# HG changeset patch
# User sanbi-uwc
# Date 1459845941 14400
# Node ID 8dff744880cd419b00ea917c5ec80be40bf6f1ab
# Parent 465131fb4ce900b02bde603e13643b94a2b5f90f
planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
diff -r 465131fb4ce9 -r 8dff744880cd qualimap_bamqc.xml
--- a/qualimap_bamqc.xml Tue Apr 05 03:53:28 2016 -0400
+++ b/qualimap_bamqc.xml Tue Apr 05 04:45:41 2016 -0400
@@ -10,10 +10,10 @@
qualimap_bamqc.py
- --input_file ${input_realigned_bam_file}
- --out_genome_file ${genomecov_file}
- --out_dir ${genomecov_file.files_path}
- --java_mem_size ${mem_size}
+ --input_file $input_realigned_bam_file
+ --out_genome_file $genomecov_file
+ --out_dir $genomecov_file.files_path
+ --java_mem_size $mem_size
diff -r 465131fb4ce9 -r 8dff744880cd qualimap_multi_bamqc.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qualimap_multi_bamqc.py Tue Apr 05 04:45:41 2016 -0400
@@ -0,0 +1,43 @@
+#!/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
diff -r 465131fb4ce9 -r 8dff744880cd qualimap_multi_bamqc.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qualimap_multi_bamqc.xml Tue Apr 05 04:45:41 2016 -0400
@@ -0,0 +1,32 @@
+
+
+ Tool to to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.
+
+ qualimap
+
+
+
+
+
+
+ qualimap_multi_bamqc.py
+ --input_file $input_realigned_bam_file
+ --out_dir $output1.files_path
+ --java_mem_size $mem_size
+
+
+
+
+
+
+
+
+ Help!
+
+
+
+
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+