# HG changeset patch
# User scottx611x
# Date 1532532773 14400
# Node ID 5b36882f64553ca3185d82d6aa7e6df9b6fef576
# Parent  716e406ce6ea30f25db9876093cc3a8ca919bbb7
planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty

diff -r 716e406ce6ea -r 5b36882f6455 qualimap_bamqc.py
--- a/qualimap_bamqc.py	Wed Jul 25 10:59:11 2018 -0400
+++ b/qualimap_bamqc.py	Wed Jul 25 11:32:53 2018 -0400
@@ -28,7 +28,7 @@
         description="Generate Bam Quality Statistics"
     )
     parser.add_argument('--input_file')
-    parser.add_argument('--out_genome_file', default="genome_results.txt")
+    parser.add_argument('--out_genome_file', default="genome_coverage.txt")
     parser.add_argument('--out_dir')
     parser.add_argument('--java_mem_size', default="8G")
 
diff -r 716e406ce6ea -r 5b36882f6455 qualimap_bamqc.xml
--- a/qualimap_bamqc.xml	Wed Jul 25 10:59:11 2018 -0400
+++ b/qualimap_bamqc.xml	Wed Jul 25 11:32:53 2018 -0400
@@ -11,7 +11,6 @@
     <command interpreter="python">
         qualimap_bamqc.py
             --input_file $input_realigned_bam_file
-            --out_genome_file $genome_results
             --out_dir qualimap_results
             --java_mem_size $mem_size
     </command>
@@ -23,6 +22,7 @@
         <data format="txt" name="genome_results" label="Qualimap BamQC report">
           <discover_datasets pattern="genome_results*" visible="true" ext="txt" directory="qualimap_results" assign_primary_output="true"/>
         </data>
+        <data format="txt" name="genome_coverage" label="Qualimap BamQC coverage report"></data>
         <data format="html" name="qualimap_html_results" label="Qualimap BamQC HTML report">
           <discover_datasets pattern="qualimapReport*" visible="true" ext="html" directory="qualimap_results" assign_primary_output="true"/>
         </data>
@@ -31,15 +31,11 @@
     <tests>
         <test>
           <param name="input_realigned_bam_file" value="test.bam"></param>
-          <output name="genome_results">
-            <assert_contents>
-              <has_text text="BamQC report" />
-            </assert_contents>
+          <output name="genome_results" file="genome_results.txt" ftype="txt">
           </output>
-          <output name="qualimap_html_results">
-            <assert_contents>
-              <has_text text="Qualimap report: BAM QC" />
-            </assert_contents>
+          <output name="genome_coverage" file="genome_coverage.txt" ftype="txt">
+          </output>
+          <output name="qualimap_html_results" file="qualimapReport.html" ftype="html">
           </output>
         </test>
     </tests>