Mercurial > repos > jjohnson > defuse
changeset 15:337dc0fe0da1
add defuse_bamfastq
author | landsj <lands065@umn.edu> |
---|---|
date | Wed, 12 Jun 2013 15:41:12 -0500 |
parents | d975e466d443 |
children | 3df516ce3ad6 |
files | defuse_bamfastq.xml |
diffstat | 1 files changed, 65 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/defuse_bamfastq.xml Wed Jun 12 15:41:12 2013 -0500 @@ -0,0 +1,65 @@ +<?xml version="1.0"?> +<tool id="defuse_bamfastq" name="Defuse BamFastq" version="0.6.1"> + <description>converts a bam file to fastq files.</description> + + <requirements> + <requirement type="package" version="0.6.1">defuse</requirement> + </requirements> + + <version_command>bamfastq --version</version_command> + + <command>bamfastq + #if $pair == True : + $pair + #end if + + #if $multiple == True : + $multiple + #end if + + #if $rename == True : + $rename + #end if + + -2 $fastq2 + -1 $fastq1 + -b $bamname + + + </command> + + <inputs> + <param name="bamname" type="data" format="bam" label="Bam filename."/> + <param name="pair" type="boolean" truevalue="-p" falsevalue="" checked="true" label="Name contains pair info as /1 /2."/> + <param name="multiple" type="boolean" truevalue="-m" falsevalue="" checked="true" label="Bam contains multiple mappings per read."/> + <param name="rename" type="boolean" truevalue="-r" falsevalue="" checked="true" label="Rename with integer IDs."/> + + + + <stdio> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + + </inputs> + + <outputs> + <data format="fastqsanger,fastqillumina" name="fastq1" label="fastq1" /> + <data format="fastqsanger,fastqillumina" name="fastq2" label="fastq2" /> + </outputs> + + <tests> + <test> + <param name="bamname" ftype="bam" value="tophat_out2h.bam" /> + <param name="pair" value="True" /> + <param name="multiple" value="True" /> + <param name="rename" value="True" /> + <output name="fastq1" file="testout_defuse1.fq" /> + <output name="fastq2" file="testout_defuse2.fq" /> + + </test> + </tests> + + <help> + Turn your dry, flavorless BAM file into delicious fastq files! + </help> +</tool>