Update wrapper

bgruening · Aug 30, 2023 · dcc2a4f · dcc2a4f
1 parent 27d51fb
commit dcc2a4f
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Showing 30 changed files with 4,064 additions and 4,128 deletions.
diff --git a/tools/rna_tools/sortmerna/macros.xml b/tools/rna_tools/sortmerna/macros.xml
@@ -11,6 +11,17 @@
  <param name="seed_length" type="integer" min="0" max="100" value="18" label="Seed length for database indexing" help="(-L)"/>
  <param name="max_pos" type="integer" min="0" max="100000" value="10000" label="Maximum number of positions to store for each k-mer for database indexing" help="With 0, all positions are stored (--max_pos)"/>
  </xml>
+ <xml name="reads_macro">
+ <param argument="--reads" type="data" format="fasta,fastq,fastq.gz" label="Querying sequences"/>
+ </xml>
+ <xml name="paired_type_macro">
+ <param name="paired_type" type="select" display="radio" label="If one of the paired-end reads aligns and the other one does not">
+ <option value="">Leave the reads split between aligned and rejected files</option>
+ <option value="--paired_in">Output both reads to aligned file (--paired_in)</option>
+ <option value="--paired_out">Output both reads to rejected file (--paired_out)</option>
+ <option value="--sout">Separate paired and singleton aligned reads (--sout)</option>
+ </param>
+ </xml>
  <xml name="output_alignments">
  <param name="print_all_reads" type="boolean" checked="false" truevalue="--print_all_reads" falsevalue="" label="Output null alignment strings for non-aligned reads"/>
  <conditional name="blast">
@@ -39,21 +50,17 @@
  <when value="True">
  <param argument="--id" type="float" value="0.97" label="Percentage id similarity threshold" help="The alignment must still pass the E-value threshold" />
  <param argument="--coverage" type="float" value="0.97" label="Percentage query coverage threshold" help="The alignment must still pass the E-value threshold" />
- <param name="de_novo_otu" type="boolean" truevalue="True" falsevalue="False" label="FASTA/FASTQ file for reads matching database below percentage id" help="--de_novo_otu" />
+ <param name="de_novo_otu" type="boolean" truevalue="--de_novo_otu" falsevalue="" label="FASTA/FASTQ file for reads matching database below percentage id" help="--de_novo_otu" />
  </when>
  <when value="False"/>
  </conditional>
  </xml>
- <xml name="evalue_macro">
- <param name="e_value" argument="-e" type="float" min="0" max="10" value="1" label="E-value threshold" help="Defines the 'statistical significance' of a local alignment. Exponentially 
- correllates with the Minimal Alignment score. Higher E-values (100, 1000, ...) cause more reads to pass the alignment threshold."/>
- </xml>
- <token name="@OTUS@">
