>i-GT6;QLr^-uF5 z%Deg2CutK1=_iC^xm3+()fJ(O>XA7v6oA3ar9#rCOD%q6F*8giU7LH?V2`-la0Y&GL z)DrwMIYO|694^Lb;C%NTJS!Yl_m<+nI0YA=7ERt-;;F-0(o%;FZM=fS+OQnBQfyeu zT_B@cWn%lMoPyL)17>GxPz?0GLa%%xm1HW3VKZ6f zh>h-Wc&Ue-SSuQd;>a80MluFVV zC{T@Aq%o7GXcskI9tmMT9hBnqK~NjX3I|RAbt`MNdsIPk zOQu7sfq2R!c`mJ#%b_d@BT2Od`Fd1fr!3cgQZke8z$RG83t=jub6byx_^wxF6E!_v zcTq^z{Edv@MbC(k*LbIIom5L^wXoN>`)rMz6xCh}O$vN4S zf{H(dZFRIjVQThP_)lrqfg6P!8l~cYWQKi!HIXBqdsDlbRwg~PmP0No{@9HVwJZk{ zsjvn>Hz1FPJ@0q#$w$ad#UEe0R43%IdZ%z5I@rsv+piN?3hKSjyU0z|F}q_KIEi$- zu?Fg{VlS^wP$!e_9*ys*E@yM%`aQis-`DKDZKrn8StQwo(}}DDM*+!wc8BeAFu9zC zvx%V_%OUBh11`hw`F7_3)=UoW@=myf4h(-=$;EC;f4qb8jO?cKcY7tCGD~~9XrO(0 zUgysUmI^56dWvFkAssWJsGCJEpuX8eXZdN0(zBr!F!(6T zIg27VT7jm!N y-~+&a7vyOtEy=jir#6x5E*uNxu41-zwNq`sbm9ng5Dkt{I{kHP5L#P@>F$4R95k8$ diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__cull_seqs.xml b/tools/suite_qiime2__rescript/qiime2__rescript__cull_seqs.xml index 6d847c5..bcd6168 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__cull_seqs.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__cull_seqs.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Removes sequences that contain at least the specified number of degenerate bases and/or homopolymers of a given length. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version rescript q2galaxy run rescript cull_seqs '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__degap_seqs.xml b/tools/suite_qiime2__rescript/qiime2__rescript__degap_seqs.xml index 1cf18c3..06584eb 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__degap_seqs.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__degap_seqs.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Remove gaps from DNA sequence alignments. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version rescript q2galaxy run rescript degap_seqs '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__dereplicate.xml b/tools/suite_qiime2__rescript/qiime2__rescript__dereplicate.xml index 6e24bbf..f30a80a 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__dereplicate.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__dereplicate.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Dereplicate features with matching sequences and taxonomies. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version rescript q2galaxy run rescript dereplicate '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__edit_taxonomy.xml b/tools/suite_qiime2__rescript/qiime2__rescript__edit_taxonomy.xml index dbc293d..5b14e24 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__edit_taxonomy.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__edit_taxonomy.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Edit taxonomy strings with find and replace terms. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version rescript q2galaxy run rescript edit_taxonomy '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_classifications.xml b/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_classifications.xml index 88c5a9e..49a227c 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_classifications.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_classifications.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Interactively evaluate taxonomic classification accuracy. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version rescript q2galaxy run rescript evaluate_classifications '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_cross_validate.xml b/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_cross_validate.xml index 02a952d..a435750 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_cross_validate.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_cross_validate.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Evaluate DNA sequence reference database via cross-validated taxonomic classification. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version rescript q2galaxy run rescript evaluate_cross_validate '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_fit_classifier.xml b/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_fit_classifier.xml index 6acf884..7991f17 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_fit_classifier.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_fit_classifier.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Evaluate and train naive Bayes classifier on reference sequences. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version rescript q2galaxy run rescript evaluate_fit_classifier '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_seqs.xml b/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_seqs.xml index e727ecf..8dce81f 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_seqs.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_seqs.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Compute summary statistics on sequence artifact(s). - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version rescript q2galaxy run rescript evaluate_seqs '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_taxonomy.xml b/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_taxonomy.xml index eedecdd..2956f37 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_taxonomy.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_taxonomy.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Compute summary statistics on taxonomy artifact(s). - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version rescript q2galaxy run rescript evaluate_taxonomy '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__extract_seq_segments.xml b/tools/suite_qiime2__rescript/qiime2__rescript__extract_seq_segments.xml index 8792377..97521c5 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__extract_seq_segments.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__extract_seq_segments.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Use reference sequences to extract shorter matching sequence segments from longer sequences based on a user-defined 'perc-identity' value. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version rescript q2galaxy run rescript extract_seq_segments '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__filter_seqs_length.xml b/tools/suite_qiime2__rescript/qiime2__rescript__filter_seqs_length.xml index 232121e..f517cce 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__filter_seqs_length.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__filter_seqs_length.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Filter sequences by length. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version rescript q2galaxy run rescript filter_seqs_length '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__filter_seqs_length_by_taxon.xml b/tools/suite_qiime2__rescript/qiime2__rescript__filter_seqs_length_by_taxon.xml index 7587e15..dc0dc6d 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__filter_seqs_length_by_taxon.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__filter_seqs_length_by_taxon.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Filter sequences by length and taxonomic group. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version rescript q2galaxy run rescript filter_seqs_length_by_taxon '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__filter_taxa.xml b/tools/suite_qiime2__rescript/qiime2__rescript__filter_taxa.xml index 6f35e98..a7d829b 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__filter_taxa.