Update Galaxy Tools

qiime2 · Jun 3, 2024 · 30e631d · 30e631d
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diff --git 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)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.2.1)
+    q2galaxy (version: 2024.5.0)
 for:
-    qiime2 (version: 2024.2.0)
+    qiime2 (version: 2024.5.0)
 -->
-<tool name="qiime2 alignment mafft" id="qiime2__alignment__mafft" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 alignment mafft" id="qiime2__alignment__mafft" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
     <description>De novo multiple sequence alignment with MAFFT</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
     </requirements>
     <version_command>q2galaxy version alignment</version_command>
     <command detect_errors="exit_code">q2galaxy run alignment mafft '$inputs'</command>

diff --git 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)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.2.1)
+    q2galaxy (version: 2024.5.0)
 for:
-    qiime2 (version: 2024.2.0)
+    qiime2 (version: 2024.5.0)
 -->
-<tool name="qiime2 alignment mafft-add" id="qiime2__alignment__mafft_add" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 alignment mafft-add" id="qiime2__alignment__mafft_add" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
     <description>Add sequences to multiple sequence alignment with MAFFT.</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
     </requirements>
     <version_command>q2galaxy version alignment</version_command>
     <command detect_errors="exit_code">q2galaxy run alignment mafft_add '$inputs'</command>

diff --git 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)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.2.1)
+    q2galaxy (version: 2024.5.0)
 for:
-    qiime2 (version: 2024.2.0)
+    qiime2 (version: 2024.5.0)
 -->
-<tool name="qiime2 alignment mask" id="qiime2__alignment__mask" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 alignment mask" id="qiime2__alignment__mask" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
     <description>Positional conservation and gap filtering.</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
     </requirements>
     <version_command>q2galaxy version alignment</version_command>
     <command detect_errors="exit_code">q2galaxy run alignment mask '$inputs'</command>

diff --git 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)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.2.1)
+    q2galaxy (version: 2024.5.0)
 for:
-    qiime2 (version: 2024.2.0)
+    qiime2 (version: 2024.5.0)
 -->
-<tool name="qiime2 composition add-pseudocount" id="qiime2__composition__add_pseudocount" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 composition add-pseudocount" id="qiime2__composition__add_pseudocount" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
     <description>Add pseudocount to table.</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
     </requirements>
     <version_command>q2galaxy version composition</version_command>
     <command detect_errors="exit_code">q2galaxy run composition add_pseudocount '$inputs'</command>

diff --git 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)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.2.1)
+    q2galaxy (version: 2024.5.0)
 for:
-    qiime2 (version: 2024.2.0)
+    qiime2 (version: 2024.5.0)
 -->
-<tool name="qiime2 composition ancom" id="qiime2__composition__ancom" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 composition ancom" id="qiime2__composition__ancom" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
     <description>Apply ANCOM to identify features that differ in abundance.</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
     </requirements>
     <version_command>q2galaxy version composition</version_command>
     <command detect_errors="exit_code">q2galaxy run composition ancom '$inputs'</command>

diff --git 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)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.2.1)
+    q2galaxy (version: 2024.5.0)
 for:
-    qiime2 (version: 2024.2.0)
+    qiime2 (version: 2024.5.0)
 -->
-<tool name="qiime2 composition ancombc" id="qiime2__composition__ancombc" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 composition ancombc" id="qiime2__composition__ancombc" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
     <description>Analysis of Composition of Microbiomes with Bias Correction</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
     </requirements>
     <version_command>q2galaxy version composition</version_command>
     <command detect_errors="exit_code">q2galaxy run composition ancombc '$inputs'</command>

diff --git 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)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.2.1)
+    q2galaxy (version: 2024.5.0)
 for:
-    qiime2 (version: 2024.2.0)
+    qiime2 (version: 2024.5.0)
 -->
-<tool name="qiime2 composition da-barplot" id="qiime2__composition__da_barplot" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 composition da-barplot" id="qiime2__composition__da_barplot" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
     <description>Differential abundance bar plots</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
     </requirements>
     <version_command>q2galaxy version composition</version_command>
     <command detect_errors="exit_code">q2galaxy run composition da_barplot '$inputs'</command>

