# HG changeset patch
# User scottx611x
# Date 1532633814 14400
# Node ID ffc7fdae906ced3c0e7ecc40669a1d8d5fe305e9
# Parent  1d2705d9bdd2b44c26d816132c5bf08bb7c4bf49
planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty

diff -r 1d2705d9bdd2 -r ffc7fdae906c qualimap_bamqc.xml
--- a/qualimap_bamqc.xml	Thu Jul 26 14:48:55 2018 -0400
+++ b/qualimap_bamqc.xml	Thu Jul 26 15:36:54 2018 -0400
@@ -20,14 +20,12 @@
         <param name="mem_size" type="text" value="8G" format="txt" label="Java memory size (default Gig)" help="Specify the size of memory to allocate. (Default 8 Gig)"/>
     </inputs>
     <outputs>
-        <data format="txt" name="genome_coverage" label="Qualimap BamQC Coverage Report">
-          <discover_datasets visible="true" ext="txt"/>
-        </data>
+        <data format="txt" name="genome_coverage" label="Qualimap BamQC Coverage Report"></data>
         <data format="txt" name="genome_results" label="Qualimap BamQC Results">
-          <discover_datasets pattern="genome_results.txt" visible="true" ext="txt" directory="qualimap_results"/>
+          <discover_datasets pattern="genome_results.txt" 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.html" visible="true" ext="html" directory="qualimap_results"/>
+          <discover_datasets pattern="qualimapReport.html" visible="true" ext="html" directory="qualimap_results" assign_primary_output="true"/>
         </data>
         <data format="txt" name="qualimap_raw_data_results" label="Qualimap Raw Data Results">
           <discover_datasets pattern="__designation_and_ext__" visible="true" ext="txt" directory="qualimap_results/raw_data_qualimapReport"/>
@@ -36,19 +34,25 @@
    
     <tests>
         <test>
+          <param name="mem_size"  value="2G"></param>
           <param name="input_realigned_bam_file" value="test.bam"></param>
            <output name="genome_coverage">
             <assert_contents>
-              <has_text text="" />
+              <has_text text="#chr  pos coverage" />
             </assert_contents>
           </output>
           <output name="genome_results">
           	<assert_contents>
-              <has_text text="" />
+              <has_text text="BamQC report" />
             </assert_contents>
           </output>
           <output name="qualimap_html_results">
           	<assert_contents>
+              <has_text text="Qualimap Report: BAM QC" />
+            </assert_contents>
+          </output>
+          <output name="qualimap_raw_data_results">
+            <assert_contents>
               <has_text text="" />
             </assert_contents>
           </output>