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__filter_taxa.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Filter taxonomy by list of IDs or search criteria. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version rescript q2galaxy run rescript filter_taxa '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__get_gtdb_data.xml b/tools/suite_qiime2__rescript/qiime2__rescript__get_gtdb_data.xml index a0db1a7..b77d01f 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__get_gtdb_data.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__get_gtdb_data.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Download, parse, and import SSU GTDB reference data. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version rescript q2galaxy run rescript get_gtdb_data '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__get_ncbi_data.xml b/tools/suite_qiime2__rescript/qiime2__rescript__get_ncbi_data.xml index 17a2c82..3562e7f 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__get_ncbi_data.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__get_ncbi_data.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Download, parse, and import NCBI sequences and taxonomies - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version rescript q2galaxy run rescript get_ncbi_data '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__get_ncbi_data_protein.xml b/tools/suite_qiime2__rescript/qiime2__rescript__get_ncbi_data_protein.xml index 12751ac..e4877b6 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__get_ncbi_data_protein.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__get_ncbi_data_protein.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Download, parse, and import NCBI protein sequences and taxonomies - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version rescript q2galaxy run rescript get_ncbi_data_protein '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__get_ncbi_genomes.xml b/tools/suite_qiime2__rescript/qiime2__rescript__get_ncbi_genomes.xml index 260d5b0..350c0c5 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__get_ncbi_genomes.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__get_ncbi_genomes.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Fetch entire genomes and associated taxonomies and metadata using NCBI Datasets. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version rescript q2galaxy run rescript get_ncbi_genomes '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__get_silva_data.xml b/tools/suite_qiime2__rescript/qiime2__rescript__get_silva_data.xml index d3e0f78..9a1840d 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__get_silva_data.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__get_silva_data.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Download, parse, and import SILVA database. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version rescript q2galaxy run rescript get_silva_data '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__get_unite_data.xml b/tools/suite_qiime2__rescript/qiime2__rescript__get_unite_data.xml index 26ca2a8..fcea920 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__get_unite_data.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__get_unite_data.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Download and import UNITE reference data. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version rescript q2galaxy run rescript get_unite_data '$inputs' @@ -22,8 +22,9 @@ for:
- - + + + diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__merge_taxa.xml b/tools/suite_qiime2__rescript/qiime2__rescript__merge_taxa.xml index b9d63ed..b1a5f09 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__merge_taxa.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__merge_taxa.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Compare taxonomies and select the longest, highest scoring, or find the least common ancestor. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version rescript q2galaxy run rescript merge_taxa '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__orient_seqs.xml b/tools/suite_qiime2__rescript/qiime2__rescript__orient_seqs.xml index 92c2310..12ed70e 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__orient_seqs.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__orient_seqs.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Orient input sequences by comparison against reference. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version rescript q2galaxy run rescript orient_seqs '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__parse_silva_taxonomy.xml b/tools/suite_qiime2__rescript/qiime2__rescript__parse_silva_taxonomy.xml index 7d72aa1..af2a48c 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__parse_silva_taxonomy.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__parse_silva_taxonomy.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Generates a SILVA fixed-rank taxonomy. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version rescript q2galaxy run rescript parse_silva_taxonomy '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__reverse_transcribe.xml b/tools/suite_qiime2__rescript/qiime2__rescript__reverse_transcribe.xml index 9b766f5..4318645 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__reverse_transcribe.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__reverse_transcribe.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Reverse transcribe RNA to DNA sequences. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version rescript q2galaxy run rescript reverse_transcribe '$inputs' @@ -23,8 +23,8 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[AlignedRNASequence]', 'FeatureData[RNASequence]'] diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__subsample_fasta.xml b/tools/suite_qiime2__rescript/qiime2__rescript__subsample_fasta.xml index 789f2a8..a2e53d3 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__subsample_fasta.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__subsample_fasta.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Subsample an indicated number of sequences from a FASTA file. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version rescript q2galaxy run rescript subsample_fasta '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__trim_alignment.xml b/tools/suite_qiime2__rescript/qiime2__rescript__trim_alignment.xml index c2bd10a..89f5183 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__trim_alignment.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__trim_alignment.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Trim alignment based on provided primers or specific positions. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version rescript q2galaxy run rescript trim_alignment '$inputs' diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__classify_samples.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__classify_samples.xml index 741d587..05934de 100644 --- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__classify_samples.xml +++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__classify_samples.