Add ftype

bgruening · Sep 1, 2023 · 2ea8802 · 2ea8802
1 parent d1a2afb
commit 2ea8802
Showing 1 changed file with 7 additions and 7 deletions.
diff --git a/tools/rna_tools/sortmerna/sortmerna.xml b/tools/rna_tools/sortmerna/sortmerna.xml
@@ -304,7 +304,7 @@ sortmerna --version 2>&1|grep 'SortMeRNA version'
  <param name="N" value="True"/>
  <output name="aligned" file="test1_aligned.fastq" />
  <output name="unaligned" file="test1_unaligned.fastq" />
- <output name="output_bam" file="test1_bam.bam" lines_diff="2"/>
+ <output name="output_bam" file="test1_bam.bam" lines_diff="2" ftype="bam"/>
  <output name="output_blast" file="test1_blast.tabular"/>
  </test>
  <test expect_num_outputs="1">
@@ -373,7 +373,7 @@ sortmerna --version 2>&1|grep 'SortMeRNA version'
  <output name="aligned_reverse" file="test3_aligned_reverse.fastq" />
  <output name="unaligned_forward" file="test3_unaligned_forward.fastq" />
  <output name="unaligned_reverse" file="test3_unaligned_reverse.fastq" />
- <output name="output_bam" file="test3_bam.bam" lines_diff="2"/>
+ <output name="output_bam" file="test3_bam.bam" lines_diff="2" ftype="bam"/>
  </test>
  <test expect_num_outputs="3">
  <conditional name="sequencing_type">
@@ -452,7 +452,7 @@ sortmerna --version 2>&1|grep 'SortMeRNA version'
  <param name="N" value="True"/>
  <output name="aligned_forward" file="test5_aligned_forward.fasta" />
  <output name="aligned_reverse" file="test5_aligned_reverse.fasta" />
- <output name="output_bam" file="test5_bam.bam" lines_diff="2"/>
+ <output name="output_bam" file="test5_bam.bam" lines_diff="2" ftype="bam"/>
  </test>
  <test expect_num_outputs="5">
  <conditional name="sequencing_type">
@@ -495,7 +495,7 @@ sortmerna --version 2>&1|grep 'SortMeRNA version'
  <output name="aligned_reverse" file="test6_aligned_reverse.fasta" />
  <output name="unaligned_forward" file="test6_unaligned_forward.fasta" />
  <output name="unaligned_reverse" file="test6_unaligned_reverse.fasta" />
- <output name="output_bam" file="test6_bam.bam" lines_diff="2"/>
+ <output name="output_bam" file="test6_bam.bam" lines_diff="2" ftype="bam"/>
  </test>
  <test expect_num_outputs="1">
  <conditional name="sequencing_type">
@@ -514,7 +514,7 @@ sortmerna --version 2>&1|grep 'SortMeRNA version'
  <param name="report_type" value="min_lis" />
  <param name="min_lis" value="1"/>
  </conditional>
- <output name="output_bam" file="test7_bam.bam" lines_diff="2"/>
+ <output name="output_bam" file="test7_bam.bam" lines_diff="2" ftype="bam"/>
  </test>
  <test expect_num_outputs="9">
  <conditional name="sequencing_type">
@@ -555,7 +555,7 @@ sortmerna --version 2>&1|grep 'SortMeRNA version'
  <param name="N" value="True"/>
  <output name="aligned_forward_singleton" file="test8_aligned_forward_singleton.fastq" />
  <output name="aligned_reverse_singleton" file="test8_aligned_reverse_singleton.fastq" />
- <output name="output_bam" file="test8_bam.bam" lines_diff="2"/>
+ <output name="output_bam" file="test8_bam.bam" lines_diff="2" ftype="bam"/>
  </test>
  <test expect_num_outputs="1">
  <conditional name="sequencing_type">
@@ -588,7 +588,7 @@ sortmerna --version 2>&1|grep 'SortMeRNA version'
  <conditional name="report">
  <param name="report_type" value="number_alignments" />
  </conditional>
- <output name="output_bam" file="test10_bam.bam" lines_diff="2"/>
+ <output name="output_bam" file="test10_bam.bam" lines_diff="2" ftype="bam"/>
  </test>
  </tests>
  <help>