# HG changeset patch
# User sanbi-uwc
# Date 1459842808 14400
# Node ID 465131fb4ce900b02bde603e13643b94a2b5f90f
# Parent  a19abfa30ca7acd30a0293542a4b6f7199c13528
planemo upload for repository https://github.com/zipho/qualimap2 commit 5a0a3d24e87ed5d8d027c1c5ecae6f5cd7b1f64d

diff -r a19abfa30ca7 -r 465131fb4ce9 qualimap_bamqc.py
--- a/qualimap_bamqc.py	Tue Apr 05 03:34:34 2016 -0400
+++ b/qualimap_bamqc.py	Tue Apr 05 03:53:28 2016 -0400
@@ -10,10 +10,10 @@
 
 
 def qualimap_bamqc(bam_filename, genomecov_file, out_dir, jv_mem_size):
-    cmdline_str = "qualimap bamqc -bam {} -oc {} -outdir {} --outfile {} --java-mem-size={}".format(bam_filename,
-                                                                                                    genomecov_file,
-                                                                                                    out_dir,
-                                                                                                    jv_mem_size)
+    cmdline_str = "qualimap bamqc -bam {} -oc {} -outdir {} --java-mem-size={}".format(bam_filename,
+                                                                                       genomecov_file,
+                                                                                       out_dir,
+                                                                                       jv_mem_size)
     cmdline = new_split(cmdline_str)
     try:
         check_call(cmdline)