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Train and test a cross-validated supervised learning classifier. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version sample_classifier q2galaxy run sample_classifier classify_samples '$inputs' @@ -23,10 +23,10 @@ for: - - + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__classify_samples_from_dist.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__classify_samples_from_dist.xml index 569c461..e5c4888 100644 --- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__classify_samples_from_dist.xml +++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__classify_samples_from_dist.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Run k-nearest-neighbors on a labeled distance matrix. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version sample_classifier q2galaxy run sample_classifier classify_samples_from_dist '$inputs' diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__classify_samples_ncv.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__classify_samples_ncv.xml index fe8b023..f3c9e3d 100644 --- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__classify_samples_ncv.xml +++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__classify_samples_ncv.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Nested cross-validated supervised learning classifier. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version sample_classifier q2galaxy run sample_classifier classify_samples_ncv '$inputs' @@ -23,10 +23,10 @@ for: - - + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__confusion_matrix.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__confusion_matrix.xml index de9b553..d3e43f4 100644 --- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__confusion_matrix.xml +++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__confusion_matrix.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Make a confusion matrix from sample classifier predictions. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version sample_classifier q2galaxy run sample_classifier confusion_matrix '$inputs' diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__fit_classifier.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__fit_classifier.xml index 58cc279..9f1b417 100644 --- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__fit_classifier.xml +++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__fit_classifier.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Fit a supervised learning classifier. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version sample_classifier q2galaxy run sample_classifier fit_classifier '$inputs' @@ -23,10 +23,10 @@ for: - - + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__fit_regressor.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__fit_regressor.xml index 53e6053..def7f2e 100644 --- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__fit_regressor.xml +++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__fit_regressor.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Fit a supervised learning regressor. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version sample_classifier q2galaxy run sample_classifier fit_regressor '$inputs' @@ -23,10 +23,10 @@ for: - - + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__heatmap.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__heatmap.xml index 2effa73..33cc6a7 100644 --- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__heatmap.xml +++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__heatmap.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Generate heatmap of important features. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version sample_classifier q2galaxy run sample_classifier heatmap '$inputs' @@ -23,10 +23,10 @@ for: - - + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__metatable.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__metatable.xml index 845c507..c9660db 100644 --- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__metatable.xml +++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__metatable.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Convert (and merge) positive numeric metadata (in)to feature table. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version sample_classifier q2galaxy run sample_classifier metatable '$inputs' @@ -38,10 +38,10 @@ for:
- - + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__predict_classification.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__predict_classification.xml index 682c36e..3473243 100644 --- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__predict_classification.xml +++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__predict_classification.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Use trained classifier to predict target values for new samples. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version sample_classifier q2galaxy run sample_classifier predict_classification '$inputs' @@ -23,10 +23,10 @@ for: - - + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__predict_regression.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__predict_regression.xml index 3f9dca1..64cad4c 100644 --- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__predict_regression.xml +++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__predict_regression.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Use trained regressor to predict target values for new samples. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version sample_classifier q2galaxy run sample_classifier predict_regression '$inputs' @@ -23,10 +23,10 @@ for: - - + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__regress_samples.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__regress_samples.xml index a03e34e..f852d95 100644 --- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__regress_samples.xml +++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__regress_samples.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Train and test a cross-validated supervised learning regressor. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version sample_classifier q2galaxy run sample_classifier regress_samples '$inputs' @@ -23,10 +23,10 @@ for: - - + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__regress_samples_ncv.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__regress_samples_ncv.xml index 51e1b5f..0153d28 100644 --- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__regress_samples_ncv.xml +++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__regress_samples_ncv.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Nested cross-validated supervised learning regressor. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version sample_classifier q2galaxy run sample_classifier regress_samples_ncv '$inputs' @@ -23,10 +23,10 @@ for: - - + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__scatterplot.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__scatterplot.xml index 57b8403..40deb94 100644 --- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__scatterplot.xml +++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__scatterplot.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Make 2D scatterplot and linear regression of regressor predictions. