# HG changeset patch
# User scottx611x
# Date 1532621652 14400
# Node ID 4e5e0a116434fa3d3f4f9c58d3b371005dcef648
# Parent  e14c864ee2b0aaeb89761d0d12b5d62015f7a102
planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty

diff -r e14c864ee2b0 -r 4e5e0a116434 qualimap_bamqc.py
--- a/qualimap_bamqc.py	Thu Jul 26 11:44:20 2018 -0400
+++ b/qualimap_bamqc.py	Thu Jul 26 12:14:12 2018 -0400
@@ -29,11 +29,11 @@
     )
     parser.add_argument('--input_file')
     parser.add_argument('--out_genome_file', default="genome_coverage.txt")
-    parser.add_argument('--out_dir')
+    parser.add_argument('--out_dir', default="qualimap_results")
     parser.add_argument('--java_mem_size', default="8G")
 
     args = parser.parse_args()
-    
+
     qualimap_bamqc(
         args.input_file,
         args.out_genome_file,
diff -r e14c864ee2b0 -r 4e5e0a116434 qualimap_bamqc.xml
--- a/qualimap_bamqc.xml	Thu Jul 26 11:44:20 2018 -0400
+++ b/qualimap_bamqc.xml	Thu Jul 26 12:14:12 2018 -0400
@@ -21,13 +21,13 @@
     </inputs>
     <outputs>
         <data format="txt" name="genome_coverage" label="Qualimap BamQC coverage report">
-          <discover_datasets pattern="genome_coverage*" visible="true" ext="txt" assign_primary_output="true"/>
+          <discover_datasets visible="true" ext="txt" assign_primary_output="true"/>
         </data>
         <data format="txt" name="genome_results" label="Qualimap BamQC results">
-          <discover_datasets pattern="genome_results*" visible="true" ext="txt" directory="qualimap_results" assign_primary_output="true"/>
+          <discover_datasets pattern="__designation__" visible="true" ext="txt" directory="qualimap_results" assign_primary_output="true"/>
         </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"/>
+          <discover_datasets pattern="__designation__" visible="true" ext="html" directory="qualimap_results" assign_primary_output="true"/>
         </data>
     </outputs>