# HG changeset patch
# User scottx611x
# Date 1532638348 14400
# Node ID 7e359370b5a23fbeee5ddbc3694c8108b9ea6358
# Parent  0ea51e29a0ceff0cfd8e1cdbe53ed05241657fb7
planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty

diff -r 0ea51e29a0ce -r 7e359370b5a2 qualimap_bamqc.py
--- a/qualimap_bamqc.py	Thu Jul 26 16:47:12 2018 -0400
+++ b/qualimap_bamqc.py	Thu Jul 26 16:52:28 2018 -0400
@@ -9,12 +9,12 @@
 OUTPUT_DIR = "qualimap_results"
 
 
-def qualimap_bamqc(bam_filename, genomecov_file, jv_mem_size):
+def qualimap_bamqc(bam_filename, genomecov_file, out_dir, jv_mem_size):
     qualimap_command = [
         "qualimap", "bamqc",
         "-bam " + bam_filename,
         "-oc " + genomecov_file,
-        "-outdir " + OUTPUT_DIR,
+        "-outdir " + out_dir,
         "--java-mem-size=" + jv_mem_size
     ]
 
@@ -30,24 +30,26 @@
     )
     parser.add_argument('--input_file')
     parser.add_argument('--out_genome_file')
+    parser.add_argument('--out_dir')
     parser.add_argument('--java_mem_size')
 
     args = parser.parse_args()
 
-    print(os.listdir(os.getcwd()))
+    print(os.listdir(args.out_dir))
 
     qualimap_bamqc(
         args.input_file,
         args.out_genome_file,
+        args.out_dir,
         args.java_mem_size
     )
 
-    shutil.move(OUTPUT_DIR + "/genome_results.txt", "./genome_results.txt")
-    shutil.move(OUTPUT_DIR + "/qualimapReport.html", "./qualimapReport.html")
+    shutil.move(args.out_dir + "/genome_results.txt", "./genome_results.txt")
+    shutil.move(args.out_dir + "/qualimapReport.html", "./qualimapReport.html")
     shutil.make_archive(
         './raw_data_qualimapReport',
         'zip',
-        OUTPUT_DIR + '/raw_data_qualimapReport'
+        args.out_dir + '/raw_data_qualimapReport'
     )
 
 
diff -r 0ea51e29a0ce -r 7e359370b5a2 qualimap_bamqc.xml
--- a/qualimap_bamqc.xml	Thu Jul 26 16:47:12 2018 -0400
+++ b/qualimap_bamqc.xml	Thu Jul 26 16:52:28 2018 -0400
@@ -11,6 +11,7 @@
     <command interpreter="python">
         qualimap_bamqc.py
             --input_file $input_realigned_bam_file
+            --out_dir qualimap_results
             --out_genome_file $genome_coverage
             --java_mem_size $mem_size
     </command>