Collapsable tsv outputs

phac-nml · Mar 24, 2023 · ee57f70 · ee57f70
1 parent 912ed87
commit ee57f70
Show file tree

Hide file tree

Showing 3 changed files with 7 additions and 19 deletions.
diff --git a/tools/spatyper/spatyper.xml b/tools/spatyper/spatyper.xml
@@ -6,22 +6,18 @@
  <requirement type="package" version="@VERSION@">spatyper</requirement>
  </requirements>
  <command detect_errors="aggressive"> <![CDATA[
- spaTyper -f '${input1}' > '${output1}' 
+ spaTyper -f '${input}' --output '${output}' 
  ]]> </command>
  <inputs>
- <param type="data" name="input1" format="fasta" label="SPA Fasta file" help="Staphylococcus aureus - staphylococcal protein A fasta file. This will be assigned a type based on its repeat region."/>
+ <param type="data" name="input" format="fasta" label="SPA Fasta file" help="Staphylococcus aureus - staphylococcal protein A fasta file. This will be assigned a type based on its repeat region."/>
  </inputs>
  <outputs>
- <data name="output1" format="txt" />
+ <data name="output" format="tsv"/>
  </outputs>
  <tests>
  <test>
- <param name="input1" value="input.fasta"/>
- <output name="output1">
- <assert_contents>
- <has_text text = "t11215" />
- </assert_contents>
- </output>
+ <param name="input" value="input.fasta"/>
+ <output name="output" file="output.tsv" ftype="tsv"/>
  </test>
  </tests>
  <help><![CDATA[

diff --git a/tools/spatyper/test-data/output.tsv b/tools/spatyper/test-data/output.tsv
@@ -0,0 +1,2 @@
+Sequence name Repeats Type
+AJ829762.1 Staphylococcus aureus subsp. aureus partial spa gene for protein A 99-20-69-31-70-13-17-16-16-16-16 t11215
diff --git a/tools/spatyper/test-data/output.txt b/tools/spatyper/test-data/output.txt