Mercurial > repos > scottx611x > qualimap2_bamqc

changeset 3:c9afc13316ec draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/scottx611x/qualimap2 commit 659800a1d841117a6fedc8ae394002c5744d1f2a
author scottx611x
date Wed, 25 Jul 2018 12:05:20 -0400
parents 5b36882f6455
children 10a0b8ee05fc
files qualimap_bamqc.xml
diffstat 1 files changed, 13 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/qualimap_bamqc.xml	Wed Jul 25 11:32:53 2018 -0400
+++ b/qualimap_bamqc.xml	Wed Jul 25 12:05:20 2018 -0400
@@ -12,6 +12,7 @@
         qualimap_bamqc.py
             --input_file $input_realigned_bam_file
             --out_dir qualimap_results
+            --out_genome_file $genome_coverage
             --java_mem_size $mem_size
     </command>
     <inputs>
@@ -31,11 +32,20 @@
     <tests>
         <test>
           <param name="input_realigned_bam_file" value="test.bam"></param>
-          <output name="genome_results" file="genome_results.txt" ftype="txt">
+          <output name="genome_results">
+          	<assert_contents>
+              <has_text text="" />
+            </assert_contents>
           </output>
-          <output name="genome_coverage" file="genome_coverage.txt" ftype="txt">
+          <output name="genome_coverage">
+          	<assert_contents>
+              <has_text text="" />
+            </assert_contents>
           </output>
-          <output name="qualimap_html_results" file="qualimapReport.html" ftype="html">
+          <output name="qualimap_html_results">
+          	<assert_contents>
+              <has_text text="" />
+            </assert_contents>
           </output>
         </test>
     </tests>