Mercurial > repos > iuc > bedtools
comparison tagBed.xml @ 0:4fb5ea02b441 draft
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| author | iuc |
|---|---|
| date | Tue, 15 Jul 2014 14:42:23 -0400 |
| parents | |
| children | 7511823bdea1 |
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| -1:000000000000 | 0:4fb5ea02b441 |
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| 1 <tool id="bedtools_tagbed" name="TagBed" version="@WRAPPER_VERSION@.0"> | |
| 2 <description></description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <command> | |
| 9 bedtools tag | |
| 10 -i $inputA | |
| 11 -files | |
| 12 #for $bed in beds: | |
| 13 $bed.input | |
| 14 #end for | |
| 15 -f $overlap | |
| 16 $strand | |
| 17 -tag $tag | |
| 18 $field | |
| 19 > $output | |
| 20 </command> | |
| 21 <inputs> | |
| 22 <param format="bam" name="inputA" type="data" label="BAM file"/> | |
| 23 | |
| 24 <repeat name="beds" title="Add files" > | |
| 25 <param name="input" format="bed,gff,vcf" type="data" label="BED/VCF/GFF file" /> | |
| 26 </repeat> | |
| 27 <expand macro="strand2" /> | |
| 28 <expand macro="overlap" /> | |
| 29 | |
| 30 <param name="tag" type="text" value="YB" label="Dictate what the tag should be." /> | |
| 31 <param name="field" type="select" label="Use which field from the annotation files to populate tags?"> | |
| 32 <option value="-labels" selected="True">labels</option> | |
| 33 <option value="-scores">Scores</option> | |
| 34 <option value="-names">Names</option> | |
| 35 <option value="-labels -intervals">Intervals</option> | |
| 36 </param> | |
| 37 </inputs> | |
| 38 <outputs> | |
| 39 <data format="bed" name="output" label="" /> | |
| 40 </outputs> | |
| 41 <help> | |
| 42 | |
| 43 **What it does** | |
| 44 | |
| 45 Annotates a BAM file based on overlaps with multiple BED/GFF/VCF files on the intervals in an input bam file | |
| 46 | |
| 47 @REFERENCES@ | |
| 48 | |
| 49 </help> | |
| 50 </tool> |