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comparison bedpeToBam.xml @ 0:4fb5ea02b441 draft

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author iuc
date Tue, 15 Jul 2014 14:42:23 -0400
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1 <tool id="bedtools_bedpetobam" name="Convert from BEDPE to BAM" version="@WRAPPER_VERSION@.0">
2 <description></description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="stdio" />
8 <command>
9 bedtools bedpetobam
10 $ubam
11 -mapq $mapq
12 -i '$input'
13 -g $genome
14 &gt; '$output'
15 </command>
16 <inputs>
17 <param format="bed,gff,vcf" name="input" type="data" label="BED/VCF/GFF file"/>
18 <expand macro="genome" />
19 <param name="mapq" type="integer" label="Set a mapping quality (SAM MAPQ field) value for all BED entries" value="255" />
20 <param name="ubam" type="boolean" label="Write uncompressed BAM output." truevalue="-ubam" falsevalue="" checked="false"/>
21 </inputs>
22 <outputs>
23 <data format="bam" name="output" metadata_source="input" label="${input.name} (as BAM)"/>
24 </outputs>
25 <help>
26
27 **What it does**
28
29 Converts feature records to BAM format.
30
31 .. class:: warningmark
32
33 BED files must be at least BED4 to create BAM (needs name field).
34
35 @REFERENCES@
36 </help>
37 </tool>