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version sample_classifier q2galaxy run sample_classifier scatterplot '$inputs' diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__split_table.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__split_table.xml index f80f72e..fa4808f 100644 --- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__split_table.xml +++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__split_table.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Split a feature table into training and testing sets. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version sample_classifier q2galaxy run sample_classifier split_table '$inputs' @@ -23,13 +23,13 @@ for: - - + - - - + + + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Balance]', 'FeatureTable[Composition]', 'FeatureTable[Design]', 'FeatureTable[Frequency]', 'FeatureTable[PercentileNormalized]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__summarize.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__summarize.xml index 0ff2297..204ee37 100644 --- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__summarize.xml +++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__summarize.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Summarize parameter and feature extraction information for a trained estimator. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version sample_classifier q2galaxy run sample_classifier summarize '$inputs' @@ -23,8 +23,8 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleEstimator[Classifier]', 'SampleEstimator[Regressor]'] diff --git a/tools/suite_qiime2__taxa/qiime2__taxa__barplot.xml b/tools/suite_qiime2__taxa/qiime2__taxa__barplot.xml index 3964ee6..941a637 100644 --- a/tools/suite_qiime2__taxa/qiime2__taxa__barplot.xml +++ b/tools/suite_qiime2__taxa/qiime2__taxa__barplot.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Visualize taxonomy with an interactive bar plot - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version taxa q2galaxy run taxa barplot '$inputs' @@ -23,8 +23,8 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]'] diff --git a/tools/suite_qiime2__taxa/qiime2__taxa__collapse.xml b/tools/suite_qiime2__taxa/qiime2__taxa__collapse.xml index 6b6e006..62f71fe 100644 --- a/tools/suite_qiime2__taxa/qiime2__taxa__collapse.xml +++ b/tools/suite_qiime2__taxa/qiime2__taxa__collapse.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Collapse features by their taxonomy at the specified level - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version taxa q2galaxy run taxa collapse '$inputs' diff --git a/tools/suite_qiime2__taxa/qiime2__taxa__filter_seqs.xml b/tools/suite_qiime2__taxa/qiime2__taxa__filter_seqs.xml index 7c00cb2..7818d9f 100644 --- a/tools/suite_qiime2__taxa/qiime2__taxa__filter_seqs.xml +++ b/tools/suite_qiime2__taxa/qiime2__taxa__filter_seqs.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Taxonomy-based feature sequence filter. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version taxa q2galaxy run taxa filter_seqs '$inputs' diff --git a/tools/suite_qiime2__taxa/qiime2__taxa__filter_table.xml b/tools/suite_qiime2__taxa/qiime2__taxa__filter_table.xml index 9102819..9254889 100644 --- a/tools/suite_qiime2__taxa/qiime2__taxa__filter_table.xml +++ b/tools/suite_qiime2__taxa/qiime2__taxa__filter_table.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Taxonomy-based feature table filter. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version taxa q2galaxy run taxa filter_table '$inputs' @@ -21,11 +21,12 @@ for: - + + - hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]'] + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]'] diff --git a/tools/suite_qiime2__taxa/test-data/barplot.test0.table.qza b/tools/suite_qiime2__taxa/test-data/barplot.test0.table.qza index ddb42205d8a4e4c476d3d80a50bee2adbe9caa3d..5d9adc8542669f240e9ee688efcbbf364ddc3965 100644 GIT binary patch delta 859 zcmca}o$1bXCf)#VW)=|!1_lm>HyaL5c4RJK2GSFG*Mq2y`|FuN^yV$h`!x7~jEKnh zhVA><7#NKCCpYMrO`f-icXNa82{w?T$=)W_V7gRi7g*CV_ZJY|Cry3{fkpV5v)I8( z&gFVfe!og}a>FY2$*y_EAhE^VO^jeg3G+TPawEBEvqrb6Fj(ee>MfY|RbXRSQ(uB5 zs`Gk=O8Os1IS+apm;EQqt|_~=Ek5( zAznr%5oSavC@hqoT)jYZa>_!m#gh{jNHZ2sUg)hcdC3Avu;v2`q?uG1Cp+q@Pi9#N z5vp344wmv?Bt7~6LK9%vK*V<~l4fc&1}Zh0%(+-t0ThZiGTvDw0mD22h;4xw29`Ab zH=fM6$Qx`<|6=LMR*S7C^Lg;_2Y918P=2vA({l64flG}i=P#B8d%fsetJz~<%*^MV z%)P`99J+PQypwyD^MFm8y=Yc-!1inAhSE#iw@Da63=)PjMb5JlVmP^dO%uxl8BuKAt; z779pJom{^h5>y~ZUMYYJ+vTxOR#?FUcF}By{Z6nT%Rw=^u@J1`z%o0q(fU9ij4UtfK*HZDtHazB~Gqe0tp4CHD4XS3NkR1nW1~< cY%f@$+cFUmR$!PjFo*$RDK`T{-~td20FC)nxBvhE delta 903 zcmZ8fT}V@57=F(;bFm*aC#(D*yO9d|Avd!Y4V579Bu!VKS4kB8k4;*TUet&dLN|ocC;N+c_8C`#nGJ_kIuG{4ATFWmb=9 zD5(N~weacj{ef!}26dUN6Rt9?7_jZZ{GTb@b|rhLuVx-a5aN z6_+Cm1en6^Qj#wEMZ7asi!UQCBIf$9RGRY+$7tXO5hZ8m^yZ8HQ386p`)yhwziSr= zc-nFPb2I!TVRR3arYIyBj7Yj=j=0OiLTJCRiQg!ZU0X>hXNc zLP(dynbUwx!WL8{>VrM8(`Bl->m!4lxt;2^4rd(3a*tRz+g+KXOWu#G4Q4!^(5I=9IeT%4EDN#` zgYpLI^k|eLSKJh3^_YGYUxKr+NYX#UCZc{ObSgH?*_*ZkDm-eV!P$7KDYXvZ@*aRd zc4~E1LYLa}4Eu0p$V7&Rjjx*Z5CAR|7?w|F47)HLu;TQH9*rj%`QkMKe5@!od_9#j z+!+2p>FbLbxS8%cGs2nAms7STHW9ot&RIH?flc%P#^coFp2C@MJ&&owK1GjH3&M9h zkJ4U^5o_Z5s1F9qIun%u-}V-V!TSnK?xRNhHME`rxz#a!*e3v_7(jPHAl@fMCY#+O Su2EkJfL;BAW`H(H+x-LPBV307 diff --git a/tools/suite_qiime2__taxa/test-data/barplot.test0.taxonomy.qza b/tools/suite_qiime2__taxa/test-data/barplot.test0.taxonomy.qza index 32e960044848a0b89f8c375997fd160fbf50d6c6..d42f047411bd815246adfda234db5cf2140eb352 100644 GIT binary patch delta 2366 zcmZWqYfMyU5WNGqEQJ*Ws}ULs#Enq5RY8PO5p0wcd2}(YqNQ0EYvNLQ6dJ7xtVqBI zx}cvrf+4u-j|P8GT|8Bu zHy6txJ+9mXI=q+yrIX}jK)nBzF(Nrj%09t@R48^XT?mm{uJBt)UEMN`Bn^e&q)5ob zFfHhvaY0b3ahH)}7_%D!g=IKND^n(3js8Zok7mj64jJgo2!k^Uqy2OJqUFT+ioz%! 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(SPDX: BSD-3-Clause) --> - + Closed-reference clustering of features. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version vsearch q2galaxy run vsearch cluster_features_closed_reference '$inputs' diff --git a/tools/suite_qiime2__vsearch/qiime2__vsearch__cluster_features_de_novo.xml b/tools/suite_qiime2__vsearch/qiime2__vsearch__cluster_features_de_novo.xml index e3f46f6..94a8c55 100644 --- a/tools/suite_qiime2__vsearch/qiime2__vsearch__cluster_features_de_novo.xml +++ b/tools/suite_qiime2__vsearch/qiime2__vsearch__cluster_features_de_novo.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + De novo clustering of features. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version vsearch q2galaxy run vsearch cluster_features_de_novo '$inputs' diff --git a/tools/suite_qiime2__vsearch/qiime2__vsearch__cluster_features_open_reference.xml b/tools/suite_qiime2__vsearch/qiime2__vsearch__cluster_features_open_reference.xml index 06eb2c9..49b47af 100644 --- a/tools/suite_qiime2__vsearch/qiime2__vsearch__cluster_features_open_reference.xml +++ b/tools/suite_qiime2__vsearch/qiime2__vsearch__cluster_features_open_reference.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Open-reference clustering of features. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version vsearch q2galaxy run vsearch cluster_features_open_reference '$inputs' diff --git a/tools/suite_qiime2__vsearch/qiime2__vsearch__dereplicate_sequences.xml b/tools/suite_qiime2__vsearch/qiime2__vsearch__dereplicate_sequences.xml index c034f92..a655d19 100644 --- a/tools/suite_qiime2__vsearch/qiime2__vsearch__dereplicate_sequences.xml +++ b/tools/suite_qiime2__vsearch/qiime2__vsearch__dereplicate_sequences.