diff --git 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)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.2.1)
+    q2galaxy (version: 2024.5.0)
 for:
-    qiime2 (version: 2024.2.0)
+    qiime2 (version: 2024.5.0)
 -->
-<tool name="qiime2 composition tabulate" id="qiime2__composition__tabulate" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 composition tabulate" id="qiime2__composition__tabulate" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
     <description> View tabular output from ANCOM-BC.</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
     </requirements>
     <version_command>q2galaxy version composition</version_command>
     <command detect_errors="exit_code">q2galaxy run composition tabulate '$inputs'</command>

diff --git a/tools/suite_qiime2__composition/test-data/ancombc.test0.table.qza b/tools/suite_qiime2__composition/test-data/ancombc.test0.table.qza
diff --git a/tools/suite_qiime2__composition/test-data/ancombc.test1.table.qza b/tools/suite_qiime2__composition/test-data/ancombc.test1.table.qza
diff --git a/tools/suite_qiime2__cutadapt/qiime2__cutadapt__demux_paired.xml b/tools/suite_qiime2__cutadapt/qiime2__cutadapt__demux_paired.xml
@@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.2.1)
+    q2galaxy (version: 2024.5.0)
 for:
-    qiime2 (version: 2024.2.0)
+    qiime2 (version: 2024.5.0)
 -->
-<tool name="qiime2 cutadapt demux-paired" id="qiime2__cutadapt__demux_paired" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 cutadapt demux-paired" id="qiime2__cutadapt__demux_paired" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
     <description>Demultiplex paired-end sequence data with barcodes in-sequence.</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
     </requirements>
     <version_command>q2galaxy version cutadapt</version_command>
     <command detect_errors="exit_code">q2galaxy run cutadapt demux_paired '$inputs'</command>

diff --git 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)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.2.1)
+    q2galaxy (version: 2024.5.0)
 for:
-    qiime2 (version: 2024.2.0)
+    qiime2 (version: 2024.5.0)
 -->
-<tool name="qiime2 cutadapt demux-single" id="qiime2__cutadapt__demux_single" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 cutadapt demux-single" id="qiime2__cutadapt__demux_single" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
     <description>Demultiplex single-end sequence data with barcodes in-sequence.</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
     </requirements>
     <version_command>q2galaxy version cutadapt</version_command>
     <command detect_errors="exit_code">q2galaxy run cutadapt demux_single '$inputs'</command>

diff --git 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)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.2.1)
+    q2galaxy (version: 2024.5.0)
 for:
-    qiime2 (version: 2024.2.0)
+    qiime2 (version: 2024.5.0)
 -->
-<tool name="qiime2 cutadapt trim-paired" id="qiime2__cutadapt__trim_paired" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 cutadapt trim-paired" id="qiime2__cutadapt__trim_paired" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
     <description>Find and remove adapters in demultiplexed paired-end sequences.</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
     </requirements>
     <version_command>q2galaxy version cutadapt</version_command>
     <command detect_errors="exit_code">q2galaxy run cutadapt trim_paired '$inputs'</command>

diff --git 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)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.2.1)
+    q2galaxy (version: 2024.5.0)
 for:
-    qiime2 (version: 2024.2.0)
+    qiime2 (version: 2024.5.0)
 -->
-<tool name="qiime2 cutadapt trim-single" id="qiime2__cutadapt__trim_single" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 cutadapt trim-single" id="qiime2__cutadapt__trim_single" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
     <description>Find and remove adapters in demultiplexed single-end sequences.</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
     </requirements>
     <version_command>q2galaxy version cutadapt</version_command>
     <command detect_errors="exit_code">q2galaxy run cutadapt trim_single '$inputs'</command>

