Mercurial > repos > xuebing > sharplabtool
comparison mytools/bed_to_bam.xml @ 7:f0dc65e7f6c0
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| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:59:07 -0500 |
| parents | |
| children |
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| 6:094f377db4e5 | 7:f0dc65e7f6c0 |
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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/galaxy-dist/tool-data/genome/chrsize/mouse.mm9.genome" selected="true">mm9</option> | |
| 8 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm8.genome">mm8</option> | |
| 9 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg18.genome">hg18</option> | |
| 10 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.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 </tool> |