Mercurial > repos > jjohnson > defuse
view defuse_bamfastq.xml @ 22:68494d6aabeb
Update datamanager and defuse.xml config file generation
author | Jim Johnson <jj@umn.edu> |
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date | Thu, 27 Jun 2013 13:11:50 -0500 |
parents | 547d8db4673e |
children | 225750bf3770 |
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<?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 -b $bamfile -1 $fastq1 -2 $fastq2 </command> <inputs> <param name="bamfile" type="data" format="bam" label="Bam file"/> <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."/> </inputs> <stdio> <exit_code range="1:" level="fatal" description="Error" /> </stdio> <outputs> <data format="fastqsanger" name="fastq1" label="fastq1" /> <data format="fastqsanger" name="fastq2" label="fastq2" /> </outputs> <tests> <test> <param name="bamfile" ftype="bam" value="tophat_out2h.bam" /> <param name="pair" value="True" /> <param name="multiple" value="True" /> <param name="rename" value="True" /> <output name="fastq1"> <assert_contents> <has_text text="@test_mRNA_36_146_27/1" /> <not_has_text text="@test_mRNA_36_146_27/2" /> <not_has_text text="test_mRNA_150_290_0" /> </assert_contents> </output> <output name="fastq2"> <assert_contents> <has_text text="@test_mRNA_36_146_27/2" /> <not_has_text text="@test_mRNA_36_146_27/1" /> <not_has_text text="test_mRNA_150_290_0" /> </assert_contents> </output> </test> </tests> <help> bamfastq converts a bam file input into a pair of fastq files that can be used as input to deFuse. </help> </tool>