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
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
diff --git a/tools/suite_qiime2__dada2/qiime2__dada2__denoise_ccs.xml b/tools/suite_qiime2__dada2/qiime2__dada2__denoise_ccs.xml
@@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.2.1)
+    q2galaxy (version: 2024.5.0)
 for:
-    qiime2 (version: 2024.2.0)
+    qiime2 (version: 2024.5.0)
 -->
-<tool name="qiime2 dada2 denoise-ccs" id="qiime2__dada2__denoise_ccs" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 dada2 denoise-ccs" id="qiime2__dada2__denoise_ccs" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
     <description>Denoise and dereplicate single-end Pacbio CCS</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
     </requirements>
     <version_command>q2galaxy version dada2</version_command>
     <command detect_errors="exit_code">q2galaxy run dada2 denoise_ccs '$inputs'</command>

diff --git 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)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.2.1)
+    q2galaxy (version: 2024.5.0)
 for:
-    qiime2 (version: 2024.2.0)
+    qiime2 (version: 2024.5.0)
 -->
-<tool name="qiime2 dada2 denoise-paired" id="qiime2__dada2__denoise_paired" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 dada2 denoise-paired" id="qiime2__dada2__denoise_paired" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
     <description>Denoise and dereplicate paired-end sequences</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
     </requirements>
     <version_command>q2galaxy version dada2</version_command>
     <command detect_errors="exit_code">q2galaxy run dada2 denoise_paired '$inputs'</command>

diff --git 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)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.2.1)
+    q2galaxy (version: 2024.5.0)
 for:
-    qiime2 (version: 2024.2.0)
+    qiime2 (version: 2024.5.0)
 -->
-<tool name="qiime2 dada2 denoise-pyro" id="qiime2__dada2__denoise_pyro" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 dada2 denoise-pyro" id="qiime2__dada2__denoise_pyro" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
     <description>Denoise and dereplicate single-end pyrosequences</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
     </requirements>
     <version_command>q2galaxy version dada2</version_command>
     <command detect_errors="exit_code">q2galaxy run dada2 denoise_pyro '$inputs'</command>

diff --git 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. (SPDX: BSD-3-Clause)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.2.1)
+    q2galaxy (version: 2024.5.0)
 for:
-    qiime2 (version: 2024.2.0)
+    qiime2 (version: 2024.5.0)
 -->
-<tool name="qiime2 dada2 denoise-single" id="qiime2__dada2__denoise_single" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 dada2 denoise-single" id="qiime2__dada2__denoise_single" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
     <description>Denoise and dereplicate single-end sequences</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
     </requirements>
     <version_command>q2galaxy version dada2</version_command>
     <command detect_errors="exit_code">q2galaxy run dada2 denoise_single '$inputs'</command>

diff --git a/tools/suite_qiime2__dada2/test-data/denoise_paired.test0.demux-paired.qza b/tools/suite_qiime2__dada2/test-data/denoise_paired.test0.demux-paired.qza
diff --git a/tools/suite_qiime2__dada2/test-data/denoise_single.test0.demux-single.qza b/tools/suite_qiime2__dada2/test-data/denoise_single.test0.demux-single.qza
diff --git a/tools/suite_qiime2__deblur/qiime2__deblur__denoise_16S.xml b/tools/suite_qiime2__deblur/qiime2__deblur__denoise_16S.xml
@@ -6,14 +6,14 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.2.1)
+    q2galaxy (version: 2024.5.0)
 for:
-    qiime2 (version: 2024.2.0)
+    qiime2 (version: 2024.5.0)
 -->
-<tool name="qiime2 deblur denoise-16S" id="qiime2__deblur__denoise_16S" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 deblur denoise-16S" id="qiime2__deblur__denoise_16S" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
     <description>Deblur sequences using a 16S positive filter.</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
     </requirements>
     <version_command>q2galaxy version deblur</version_command>
     <command detect_errors="exit_code">q2galaxy run deblur denoise_16S '$inputs'</command>
@@ -23,9 +23,9 @@ for:
     <inputs>
         <param name="demultiplexed_seqs" type="data" format="qza" label="demultiplexed_seqs: SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality]" help="[required]  The demultiplexed sequences to be denoised.">
             <options options_filter_attribute="metadata.semantic_type">
-                <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/>
-                <filter type="add_value" value="SampleData[JoinedSequencesWithQuality]"/>
                 <filter type="add_value" value="SampleData[SequencesWithQuality]"/>
+                <filter type="add_value" value="SampleData[JoinedSequencesWithQuality]"/>
+                <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/>
             </options>
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[JoinedSequencesWithQuality]', 'SampleData[PairedEndSequencesWithQuality]', 'SampleData[SequencesWithQuality]']</validator>
         </param>