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1 <tool id="bedToBam" name="bedToBam">
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2 <description>convert BED or GFF or VCF to BAM</description>
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3 <command>bedToBam -i $input -g $genome $bed12 $mapq $ubam > $outfile </command>
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4 <inputs>
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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)"/>
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6 <param name="genome" type="select" label="Select genome">
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7 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm9.genome" selected="true">mm9</option>
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8 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm8.genome">mm8</option>
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9 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg18.genome">hg18</option>
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10 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg19.genome">hg19</option>
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11 </param>
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12 <param name="mapq" size="10" type="integer" value="255" label="Set the mappinq quality for the BAM records"/>
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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"/>
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14 <param name="ubam" label="Write uncompressed BAM output" help="Default is to write compressed BAM" type="boolean" truevalue="-ubam" falsevalue="" checked="False"/>
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15 </inputs>
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16 <outputs>
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17 <data format="bam" name="outfile" />
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18 </outputs>
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19 </tool>
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