# HG changeset patch
# User iuc
# Date 1589636875 14400
# Node ID 5f8e69cc4c6e08af41bb1652c4f9b1ba6dd4abf2
# Parent  e7fd6754d093d597654d9c4075dda5da515fcece
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875"

diff -r e7fd6754d093 -r 5f8e69cc4c6e qualimap_bamqc.xml
--- a/qualimap_bamqc.xml	Mon Jan 13 13:04:33 2020 -0500
+++ b/qualimap_bamqc.xml	Sat May 16 09:47:55 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="qualimap_bamqc" name="QualiMap BamQC" version="@VERSION@+galaxy1">
+<tool id="qualimap_bamqc" name="QualiMap BamQC" version="@VERSION@+galaxy2">
     <macros>
         <import>qualimap_macros.xml</import>
     </macros>
@@ -6,6 +6,7 @@
     <expand macro="version_command" />
     <command detect_errors="exit_code"><![CDATA[
         #import os
+        #import re
         @SET_JAVA_OPTS@ &&
 
         ## Set some default file names and paths
@@ -39,8 +40,11 @@
             #end if
         #end if
 
+        #set input_name = re.sub('[^\s\w\-]', '_', str($input1.name))
+        ln -s '$input1' '$input_name' &&
+
         qualimap bamqc
-        -bam '$input1' -outdir results -outformat html
+        -bam '$input_name' -outdir results -outformat html
         --collect-overlap-pairs
         #if str($stats_regions.region_select) == 'custom_regions':
             -gff ${regions_file} ${stats_regions.outside_stats}