+ <token name="@OTU_PICKING@">
  #if $report.otu.otu_map == 'True'
  --otu_map
  --id '$report.otu.id'
  --coverage '$report.otu.coverage'
- --de_novo_otu $report.otu.de_novo_otu
+ $report.otu.de_novo_otu
  #end if
  </token>
  <token name="@ALIGNMENTS@">

diff --git a/tools/rna_tools/sortmerna/sortmerna.xml b/tools/rna_tools/sortmerna/sortmerna.xml
diff --git a/tools/rna_tools/sortmerna/test-data/interlaced_reads.fastq.gz b/tools/rna_tools/sortmerna/test-data/interlaced_reads.fastq.gz
diff --git a/tools/rna_tools/sortmerna/test-data/read_small.fastq.gz b/tools/rna_tools/sortmerna/test-data/read_small.fastq.gz
diff --git a/tools/rna_tools/sortmerna/test-data/reads_small.fastq.gz b/tools/rna_tools/sortmerna/test-data/reads_small.fastq.gz
diff --git a/tools/rna_tools/sortmerna/test-data/ref_small.fasta.gz b/tools/rna_tools/sortmerna/test-data/ref_small.fasta.gz
diff --git a/tools/rna_tools/sortmerna/test-data/test1_aligned.fastq b/tools/rna_tools/sortmerna/test-data/test1_aligned.fastq
@@ -1,4 +1,4 @@
 @read1
 GCCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATACCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACC
-+read1
++
 IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff --git a/tools/rna_tools/sortmerna/test-data/test1_bam.bam b/tools/rna_tools/sortmerna/test-data/test1_bam.bam
diff --git a/tools/rna_tools/sortmerna/test-data/test2_aligned.fasta b/tools/rna_tools/sortmerna/test-data/test2_aligned.fasta
@@ -1,2 +0,0 @@
->read1
-GCCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATACCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACC

diff --git a/tools/rna_tools/sortmerna/test-data/test2_log.txt b/tools/rna_tools/sortmerna/test-data/test2_log.txt
diff --git a/tools/rna_tools/sortmerna/test-data/test3_bam.bam b/tools/rna_tools/sortmerna/test-data/test3_bam.bam
diff --git a/tools/rna_tools/sortmerna/test-data/test4_bam.bam b/tools/rna_tools/sortmerna/test-data/test4_bam.bam
diff --git a/tools/rna_tools/sortmerna/test-data/test4_de_novo.fasta b/tools/rna_tools/sortmerna/test-data/test4_de_novo.fasta
@@ -1,23 +1,13 @@
 >1p_error_2 reference=AY466476 amplicon=432..713 errors=76%G
 GUGCCAGCAGCCGCGGUAAUACGAAGGGGGCUAGCGUUGUUCGGAGUUACUGGCGUAAAGGCGCGUAGCGGCCUGGAAGUUAGCGUGAAGCCCUGGCUCA
->1p_error_3 reference=JN430627 amplicon=421..712 errors=1%C
-CUGCCAGCAGCCGCGGUAACACGUAAGGGGCGAGCGUUGUUCGGAAUUAUUGGGCGUAAAGGGCACGUAGGCGGCACGGUAAGCCUGGUGUGAAAGACCG
 >1p_error_5 reference=FJ890890 amplicon=455..746 description="Bacteria;Cyanobacteria;Chloroplast
 GUGCCAGCAGCCGCGGUAAGACAGAGGAUGCAAGCGUUAUCCGGAAUGAUUGGGCGUAAAGCGUCUGUAGGUUGUUUAAAAAGUAUUUUGUUAAAGAUUA
->1p_error_6 reference=JN449148 amplicon=487..779 errors=39%C