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Dereplicate sequences. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version vsearch q2galaxy run vsearch dereplicate_sequences '$inputs' diff --git a/tools/suite_qiime2__vsearch/qiime2__vsearch__fastq_stats.xml b/tools/suite_qiime2__vsearch/qiime2__vsearch__fastq_stats.xml index 544d36a..703614b 100644 --- a/tools/suite_qiime2__vsearch/qiime2__vsearch__fastq_stats.xml +++ b/tools/suite_qiime2__vsearch/qiime2__vsearch__fastq_stats.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Fastq stats with vsearch. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version vsearch q2galaxy run vsearch fastq_stats '$inputs' diff --git a/tools/suite_qiime2__vsearch/qiime2__vsearch__merge_pairs.xml b/tools/suite_qiime2__vsearch/qiime2__vsearch__merge_pairs.xml index 121debe..9aa92e9 100644 --- a/tools/suite_qiime2__vsearch/qiime2__vsearch__merge_pairs.xml +++ b/tools/suite_qiime2__vsearch/qiime2__vsearch__merge_pairs.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Merge paired-end reads. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version vsearch q2galaxy run vsearch merge_pairs '$inputs' diff --git a/tools/suite_qiime2__vsearch/qiime2__vsearch__uchime_denovo.xml b/tools/suite_qiime2__vsearch/qiime2__vsearch__uchime_denovo.xml index 20a9ad4..09dfff3 100644 --- a/tools/suite_qiime2__vsearch/qiime2__vsearch__uchime_denovo.xml +++ b/tools/suite_qiime2__vsearch/qiime2__vsearch__uchime_denovo.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + De novo chimera filtering with vsearch. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version vsearch q2galaxy run vsearch uchime_denovo '$inputs' diff --git a/tools/suite_qiime2__vsearch/qiime2__vsearch__uchime_ref.xml b/tools/suite_qiime2__vsearch/qiime2__vsearch__uchime_ref.xml index 3f62f5d..623842b 100644 --- a/tools/suite_qiime2__vsearch/qiime2__vsearch__uchime_ref.xml +++ b/tools/suite_qiime2__vsearch/qiime2__vsearch__uchime_ref.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Reference-based chimera filtering with vsearch. - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy version vsearch q2galaxy run vsearch uchime_ref '$inputs' diff --git a/tools/suite_qiime2_core__tools/qiime2_core__tools__export.xml b/tools/suite_qiime2_core__tools/qiime2_core__tools__export.xml index 16f7f4e..c4d000b 100644 --- a/tools/suite_qiime2_core__tools/qiime2_core__tools__export.xml +++ b/tools/suite_qiime2_core__tools/qiime2_core__tools__export.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Export data from a QIIME 2 artifact - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy run tools export '$inputs' @@ -36,6 +36,7 @@ for: + @@ -44,18 +45,28 @@ for: + + + + + + + + + + @@ -71,6 +82,9 @@ for: + + + @@ -80,6 +94,10 @@ for: + + + + @@ -90,6 +108,8 @@ for: + + @@ -123,6 +143,12 @@ for: + + + + + + @@ -150,6 +176,7 @@ for: + @@ -170,12 +197,24 @@ for: + + + + + + + + + + + + @@ -200,6 +239,42 @@ for: + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -237,12 +312,24 @@ for: + + + + + + + + + + + + @@ -259,6 +346,7 @@ for: + @@ -266,6 +354,7 @@ for: + @@ -273,6 +362,7 @@ for: + @@ -280,6 +370,7 @@ for: + @@ -287,6 +378,7 @@ for: + @@ -294,6 +386,7 @@ for: + @@ -301,6 +394,7 @@ for: + @@ -340,6 +434,23 @@ for: + + + + + + + + + + + + + + + + + @@ -394,6 +505,30 @@ for: + + + + + + + + + + + + + + + + + + + + + + + + @@ -456,9 +591,22 @@ for: + + + + + + + + + + + + + @@ -554,7 +702,7 @@ for: - fmt_finder['output_format'] == 'None' and fmt_peek not in {'PairedDNASequencesDirectoryFormat', 'DataLoafPackageDirFmt', 'BIOMV210Format', 'BLAST6DirectoryFormat', 'ProteinFASTAFormat', 'ProbabilitiesFormat', 'MultiBowtie2IndexDirFmt', 'MultiMAGSequencesDirFmt', 'ImmutableMetadataFormat', 'DecontamScoreFormat', 'SILVATaxidMapFormat', 'AlignedProteinFASTAFormat', 'NewickFormat', 'PredictionsFormat', 'AlignedProteinSequencesDirectoryFormat', 'SeppReferenceDirFmt', 'TaxonomicClassiferTemporaryPickleDirFmt', 'PlacementsDirFmt', 'ImmutableMetadataDirectoryFormat', 'CasavaOneEightSingleLanePerSampleDirFmt', 'EMPPairedEndDirFmt', 'RNAFASTAFormat', 'EMPSingleEndDirFmt', 'ProcrustesStatisticsDirFmt', 'DADA2StatsDirFmt', 'ErrorCorrectionDetailsDirFmt', 'ProbabilitiesDirectoryFormat', 'MultiBAMDirFmt', 'SeedOrthologDirFmt', 'AlignedRNASequencesDirectoryFormat', 'MAGtoContigsDirFmt', 'DifferentialDirectoryFormat', 'QualityFilterStatsDirFmt', 'SILVATaxonomyFormat', 'DADA2StatsFormat', 'UchimeStatsFmt', 'DecontamScoreDirFmt', 'SingleLanePerSamplePairedEndFastqDirFmt', 'RNASequencesDirectoryFormat', 'SingleLanePerSampleSingleEndFastqDirFmt', 'DNAFASTAFormat', 'BooleanSeriesDirectoryFormat', 'LociDirectoryFormat', 'NewickDirectoryFormat', 'ProteinSequencesDirectoryFormat', 'DeblurStatsFmt', 'BooleanSeriesFormat', 'OrdinationFormat', 'AlphaDiversityFormat', 'TSVTaxonomyFormat', 'SampleEstimatorDirFmt', 'MAGtoContigsFormat', 'SILVATaxonomyDirectoryFormat', 'QIIME1DemuxDirFmt', 'BLASTDBDirFmtV5', 'ProteinsDirectoryFormat', 'LSMatFormat', 'PredictionsDirectoryFormat', 'DifferentialFormat', 'BAMDirFmt', 'ArtificialGroupingFormat', 'ImportanceDirectoryFormat', 'DNASequencesDirectoryFormat', 'SILVATaxidMapDirectoryFormat', 'DistanceMatrixDirectoryFormat', 'QIIME1DemuxFormat', 'OrdinationDirectoryFormat', 'MultiplexedSingleEndBarcodeInSequenceDirFmt', 'QualityFilterStatsFmt', 'PairedRNASequencesDirectoryFormat', 'DeblurStatsDirFmt', 'ContigSequencesDirFmt', 'GenesDirectoryFormat', 'ImportanceFormat', 'ProcrustesStatisticsFmt', 'ArtificialGroupingDirectoryFormat', 'FirstDifferencesDirectoryFormat', 'BLAST6Format', 'TSVTaxonomyDirectoryFormat', 'AlphaDiversityDirectoryFormat', 'BIOMV210DirFmt', 'TrueTargetsDirectoryFormat', 'AlignedDNASequencesDirectoryFormat', 'FastqGzFormat', 'AlignedRNAFASTAFormat', 'AlignedDNAFASTAFormat', 'FirstDifferencesFormat', 'Bowtie2IndexDirFmt', 'UchimeStatsDirFmt', 'MultiplexedPairedEndBarcodeInSequenceDirFmt', 'PlacementsFormat'} + fmt_finder['output_format'] == 'None' and fmt_peek not in {'PredictionsDirectoryFormat', 'QualityFilterStatsDirFmt', 'ProteinSequencesDirectoryFormat', 'OrthologAnnotationDirFmt', 'FirstDifferencesDirectoryFormat', 'DecontamScoreDirFmt', 'BooleanSeriesFormat', 'Bowtie2IndexDirFmt', 'GenesDirectoryFormat', 'AlphaDiversityFormat', 'SILVATaxidMapFormat', 'RNASequencesDirectoryFormat', 'MultiBAMDirFmt', 'AlignedDNAFASTAFormat', 'SILVATaxonomyDirectoryFormat', 'SeedOrthologDirFmt', 'QIIME1DemuxDirFmt', 'ImportanceDirectoryFormat', 'BooleanSeriesDirectoryFormat', 'BLAST6DirectoryFormat', 'BAMDirFmt', 'ImmutableMetadataFormat', 'QualityFilterStatsFmt', 'Kraken2DBReportDirectoryFormat', 'SingleLanePerSamplePairedEndFastqDirFmt', 'MAGtoContigsDirFmt', 'AlignedRNASequencesDirectoryFormat', 'NewickFormat', 'NewickDirectoryFormat', 'ProcrustesStatisticsFmt', 'EMPSingleEndDirFmt', 'PlacementsFormat', 'LSMatFormat', 'OrdinationFormat', 'AlignedProteinFASTAFormat', 'DifferentialFormat', 'SILVATaxidMapDirectoryFormat', 'CasavaOneEightSingleLanePerSampleDirFmt', 'ProbabilitiesFormat', 'DADA2StatsFormat', 'DNASequencesDirectoryFormat', 'EMPPairedEndDirFmt', 'SequenceCharacteristicsFormat', 'DiamondDatabaseFileFmt', 