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comparison tools/bedtools/bedToBam.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="bedToBam" name="bedToBam">
2 <description>convert BED or GFF or VCF to BAM</description>
3 <command>bedToBam -i $input -g $genome $bed12 $mapq $ubam > $outfile </command>
4 <inputs>
5 <param name="input" format="bed,gff,vcf" type="data" label="Input file (BED,GFF,VCF)" help="BED files must be at least BED4 to be amenable to BAM (needs name field)"/>
6 <param name="genome" type="select" label="Select genome">
7 <option value="/Users/xuebing/tools/BEDTools-Version-2.13.3/genomes/mouse.mm9.genome" selected="true">mm9</option>
8 <option value="/Users/xuebing/tools/BEDTools-Version-2.13.3/genomes/mouse.mm8.genome">mm8</option>
9 <option value="/Users/xuebing/tools/BEDTools-Version-2.13.3/genomes/mouse.hg18.genome">hg18</option>
10 <option value="/Users/xuebing/tools/BEDTools-Version-2.13.3/genomes/mouse.hg19.genome">hg19</option>
11 </param>
12 <param name="mapq" size="10" type="integer" value="255" label="Set the mappinq quality for the BAM records"/>
13 <param name="bed12" label="The BED file is in BED12 format" help="The BAM CIGAR string will reflect BED blocks" type="boolean" truevalue="-bed12" falsevalue="" checked="False"/>
14 <param name="ubam" label="Write uncompressed BAM output" help="Default is to write compressed BAM" type="boolean" truevalue="-ubam" falsevalue="" checked="False"/>
15 </inputs>
16 <outputs>
17 <data format="bam" name="outfile" />
18 </outputs>
19 <help>
20
21 **What it does**
22
23 Program: bedToBam (v2.13.3)
24 Author: Aaron Quinlan (aaronquinlan@gmail.com)
25 Summary: Converts feature records to BAM format.
26
27
28 </help>
29 </tool>