diff qualimap_bamqc.py @ 23:cefa83db3ebf draft

planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty

--- a/qualimap_bamqc.py	Thu Jul 26 15:36:54 2018 -0400
+++ b/qualimap_bamqc.py	Thu Jul 26 15:58:53 2018 -0400
@@ -2,18 +2,16 @@
 from __future__ import print_function
 import argparse
 from subprocess import check_call, CalledProcessError
+import shutil
 import sys
-import logging
-
-log = logging.getLogger(__name__)
 
 
-def qualimap_bamqc(bam_filename, genomecov_file, out_dir, jv_mem_size):
+def qualimap_bamqc(bam_filename, genomecov_file, jv_mem_size):
     qualimap_command = [
         "qualimap", "bamqc",
         "-bam " + bam_filename,
         "-oc " + genomecov_file,
-        "-outdir " + out_dir,
+        "-outdir .",
         "--java-mem-size=" + jv_mem_size
     ]
 
@@ -28,19 +26,24 @@
         description="Generate Bam Quality Statistics"
     )
     parser.add_argument('--input_file')
-    parser.add_argument('--out_genome_file', default="genome_coverage.txt")
-    parser.add_argument('--out_dir', default="qualimap_results")
-    parser.add_argument('--java_mem_size', default="8G")
+    parser.add_argument('--out_genome_file')
+    parser.add_argument('--java_mem_size')
 
     args = parser.parse_args()
 
     qualimap_bamqc(
         args.input_file,
         args.out_genome_file,
-        args.out_dir,
         args.java_mem_size
     )
 
+    shutil.make_archive(
+        'raw_data_qualimapReport.zip',
+        'zip',
+        'qualimap_results/raw_data_qualimapReport/'
+    )
+
+
 
 if __name__ == "__main__":
     main()