'ImmutableMetadataDirectoryFormat', 'OrdinationDirectoryFormat', 'MultiBowtie2IndexDirFmt', 'SILVATaxonomyFormat', 'DistanceMatrixDirectoryFormat', 'TaxonomicClassiferTemporaryPickleDirFmt', 'DiamondDatabaseDirFmt', 'BIOMV210DirFmt', 'BIOMV210Format', 'LociDirectoryFormat', 'QIIME1DemuxFormat', 'Kraken2ReportDirectoryFormat', 'TSVTaxonomyFormat', 'KaijuDBDirectoryFormat', 'ErrorCorrectionDetailsFmt', 'NCBITaxonomyDirFmt', 'AlignedProteinSequencesDirectoryFormat', 'ProteinFASTAFormat', 'AlphaDiversityDirectoryFormat', 'FastqGzFormat', 'ImportanceFormat', 'ContigSequencesDirFmt', 'RNAFASTAFormat', 'ErrorCorrectionDetailsDirFmt', 'SequenceCharacteristicsDirectoryFormat', 'UchimeStatsDirFmt', 'MAGSequencesDirFmt', 'PairedRNASequencesDirectoryFormat', 'DNAFASTAFormat', 'MultiplexedSingleEndBarcodeInSequenceDirFmt', 'DataLoafPackageDirFmt', 'SingleLanePerSampleSingleEndFastqDirFmt', 'MultiFASTADirectoryFormat', 'BLASTDBDirFmtV5', 'BrackenDBDirectoryFormat', 'FirstDifferencesFormat', 'TSVTaxonomyDirectoryFormat', 'DifferentialDirectoryFormat', 'MultiMAGSequencesDirFmt', 'PlacementsDirFmt', 'BLAST6Format', 'AlignedRNAFASTAFormat', 'TrueTargetsDirectoryFormat', 'ArtificialGroupingDirectoryFormat', 'ProcrustesStatisticsDirFmt', 'ProteinsDirectoryFormat', 'MAGtoContigsFormat', 'AlignedDNASequencesDirectoryFormat', 'ArtificialGroupingFormat', 'SeppReferenceDirFmt', 'MultiplexedPairedEndBarcodeInSequenceDirFmt', 'EggnogProteinSequencesDirFmt', 'ProbabilitiesDirectoryFormat', 'DeblurStatsDirFmt', 'DADA2StatsDirFmt', 'DecontamScoreFormat', 'UchimeStatsFmt', 'SampleEstimatorDirFmt', 'EggnogRefDirFmt', 'DeblurStatsFmt', 'PairedDNASequencesDirectoryFormat', 'Kraken2OutputDirectoryFormat', 'PredictionsFormat', 'Kraken2DBDirectoryFormat'} @@ -645,6 +793,10 @@ for: + + fmt_finder['output_format'] == 'BrackenDBDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'BrackenDBDirectoryFormat') + + fmt_finder['output_format'] == 'CasavaOneEightSingleLanePerSampleDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'CasavaOneEightSingleLanePerSampleDirFmt') @@ -693,6 +845,14 @@ for: fmt_finder['output_format'] == 'DecontamScoreFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DecontamScoreFormat') + + fmt_finder['output_format'] == 'DiamondDatabaseDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DiamondDatabaseDirFmt') + + + + fmt_finder['output_format'] == 'DiamondDatabaseFileFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DiamondDatabaseFileFmt') + + fmt_finder['output_format'] == 'DifferentialDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DifferentialDirectoryFormat') @@ -716,10 +876,23 @@ for: + + fmt_finder['output_format'] == 'EggnogProteinSequencesDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'EggnogProteinSequencesDirFmt') + + + + + fmt_finder['output_format'] == 'EggnogRefDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'EggnogRefDirFmt') + + fmt_finder['output_format'] == 'ErrorCorrectionDetailsDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ErrorCorrectionDetailsDirFmt') + + fmt_finder['output_format'] == 'ErrorCorrectionDetailsFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ErrorCorrectionDetailsFmt') + + fmt_finder['output_format'] == 'FastqGzFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'FastqGzFormat') @@ -734,7 +907,7 @@ for: fmt_finder['output_format'] == 'GenesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'GenesDirectoryFormat') - + fmt_finder['output_format'] == 'ImmutableMetadataDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ImmutableMetadataDirectoryFormat') @@ -752,13 +925,41 @@ for: fmt_finder['output_format'] == 'ImportanceFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ImportanceFormat') + + fmt_finder['output_format'] == 'KaijuDBDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'KaijuDBDirectoryFormat') + + + + + + fmt_finder['output_format'] == 'Kraken2DBDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'Kraken2DBDirectoryFormat') + + + + + + fmt_finder['output_format'] == 'Kraken2DBReportDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'Kraken2DBReportDirectoryFormat') + + + + fmt_finder['output_format'] == 'Kraken2OutputDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'Kraken2OutputDirectoryFormat') + + + + fmt_finder['output_format'] == 'Kraken2ReportDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'Kraken2ReportDirectoryFormat') + + fmt_finder['output_format'] == 'LSMatFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'LSMatFormat') fmt_finder['output_format'] == 'LociDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'LociDirectoryFormat') - + + + + fmt_finder['output_format'] == 'MAGSequencesDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'MAGSequencesDirFmt') + fmt_finder['output_format'] == 'MAGtoContigsDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'MAGtoContigsDirFmt') @@ -781,6 +982,10 @@ for: + + fmt_finder['output_format'] == 'MultiFASTADirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'MultiFASTADirectoryFormat') + + fmt_finder['output_format'] == 'MultiMAGSequencesDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'MultiMAGSequencesDirFmt') @@ -798,6 +1003,12 @@ for: fmt_finder['output_format'] == 'MultiplexedSingleEndBarcodeInSequenceDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'MultiplexedSingleEndBarcodeInSequenceDirFmt') + + fmt_finder['output_format'] == 'NCBITaxonomyDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'NCBITaxonomyDirFmt') + + + + fmt_finder['output_format'] == 'NewickDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'NewickDirectoryFormat') @@ -814,6 +1025,10 @@ for: fmt_finder['output_format'] == 'OrdinationFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'OrdinationFormat') + + fmt_finder['output_format'] == 'OrthologAnnotationDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'OrthologAnnotationDirFmt') + + fmt_finder['output_format'] == 'PairedDNASequencesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'PairedDNASequencesDirectoryFormat') @@ -866,7 +1081,7 @@ for: fmt_finder['output_format'] == 'ProteinsDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ProteinsDirectoryFormat') - + fmt_finder['output_format'] == 'QIIME1DemuxDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'QIIME1DemuxDirFmt') @@ -923,6 +1138,14 @@ for: + + fmt_finder['output_format'] == 'SequenceCharacteristicsDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SequenceCharacteristicsDirectoryFormat') + + + + fmt_finder['output_format'] == 'SequenceCharacteristicsFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SequenceCharacteristicsFormat') + + fmt_finder['output_format'] == 'SingleLanePerSamplePairedEndFastqDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SingleLanePerSamplePairedEndFastqDirFmt') @@ -1031,6 +1254,20 @@ Format details: - Each sequence must be DNA and cannot be empty. +SequenceCharacteristicsFormat +***************************** + +Format for a TSV file with information about sequences like length of a +feature. The first column contains feature identifiers and is followed by +other optional columns. + +The file cannot be empty and must have at least two columns. + +Validation for additional columns can be added with a semantic validator +tied to a property. For