Mercurial > repos > xuebing > sharplabtool
diff tools/bedtools/bedToBam.xml @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/bedtools/bedToBam.xml Fri Mar 09 19:37:19 2012 -0500 @@ -0,0 +1,29 @@ +<tool id="bedToBam" name="bedToBam"> + <description>convert BED or GFF or VCF to BAM</description> + <command>bedToBam -i $input -g $genome $bed12 $mapq $ubam > $outfile </command> + <inputs> + <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)"/> + <param name="genome" type="select" label="Select genome"> + <option value="/Users/xuebing/tools/BEDTools-Version-2.13.3/genomes/mouse.mm9.genome" selected="true">mm9</option> + <option value="/Users/xuebing/tools/BEDTools-Version-2.13.3/genomes/mouse.mm8.genome">mm8</option> + <option value="/Users/xuebing/tools/BEDTools-Version-2.13.3/genomes/mouse.hg18.genome">hg18</option> + <option value="/Users/xuebing/tools/BEDTools-Version-2.13.3/genomes/mouse.hg19.genome">hg19</option> + </param> + <param name="mapq" size="10" type="integer" value="255" label="Set the mappinq quality for the BAM records"/> + <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"/> + <param name="ubam" label="Write uncompressed BAM output" help="Default is to write compressed BAM" type="boolean" truevalue="-ubam" falsevalue="" checked="False"/> + </inputs> + <outputs> + <data format="bam" name="outfile" /> + </outputs> + <help> + +**What it does** + +Program: bedToBam (v2.13.3) +Author: Aaron Quinlan (aaronquinlan@gmail.com) +Summary: Converts feature records to BAM format. + + + </help> +</tool>