view tools/mytools/bed_to_bam.xml @ 1:cdcb0ce84a1b

author xuebing
date Fri, 09 Mar 2012 19:45:15 -0500
parents 9071e359b9a3
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<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>
    <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/galaxy-dist/tool-data/genome/chrsize/mouse.mm9.genome" selected="true">mm9</option>
     <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm8.genome">mm8</option>
     <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg18.genome">hg18</option>
     <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg19.genome">hg19</option>
    <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"/>
    <data format="bam" name="outfile" />