example the "validate_seq_char_len" validator for +"FeatureData[SequenceCharacteristics % Properties("length")]" +adds validation for a numerical column called "length". + TSVTaxonomyFormat ***************** Format for a 2+ column TSV file with an expected minimal header. @@ -1048,94 +1285,110 @@ of data. Additional formats without documentation: ***************************************** - - BAMDirFmt - - TaxonomicClassiferTemporaryPickleDirFmt - - ProbabilitiesDirectoryFormat - - BooleanSeriesFormat - - ErrorCorrectionDetailsDirFmt - - AlignedRNASequencesDirectoryFormat - - ProcrustesStatisticsDirFmt - - DifferentialDirectoryFormat - - SampleEstimatorDirFmt - - PlacementsDirFmt - - SILVATaxidMapDirectoryFormat + - DataLoafPackageDirFmt + - EggnogRefDirFmt + - NCBITaxonomyDirFmt - BIOMV210DirFmt - - MultiBAMDirFmt - - QualityFilterStatsDirFmt - - TrueTargetsDirectoryFormat - - MAGtoContigsFormat - - ArtificialGroupingDirectoryFormat - - BooleanSeriesDirectoryFormat - - PlacementsFormat - - PredictionsFormat - - MultiplexedPairedEndBarcodeInSequenceDirFmt - - DeblurStatsDirFmt + - FirstDifferencesDirectoryFormat + - PredictionsDirectoryFormat + - QIIME1DemuxDirFmt + - SILVATaxonomyFormat + - MAGSequencesDirFmt + - AlphaDiversityDirectoryFormat + - Kraken2OutputDirectoryFormat + - BAMDirFmt + - TSVTaxonomyDirectoryFormat + - EggnogProteinSequencesDirFmt + - ImmutableMetadataFormat + - LSMatFormat - SingleLanePerSampleSingleEndFastqDirFmt - AlignedProteinFASTAFormat - PairedDNASequencesDirectoryFormat - - UchimeStatsDirFmt - - DataLoafPackageDirFmt - - ArtificialGroupingFormat - - PredictionsDirectoryFormat - - SILVATaxonomyDirectoryFormat - - DNAFASTAFormat - - EMPSingleEndDirFmt - - SingleLanePerSamplePairedEndFastqDirFmt + - BooleanSeriesFormat + - MultiplexedPairedEndBarcodeInSequenceDirFmt + - DecontamScoreFormat + - OrthologAnnotationDirFmt + - GenesDirectoryFormat + - MultiBAMDirFmt + - BIOMV210Format + - DecontamScoreDirFmt + - ErrorCorrectionDetailsFmt + - DiamondDatabaseFileFmt - AlignedProteinSequencesDirectoryFormat - PairedRNASequencesDirectoryFormat - - SeppReferenceDirFmt - - MAGtoContigsDirFmt - DifferentialFormat - - UchimeStatsFmt - - SILVATaxonomyFormat - - FirstDifferencesDirectoryFormat + - Kraken2DBDirectoryFormat + - DADA2StatsFormat - DNASequencesDirectoryFormat - - GenesDirectoryFormat - - EMPPairedEndDirFmt + - ErrorCorrectionDetailsDirFmt + - DiamondDatabaseDirFmt + - ImmutableMetadataDirectoryFormat + - BooleanSeriesDirectoryFormat - AlignedDNAFASTAFormat - - SILVATaxidMapFormat - - ProteinsDirectoryFormat - - MultiMAGSequencesDirFmt - - QualityFilterStatsFmt - - AlignedDNASequencesDirectoryFormat - - LSMatFormat - - ImmutableMetadataFormat - - DeblurStatsFmt - - AlphaDiversityFormat - - MultiBowtie2IndexDirFmt - ImportanceFormat - - FirstDifferencesFormat - - DADA2StatsFormat + - NewickFormat - DistanceMatrixDirectoryFormat - - ImmutableMetadataDirectoryFormat - - OrdinationFormat - - DecontamScoreDirFmt - - CasavaOneEightSingleLanePerSampleDirFmt + - SingleLanePerSamplePairedEndFastqDirFmt + - PlacementsDirFmt + - DeblurStatsFmt + - SILVATaxidMapDirectoryFormat + - QualityFilterStatsFmt + - AlignedDNASequencesDirectoryFormat + - ImportanceDirectoryFormat + - NewickDirectoryFormat - MultiplexedSingleEndBarcodeInSequenceDirFmt - - AlphaDiversityDirectoryFormat + - MultiFASTADirectoryFormat + - ProcrustesStatisticsFmt + - SILVATaxidMapFormat + - UchimeStatsDirFmt + - Kraken2ReportDirectoryFormat + - BLAST6Format + - QualityFilterStatsDirFmt + - ProbabilitiesFormat + - SILVATaxonomyDirectoryFormat + - MultiMAGSequencesDirFmt + - EMPSingleEndDirFmt + - Bowtie2IndexDirFmt + - ProcrustesStatisticsDirFmt + - DeblurStatsDirFmt + - ArtificialGroupingDirectoryFormat + - TaxonomicClassiferTemporaryPickleDirFmt + - LociDirectoryFormat + - ArtificialGroupingFormat + - MAGtoContigsFormat + - BrackenDBDirectoryFormat - ProteinFASTAFormat - RNAFASTAFormat - - ContigSequencesDirFmt - - ImportanceDirectoryFormat - DADA2StatsDirFmt - - NewickFormat - - OrdinationDirectoryFormat - - TSVTaxonomyDirectoryFormat - - BLAST6Format - - LociDirectoryFormat + - BLAST6DirectoryFormat + - ProbabilitiesDirectoryFormat + - MultiBowtie2IndexDirFmt + - EMPPairedEndDirFmt + - OrdinationFormat + - SeedOrthologDirFmt + - MAGtoContigsDirFmt + - SampleEstimatorDirFmt + - PlacementsFormat - ProteinSequencesDirectoryFormat - RNASequencesDirectoryFormat - - BIOMV210Format - - ProbabilitiesFormat - - BLASTDBDirFmtV5 - - DecontamScoreFormat + - DNAFASTAFormat + - UchimeStatsFmt - AlignedRNAFASTAFormat - - NewickDirectoryFormat - - ProcrustesStatisticsFmt - - BLAST6DirectoryFormat - - SeedOrthologDirFmt - - QIIME1DemuxDirFmt - - Bowtie2IndexDirFmt + - TrueTargetsDirectoryFormat + - Kraken2DBReportDirectoryFormat + - KaijuDBDirectoryFormat + - ContigSequencesDirFmt + - FirstDifferencesFormat + - SeppReferenceDirFmt + - OrdinationDirectoryFormat + - PredictionsFormat + - ProteinsDirectoryFormat + - BLASTDBDirFmtV5 + - AlignedRNASequencesDirectoryFormat + - SequenceCharacteristicsDirectoryFormat + - AlphaDiversityFormat + - CasavaOneEightSingleLanePerSampleDirFmt + - DifferentialDirectoryFormat 10.1038/s41587-019-0209-9 diff --git a/tools/suite_qiime2_core__tools/qiime2_core__tools__import.xml b/tools/suite_qiime2_core__tools/qiime2_core__tools__import.xml index 7e90f0b..bf27578 100644 --- a/tools/suite_qiime2_core__tools/qiime2_core__tools__import.xml +++ b/tools/suite_qiime2_core__tools/qiime2_core__tools__import.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Import data into a QIIME 2 artifact - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy run tools import '$inputs' @@ -62,6 +62,7 @@ write(json.dumps(inputs)) + @@ -70,18 +71,28 @@ write(json.dumps(inputs)) + + + + + + + + + + @@ -97,6 +108,9 @@ write(json.dumps(inputs)) + + + @@ -106,6 +120,10 @@ write(json.dumps(inputs)) + + + + @@ -116,6 +134,8 @@ write(json.dumps(inputs)) + + @@ -235,6 +255,44 @@ write(json.dumps(inputs)) + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + database(\d{2,})mers\.kmer_distrib$ + + + + + +
+ + + @@ -391,6 +449,44 @@ write(json.dumps(inputs)) + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + .+\.bam + + + + + +
+ + + @@ -404,6 +500,44 @@ write(json.dumps(inputs)) + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + [^\.].+_contigs.(fasta|fa)$ + + + + + +
+ + + @@ -485,6 +619,234 @@ write(json.dumps(inputs)) + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + .+\.annotations + + + + + +
+ + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + .+output\.(txt|tsv)$ + + + + + +
+ + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + .+report\.(txt|tsv)$ + + + + + +
+ + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + ^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-4[0-9a-fA-F]{3}-[89abAB][0-9a-fA-F]{3}-[0-9a-fA-F]{12}\.(fa|fasta)$ + + + + + +
+ + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + .+\.annotations + + + + + +
+ + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + .+\.annotations + + + + + +
+ + + @@ -578,13 +940,33 @@ write(json.dumps(inputs)) + + + + + + +
+ + +
+ + + + + +
+ + +
+
@@ -605,6 +987,51 @@ write(json.dumps(inputs)) + + + + + + +
+ + .+(?<!\.rev)\.1\.bt2l? + + +
+
+ + .+(?<!\.rev)\.2\.bt2l? + + +
+
+ + .+\.3\.bt2l? + + +
+
