# HG changeset patch
# User sanbi-uwc
# Date 1459850814 14400
# Node ID 7923e67fa16a5410cc4fa9ae10537960bc3aec1e
# Parent  8dff744880cd419b00ea917c5ec80be40bf6f1ab
planemo upload for repository https://github.com/zipho/qualimap2 commit cdfee65aff3863f6477339300a4a11657d7a44c0

diff -r 8dff744880cd -r 7923e67fa16a qualimap_multi_bamqc.py
--- 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
diff -r 8dff744880cd -r 7923e67fa16a qualimap_multi_bamqc.xml
--- a/qualimap_multi_bamqc.xml	Tue Apr 05 04:45:41 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,32 +0,0 @@
-<?xml version="1.0" encoding="utf-8" ?>
-<tool id="qualimap_multi_bamqc" name="QualiMap Multi BamQC" version="2.2">
-    <description>Tool to to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.</description>
-    <requirements>
-        <requirement type="package" version="2.2">qualimap</requirement>
-    </requirements>
-    <stdio>
-        <exit_code range=":-1" />
-        <exit_code range="1:" />
-    </stdio>
-    <command interpreter="python">
-        qualimap_multi_bamqc.py
-            --input_file $input_realigned_bam_file
-            --out_dir $output1.files_path
-            --java_mem_size $mem_size
-    </command>
-    <inputs>
-        <param name="input_realigned_bam_file" type="data" format="bam" label="Realigned BAM dataset" help="Specify realigned BAM dataset"/>
-        <param name="mem_size" type="text" value="8G" format="txt" label="Java memory size (default Gig)" help="Specify the size of memory to allocate. (Default 8 Gig)"/>
-    </inputs>
-    <outputs>
-        <data format="pdf" name="output1" label="QualiMap: Multi BamQC PDF output"/>
-    </outputs>
-    <help>Help!</help>
-    <citations>
-        <citation></citation>
-    </citations>
-    <tests>
-        <test>
-        </test>
-    </tests>
-</tool>