diff qualimap_bamqc.py @ 42:c53375e61b33 draft

planemo upload for repository https://github.com/scottx611x/qualimap2 commit 9fafbbc012490e70d06fcef4704a1e4a45b382c5-dirty

--- a/qualimap_bamqc.py	Fri Jul 27 11:53:29 2018 -0400
+++ b/qualimap_bamqc.py	Sun Jul 29 13:53:35 2018 -0400
@@ -7,11 +7,10 @@
 import sys
 
 
-def qualimap_bamqc(bam_filename, genomecov_file, out_dir, jv_mem_size):
+def qualimap_bamqc(bam_filename, out_dir, jv_mem_size):
     qualimap_command = [
         "qualimap", "bamqc",
         "-bam " + bam_filename,
-        "-oc " + genomecov_file,
         "-outdir " + out_dir,
         "--java-mem-size=" + jv_mem_size
     ]
@@ -27,11 +26,9 @@
         description="Generate Bam Quality Statistics"
     )
     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()
@@ -39,7 +36,6 @@
 
     qualimap_bamqc(
         args.input_file,
-        args.out_genome_file,
         args.out_dir,
         args.java_mem_size
     )
@@ -47,7 +43,7 @@
     shutil.make_archive(
         'raw_data_qualimapReport',
         'zip',
-        os.path.join(args.out_dir,'raw_data_qualimapReport')
+        os.path.join(args.out_dir, 'raw_data_qualimapReport')
     )
 
     shutil.move("raw_data_qualimapReport.zip", args.out_zip)
@@ -55,10 +51,6 @@
         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()