# HG changeset patch
# User scottx611x
# Date 1532887952 14400
# Node ID 2395818cb1f1b44a14f22148edbf1816440fc42a
# Parent  c53375e61b33c4473c4da0d475c4c9b2a28550c6
planemo upload for repository https://github.com/scottx611x/qualimap2 commit 9fafbbc012490e70d06fcef4704a1e4a45b382c5-dirty

diff -r c53375e61b33 -r 2395818cb1f1 qualimap_bamqc.py
--- a/qualimap_bamqc.py	Sun Jul 29 13:53:35 2018 -0400
+++ b/qualimap_bamqc.py	Sun Jul 29 14:12:32 2018 -0400
@@ -6,12 +6,14 @@
 import shutil
 import sys
 
+QUALIMAP_OUPUT_DIR = "qualimap_results"
 
-def qualimap_bamqc(bam_filename, out_dir, jv_mem_size):
+
+def qualimap_bamqc(bam_filename, jv_mem_size):
     qualimap_command = [
         "qualimap", "bamqc",
         "-bam " + bam_filename,
-        "-outdir " + out_dir,
+        "-outdir " + QUALIMAP_OUPUT_DIR,
         "--java-mem-size=" + jv_mem_size
     ]
 
@@ -27,28 +29,27 @@
     )
     parser.add_argument('--input_file')
     parser.add_argument('--out_dir')
+    parser.add_argument('--out_results')
     parser.add_argument('--out_zip')
-    parser.add_argument('--out_html')
     parser.add_argument('--java_mem_size')
 
     args = parser.parse_args()
-    print(args)
 
     qualimap_bamqc(
         args.input_file,
-        args.out_dir,
+        QUALIMAP_OUPUT_DIR,
         args.java_mem_size
     )
 
     shutil.make_archive(
         'raw_data_qualimapReport',
         'zip',
-        os.path.join(args.out_dir, 'raw_data_qualimapReport')
+        os.path.join(QUALIMAP_OUPUT_DIR, 'raw_data_qualimapReport')
     )
 
     shutil.move("raw_data_qualimapReport.zip", args.out_zip)
     shutil.move(
-        os.path.join(args.out_dir, "genome_results.txt"),
+        os.path.join(QUALIMAP_OUPUT_DIR, "genome_results.txt"),
         args.out_results
     )
 
diff -r c53375e61b33 -r 2395818cb1f1 qualimap_bamqc.xml
--- a/qualimap_bamqc.xml	Sun Jul 29 13:53:35 2018 -0400
+++ b/qualimap_bamqc.xml	Sun Jul 29 14:12:32 2018 -0400
@@ -11,9 +11,8 @@
     <command interpreter="python">
         qualimap_bamqc.py
             --input_file $input_realigned_bam_file
-            --out_dir qualimap_results
+            --out_results $genome_results
             --out_zip $raw_data_qualimapReport
-            --out_results $genome_results
             --java_mem_size $mem_size
     </command>
     <inputs>