diff qualimap_multi_bamqc.py @ 7:7923e67fa16a draft default tip

planemo upload for repository https://github.com/zipho/qualimap2 commit cdfee65aff3863f6477339300a4a11657d7a44c0

--- a/qualimap_multi_bamqc.py	Tue Apr 05 04:45:41 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,43 +0,0 @@
-#!/usr/bin/env python
-from __future__ import print_function
-import argparse
-from subprocess import check_call, CalledProcessError
-import shlex
-import sys
-import logging
-
-log = logging.getLogger(__name__)
-
-
-def qualimap_multi_bamqc(input_file, out_dir, jv_mem_size):
-    #multi-bamqc -r -d ./bamlistinput.txt -outdir ./Kaust_kxdr/variants/qualimap -outformat PDF --java-mem-size=16G
-    cmdline_str = "qualimap multi-bamqc -r -d {} -outdir {} -outformat PDF --java-mem-size={}".format(input_file,
-                                                                                                      out_dir,
-                                                                                                      jv_mem_size)
-    cmdline = new_split(cmdline_str)
-    try:
-        check_call(cmdline)
-    except CalledProcessError:
-        print("Error running the qualimap multi bamqc", file=sys.stderr)
-
-
-def new_split(value):
-    lex = shlex.shlex(value)
-    lex.quotes = '"'
-    lex.whitespace_split = True
-    lex.commenters = ''
-    return list(lex)
-
-
-def main():
-    parser = argparse.ArgumentParser(description="Generate Bam Quality Statistics")
-    parser.add_argument('--input_file')
-    parser.add_argument('--out_dir', default="/tmp/bamstats")
-    parser.add_argument('--java_mem_size', default="8G")
-
-    args = parser.parse_args()
-
-    qualimap_multi_bamqc(args.input_file, args.out_dir, args.java_mem_size)
-
-
-if __name__ == "__main__": main()
\ No newline at end of file