# HG changeset patch
# User scottx611x
# Date 1532534720 14400
# Node ID c9afc13316ec193b486e6052cac684875e7412fb
# Parent  5b36882f64553ca3185d82d6aa7e6df9b6fef576
planemo upload for repository https://github.com/scottx611x/qualimap2 commit 659800a1d841117a6fedc8ae394002c5744d1f2a

diff -r 5b36882f6455 -r c9afc13316ec qualimap_bamqc.xml
--- 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>