Mercurial > repos > jjohnson > defuse
diff defuse_bamfastq.xml @ 11:b22f8634ff84 draft
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
author | jjohnson |
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date | Sun, 17 Jan 2016 14:11:06 -0500 |
parents | |
children | bdd93719cede |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/defuse_bamfastq.xml Sun Jan 17 14:11:06 2016 -0500 @@ -0,0 +1,63 @@ +<?xml version="1.0"?> +<tool id="defuse_bamfastq" name="Defuse BamFastq" version="@DEFUSE_VERSION@.1"> + <description>converts a bam file to fastq files.</description> + <macros> + <import>macros.xml</import> + </macros> + <requirements> + <expand macro="defuse_requirement" /> + </requirements> + <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> + <expand macro="citations"/> +</tool>