Mercurial > repos > sanbi-uwc > qualimap2
changeset 7:7923e67fa16a draft default tip
planemo upload for repository https://github.com/zipho/qualimap2 commit cdfee65aff3863f6477339300a4a11657d7a44c0
| author | sanbi-uwc |
|---|---|
| date | Tue, 05 Apr 2016 06:06:54 -0400 |
| parents | 8dff744880cd |
| children | |
| files | qualimap_multi_bamqc.py qualimap_multi_bamqc.xml |
| diffstat | 2 files changed, 0 insertions(+), 75 deletions(-) [+] |
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--- 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
--- 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>