Mercurial > repos > bgruening > bedtools_test_bag

comparison bedpeToBam.xml @ 12:c782e0edc4f1 draft default tip

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author bgruening
date Thu, 19 Jun 2014 10:12:00 -0400
parents 75d323631dce
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11:e526617a6bb9 12:c782e0edc4f1
1 <tool id="bedtools_bedpetobam" name="Convert from BEDPE to BAM" version="0.1.0"> 1 <tool id="bedtools_bedpetobam" name="Convert from BEDPE to BAM" version="@WRAPPER_VERSION@.0">
2 <description></description> 2 <description></description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
10 $ubam 10 $ubam
11 -mapq $mapq 11 -mapq $mapq
12 -i '$input' 12 -i '$input'
13 -g $genome 13 -g $genome
14 &gt; '$output' 14 &gt; '$output'
15
16 </command> 15 </command>
17 <inputs> 16 <inputs>
18 <param format="bed,gff,vcf" name="input" type="data" label="BED/VCF/GFF file"/> 17 <param format="bed,gff,vcf" name="input" type="data" label="BED/VCF/GFF file"/>
19 <expand macro="genome" /> 18 <expand macro="genome" />
20 <param name="mapq" type="integer" label="Set a mapping quality (SAM MAPQ field) value for all BED entries" value="255" /> 19 <param name="mapq" type="integer" label="Set a mapping quality (SAM MAPQ field) value for all BED entries" value="255" />
21 <param name="ubam" type="boolean" label="Write uncompressed BAM output." truevalue="-ubam" falsevalue="" checked="false"/> 20 <param name="ubam" type="boolean" label="Write uncompressed BAM output." truevalue="-ubam" falsevalue="" checked="false"/>
22
23 </inputs> 21 </inputs>
24 <outputs> 22 <outputs>
25 <data format="bam" name="output" metadata_source="input" label="${input.name} (as BAM)"/> 23 <data format="bam" name="output" metadata_source="input" label="${input.name} (as BAM)"/>
26 </outputs> 24 </outputs>
27 <help> 25 <help>