# HG changeset patch
# User scottx611x
# Date 1532706809 14400
# Node ID e856fda6f375a482eb4d40cd97804b19c2c8bce1
# Parent  98944e91463767e1289eff25679e35e3f60eaf76
planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty

diff -r 98944e914637 -r e856fda6f375 qualimap_bamqc.py
--- a/qualimap_bamqc.py	Fri Jul 27 11:45:23 2018 -0400
+++ b/qualimap_bamqc.py	Fri Jul 27 11:53:29 2018 -0400
@@ -29,13 +29,14 @@
     parser.add_argument('--input_file')
     parser.add_argument('--out_genome_file')
     parser.add_argument('--out_dir')
+    parser.add_argument('--out_zip')
+    parser.add_argument('--out_html')
+    parser.add_argument('--out_results')
     parser.add_argument('--java_mem_size')
 
     args = parser.parse_args()
     print(args)
 
-    output_dir = os.path.dirname(args.out_genome_file)
-
     qualimap_bamqc(
         args.input_file,
         args.out_genome_file,
@@ -46,21 +47,18 @@
     shutil.make_archive(
         'raw_data_qualimapReport',
         'zip',
-        args.out_dir + '/raw_data_qualimapReport'
-    )
-
-    shutil.move(
-        "raw_data_qualimapReport.zip",
-        os.path.join(output_dir, "raw_data_qualimapReport.zip")
+        os.path.join(args.out_dir,'raw_data_qualimapReport')
     )
 
-    [
-        shutil.move(
-            os.path.join(args.out_dir, file_name),
-            os.path.join(output_dir, file_name)
-        )
-        for file_name in ["genome_results.txt", "qualimapReport.html"]
-    ]
+    shutil.move("raw_data_qualimapReport.zip", args.out_zip)
+    shutil.move(
+        os.path.join(args.out_dir, "genome_results.txt"),
+        args.out_results
+    )
+    shutil.move(
+        os.path.join(args.out_dir, "qualimapReport.html"),
+        args.out_html
+    )
 
 if __name__ == "__main__":
     main()
diff -r 98944e914637 -r e856fda6f375 qualimap_bamqc.xml
--- a/qualimap_bamqc.xml	Fri Jul 27 11:45:23 2018 -0400
+++ b/qualimap_bamqc.xml	Fri Jul 27 11:53:29 2018 -0400
@@ -13,6 +13,9 @@
             --input_file $input_realigned_bam_file
             --out_dir qualimap_results
             --out_genome_file $genome_coverage
+            --out_zip $raw_data_qualimapReport
+            --out_html $qualimapReport
+            --out_results $genome_results
             --java_mem_size $mem_size
     </command>
     <inputs>