-GUGCCAGCAGCCGCGGUAAUACGUAAGGGGCGAGCGUUCCUCGGAAUUACUGGGCGUAAAGGGCGUGUAGGUGGUCUUGCAAGUCGAUUGGUAAAAGACC
 >1p_error_7 reference=EF019112 amplicon=467..758 errors=8%U,40%A
 GUGCCAGUAGCCGCGGUAAGACGUAGGGGGCGAGCGUUAAUCGGAAUUAUUGGGCGUAAAGCGUGCGUAGGCGGAUUCGUAAGUCGGGGUUGAAAUAUCC
 >1p_error_8 reference=EF020331 amplicon=491..782 errors=53+G
 GUGCCAGCAGCCGCGGUAAUACGUAGGCAGCAAGCGUUGUUCGGAAUUACUGGGGCGUAAAGAGUGUGUAGGCGGUUUUCUAAGUUUGGUGUGAAAUCUCC
->1p_error_9 reference=FJ879628 amplicon=498..789 errors=18+C
-GUGCCAGCAGCCGCGGUACAUACGUAGGGGGCAAGCGUUAUCCGGAUUUACUGGGUGUAAAGGGAGCGUAGGUGGCAGGGCAAGUCAGAUGUGAAAACCCG
 >1p_error_10 reference=EU134170 amplicon=467..758 description="Bacteria;Chloroflexi;Anaerolineae;Anaerolineales;Anaerolineaceae;uncultured
 GUGCCAGCAGCCGCGGUAAAACGUAGGAGGCGAGCGUUAUCCGGAUUUACUGGGCGUAAAGCGUGCGCAGGCGGUCCGACAGGUCGGGCGUGAAAUCUCC
->1p_error_11 reference=EU490280 amplicon=472..764 errors=63+U
-GUGCCAGCAGCCGCGGUAAAACGUAGGGGGCUAGCGUUACCCGGAUUCACUGGGCGUAAAGCGUGGUGUAGGCGGUCCGGCAAGUCGGAUGUGAAAUCCCA
->1p_error_12 reference=FJ202663 amplicon=453..744 description="Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Rhodospirillaceae;Thalassospira
-GUGCCAGCAGCCGCGGUAAUACGAAGGGAGCAAGCGUUGUUCGGAAUUACUGGGCGUAAAGGGCGUGUAGGCGGAUUAUCAAGUUAGGGGUGAAAUCCCG
 >1p_error_13 reference=DQ522159 amplicon=503..793 errors=7+C
 GUGCCAGCCAGCCGCGGUAAUACAUAGGUUGCAAGCGUUAUCCGGAUUUAUUGGGCGUAAAGCAAGCGCAGGUUGGUUAUCAAGUCUAGUGUGAAAGGCAA
 >1p_error_14 reference=EU773708 amplicon=499..791 errors=58%U
@@ -28,13 +18,9 @@ GUGCCAGCAGCCGCGGUAAUACGUAGGUCCCGAGCGUUGCGCGAAUUCACUGGGCGUAUAGCGUCCGCAGCCGGACGGGU
 AUGCCAGCAGCCGCGGUAACACGUAGGGGGCAAGCGUUGUUCGGAAUUAUUAGGCGUAAAGGGCAGGCAGGCGGACCUGCAAGUUUUCUGUUAAAGACGU
 >1p_error_17 reference=AB100473 amplicon=660..951 errors=57%C
 GUGCCAGCAGCCGCGGUAAUACGUAGGGAGCAAGCGUUGUCCGGAUUUACUGGGUGCAAAGGGCGUGUAGGCGGGAAGGCAGGUCAGAUGUGAAAUCUAU
->1p_error_18 reference=FJ802352 amplicon=495..786 errors=16%A
-GUGCCAGCAGCCGCGAUAAUACGAAGGGGGCUAGCGUUGCUCGGAAUCACUGGGCGUAAAGCGCGCGUAGGCGGCUUUCUAAGUCAGGGGUGAAAUCCCG
 >1p_error_19 reference=GQ138466 amplicon=520..812 description="Bacteria;Firmicutes;Clostridia;Clostridiales;uncultured
 GUGCCAGCAGCCGCGGUAAUACGUAGGGGGCGAGCGUUGUCCGGAAUGACUGGGCGUAAAGGGUGUGUAGGCGGUUUAGCAAGUUAGAUGUGAAAUACCC
 >1p_error_20 reference=EU857742 amplicon=514..805 errors=18%G
 GUGCCAGCAGCCGCGGUGAUACGUAAGGGGCGAGCGUUGUUCGGAAUUAUUGGGCGUAAAGGGUACGUAGGCGGAUUAACAGGCAUUAAGAUAAAGCCAA
->1p_error_21 reference=HQ588409 amplicon=540..831 errors=90%G
-GUGCCAGCAGCCGCGGUAAUACAUAGGGGGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGUAUGUAGGCGGUUUAUUAAGUCGGUAGGUGAAAGGCU
 >1p_error_22 reference=EU488153 amplicon=481..771 errors=96%C
 GUGCCAGCAGCCGCGGUAACACAUAGAGGACGAGCGUUAUCCGGAUUUACUGGGCGUAAAGAGCGUUGAGGCGGUUCCGUAAGUUGGGCGUUAAACCUCC