+ + .+\.4\.bt2l? + + +
+
+ + .+\.rev\.1\.bt2l? + + +
+
+ + .+\.rev\.2\.bt2l? + + +
+ + + @@ -836,7 +1263,7 @@ write(json.dumps(inputs)) - + @@ -850,8 +1277,8 @@ write(json.dumps(inputs)) - - (.*\_)?genes[0-9]*\.(fa|fna|fasta)$ + + .+\.(fa|fna|fasta)$ @@ -874,7 +1301,7 @@ write(json.dumps(inputs)) - + @@ -888,8 +1315,8 @@ write(json.dumps(inputs)) - - (.*\_)?loci[0-9]*\.gff$ + + .+\.gff$ @@ -912,7 +1339,7 @@ write(json.dumps(inputs)) - + @@ -926,8 +1353,8 @@ write(json.dumps(inputs)) - - (.*\_)?proteins[0-9]*\.(fa|faa|fasta)$ + + .+\.(fa|faa|fasta)$ @@ -950,15 +1377,72 @@ write(json.dumps(inputs)) - + + + + + + +
+ + +
+ + + + + + + + + +
+ + +
+
+ + +
+
+ + kaiju_db.+\.fmi + + +
+ + + + + + + + + +
+ + +
+
+ + +
+
+ + +
+ + + + - + - +
- +
@@ -1110,6 +1594,95 @@ write(json.dumps(inputs)) + + + + + + +
+ + +
+ + + + + + + + + +
+ + +
+
+ + +
+ + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + eggnog.*db.* + + + + + +
+ + + + + + + + + +
+ + +
+
+ + +
+
+ + +
+ + + @@ -1512,6 +2085,82 @@ write(json.dumps(inputs)) + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + .+output\.(txt|tsv)$ + + + + + +
+ + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + .+report\.(txt|tsv)$ + + + + + +
+ + + @@ -2275,11 +2924,10 @@ Formats: -------- These formats have documentation available. -HeaderlessTSVTaxonomyFormat -*************************** -Format for a 2+ column TSV file without a header. +FastqGzFormat +************* -This format supports comment lines starting with #, and blank lines. +A gzipped fastq file. SampleIdIndexedSingleEndPerSampleDirFmt @@ -2292,12 +2940,6 @@ Single-end reads in fastq.gz files where base filename is the sample id * `xyz.fastq.gz` is `xyz` * `sample-42_S1_L001_R1_001.fastq.gz` is `sample-42_S1_L001_R1_001` -FastqGzFormat -************* - -A gzipped fastq file. - - QIIME1DemuxFormat ***************** QIIME 1 demultiplexed FASTA format. @@ -2332,6 +2974,27 @@ Format details: - Each sequence must be DNA and cannot be empty. +HeaderlessTSVTaxonomyFormat +*************************** +Format for a 2+ column TSV file without a header. + +This format supports comment lines starting with #, and blank lines. + + +SequenceCharacteristicsFormat +***************************** + +Format for a TSV file with information about sequences like length of a +feature. The first column contains feature identifiers and is followed by +other optional columns. + +The file cannot be empty and must have at least two columns. + +Validation for additional columns can be added with a semantic validator +tied to a property. For example the "validate_seq_char_len" validator for +"FeatureData[SequenceCharacteristics % Properties("length")]" +adds validation for a numerical column called "length". + TSVTaxonomyFormat ***************** Format for a 2+ column TSV file with an expected minimal header. @@ -2349,78 +3012,90 @@ of data. Additional formats without documentation: ***************************************** - - BAMDirFmt - - TaxonomicClassiferTemporaryPickleDirFmt - - BooleanSeriesFormat - - SingleEndFastqManifestPhred33 - - SampleEstimatorDirFmt - - MultiBAMDirFmt - - MAGtoContigsFormat + - DataLoafPackageDirFmt + - EggnogRefDirFmt + - NCBITaxonomyDirFmt + - SILVATaxonomyFormat - MixedCaseAlignedRNAFASTAFormat - - PlacementsFormat - - PredictionsFormat - - SingleEndFastqManifestPhred64 - - MultiplexedPairedEndBarcodeInSequenceDirFmt + - MAGSequencesDirFmt + - Kraken2OutputDirectoryFormat + - BAMDirFmt + - EggnogProteinSequencesDirFmt + - ImmutableMetadataFormat + - EMPPairedEndCasavaDirFmt + - LSMatFormat - SingleLanePerSampleSingleEndFastqDirFmt - AlignedProteinFASTAFormat - PairedDNASequencesDirectoryFormat - - DataLoafPackageDirFmt - - ArtificialGroupingFormat - - PairedEndFastqManifestPhred33 - - DNAFASTAFormat - - EMPSingleEndDirFmt - - SingleLanePerSamplePairedEndFastqDirFmt + - BooleanSeriesFormat + - MultiplexedPairedEndBarcodeInSequenceDirFmt + - DecontamScoreFormat + - OrthologAnnotationDirFmt + - GenesDirectoryFormat + - MultiBAMDirFmt + - BIOMV210Format + - ErrorCorrectionDetailsFmt + - DiamondDatabaseFileFmt - PairedRNASequencesDirectoryFormat - - SeppReferenceDirFmt - DifferentialFormat - - UchimeStatsFmt - - SILVATaxonomyFormat - - PairedEndFastqManifestPhred64 - - GenesDirectoryFormat - - MultiFASTADirectoryFormat - - EMPPairedEndDirFmt - - CasavaOneEightLanelessPerSampleDirFmt + - Kraken2DBDirectoryFormat + - DADA2StatsFormat - AlignedDNAFASTAFormat - - SILVATaxidMapFormat - - PairedEndFastqManifestPhred33V2 - - SingleEndFastqManifestPhred33V2 + - ImportanceFormat + - SingleEndFastqManifestPhred33 + - NewickFormat + - MultiplexedFastaQualDirFmt + - SingleLanePerSamplePairedEndFastqDirFmt + - DeblurStatsFmt - MixedCaseDNAFASTAFormat - - ProteinsDirectoryFormat - - MultiMAGSequencesDirFmt - - EMPSingleEndCasavaDirFmt + - SingleEndFastqManifestPhred33V2 - QualityFilterStatsFmt - - LSMatFormat - - ImmutableMetadataFormat - - DeblurStatsFmt - - PairedEndFastqManifestPhred64V2 + - SingleEndFastqManifestPhred64 + - MultiFASTADirectoryFormat + - ProcrustesStatisticsFmt + - CasavaOneEightLanelessPerSampleDirFmt + - SILVATaxidMapFormat - SingleEndFastqManifestPhred64V2 - - AlphaDiversityFormat - - MultiBowtie2IndexDirFmt - - EMPPairedEndCasavaDirFmt - - ImportanceFormat - - FirstDifferencesFormat + - Kraken2ReportDirectoryFormat - MixedCaseAlignedDNAFASTAFormat - - MultiplexedFastaQualDirFmt - - DADA2StatsFormat - - OrdinationFormat - - CasavaOneEightSingleLanePerSampleDirFmt + - BLAST6Format + - ProbabilitiesFormat + - PairedEndFastqManifestPhred33 + - MultiMAGSequencesDirFmt + - EMPSingleEndDirFmt + - Bowtie2IndexDirFmt + - TaxonomicClassiferTemporaryPickleDirFmt + - LociDirectoryFormat + - ArtificialGroupingFormat + - MAGtoContigsFormat + - BrackenDBDirectoryFormat - ProteinFASTAFormat - RNAFASTAFormat - BIOMV100Format - - ContigSequencesDirFmt - - NewickFormat - - BLAST6Format - - LociDirectoryFormat - - BIOMV210Format - - ProbabilitiesFormat - - ErrorCorrectionDetailsFmt - - BLASTDBDirFmtV5 - - DecontamScoreFormat - - AlignedRNAFASTAFormat - - ProcrustesStatisticsFmt + - Kraken2DBReportFormat + - PairedEndFastqManifestPhred64 + - MultiBowtie2IndexDirFmt + - EMPPairedEndDirFmt + - OrdinationFormat - SeedOrthologDirFmt - - Bowtie2IndexDirFmt + - SampleEstimatorDirFmt + - PlacementsFormat + - DNAFASTAFormat + - UchimeStatsFmt + - PairedEndFastqManifestPhred33V2 + - AlignedRNAFASTAFormat + - KaijuDBDirectoryFormat + - ContigSequencesDirFmt + - EMPSingleEndCasavaDirFmt + - FirstDifferencesFormat + - SeppReferenceDirFmt + - PredictionsFormat + - ProteinsDirectoryFormat - MixedCaseRNAFASTAFormat + - PairedEndFastqManifestPhred64V2 + - BLASTDBDirFmtV5 + - AlphaDiversityFormat + - CasavaOneEightSingleLanePerSampleDirFmt 10.1038/s41587-019-0209-9 diff --git a/tools/suite_qiime2_core__tools/qiime2_core__tools__import_fastq.xml b/tools/suite_qiime2_core__tools/qiime2_core__tools__import_fastq.xml index f7883cd..13343e4 100644 --- a/tools/suite_qiime2_core__tools/qiime2_core__tools__import_fastq.xml +++ b/tools/suite_qiime2_core__tools/qiime2_core__tools__import_fastq.xml @@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Import fastq data into a QIIME 2 artifact - quay.io/qiime2/amplicon:2024.2 + quay.io/qiime2/amplicon:2024.5 q2galaxy run tools import-fastq '$inputs'