# HG changeset patch
# User scottx611x
# Date 1532619860 14400
# Node ID e14c864ee2b0aaeb89761d0d12b5d62015f7a102
# Parent  4b8ec6cb22cc467bd30a0dbb8766ff1bdcd6f06e
planemo upload for repository https://github.com/scottx611x/qualimap2 commit 070be0ead8afa05bfbb3075f075a97e7c32d619e-dirty

diff -r 4b8ec6cb22cc -r e14c864ee2b0 qualimap_bamqc.xml
--- a/qualimap_bamqc.xml	Thu Jul 26 11:36:28 2018 -0400
+++ b/qualimap_bamqc.xml	Thu Jul 26 11:44:20 2018 -0400
@@ -12,7 +12,7 @@
         qualimap_bamqc.py
             --input_file $input_realigned_bam_file
             --out_dir qualimap_results
-            --out_genome_file qualimap_results/$genome_coverage
+            --out_genome_file $genome_coverage
             --java_mem_size $mem_size
     </command>
     <inputs>
@@ -21,7 +21,7 @@
     </inputs>
     <outputs>
         <data format="txt" name="genome_coverage" label="Qualimap BamQC coverage report">
-          <discover_datasets pattern="genome_coverage*" visible="true" ext="txt" directory="qualimap_results" assign_primary_output="true"/>
+          <discover_datasets pattern="genome_coverage*" 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"/>