Mercurial > repos > portiahollyoak > breakdancer_max

comparison breakdancermax.xml @ 3:8fee2dac93a4 draft

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planemo upload for repository https://github.com/portiahollyoak/Tools commit f09b05c40adb6e529fc461466ee67bf41c3a552f
author portiahollyoak
date Mon, 23 May 2016 05:19:22 -0400
parents 2de4be065de4
children c2bb6aa52c74
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2:2de4be065de4 3:8fee2dac93a4
31 -g "$sample_name" 31 -g "$sample_name"
32 $illumina_long 32 $illumina_long
33 $copy_number_bam 33 $copy_number_bam
34 $allele_freq 34 $allele_freq
35 -y "$output_score_filter" 35 -y "$output_score_filter"
36 output_config_file && 36 output_config_file > "$breakdancer_stdout" &&
37 mv "$sample_name" "$results_bed" 37 mv "$sample_name" "$results_bed"
38 ]]></command> 38 ]]></command>
39 <inputs> 39 <inputs>
40 <param name="input_file" type="data" format="bam" label="One or more alignment files"/> 40 <param name="input_file" type="data" format="bam" label="One or more alignment files"/>
41 <param name="mean" type="integer" value="" label="Mean Insert Size"/> 41 <param name="mean" type="integer" value="" label="Mean Insert Size"/>
62 <param name="allele_freq" type="boolean" checked="false" truevalue="-h" falsevalue="" 62 <param name="allele_freq" type="boolean" checked="false" truevalue="-h" falsevalue=""
63 label="Print out Allele Frequencing column (Default= No)"/> 63 label="Print out Allele Frequencing column (Default= No)"/>
64 <param name="output_score_filter" type="integer" value="30" label="Output Score filter"/> 64 <param name="output_score_filter" type="integer" value="30" label="Output Score filter"/>
65 </inputs> 65 </inputs>
66 <outputs> 66 <outputs>
67 <data name="results_bed" type="data" format="bed" help="BED file containing SVs and supporting reads" label="${sample_name}"/> 67 <data name="results_bed" type="data" format="bed" label="${sample_name} Breakdancer BED file containing SVs and supporting reads "/>
68 <data name="results_stdout" type="data" format="bed" label="${sample_name} Breakdancer summary"/>
68 </outputs> 69 </outputs>
69 <tests> 70 <tests>
70 <test> 71 <test>
71 <param name="input_file" value="X_Hum1.bwa.bam" ftype="bam"/> 72 <param name="input_file" value="X_Hum1.bwa.bam" ftype="bam"/>
72 <param name="mean" value="227"/> 73 <param name="mean" value="227"/>