Mercurial > repos > iuc > bedtools
annotate tagBed.xml @ 4:607c0576c6ab draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
| author | iuc |
|---|---|
| date | Wed, 27 Jan 2016 15:15:59 -0500 |
| parents | 82aac94b06c3 |
| children | 95a3b2c25bd1 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="bedtools_tagbed" name="TagBed" version="@WRAPPER_VERSION@.0"> |
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4
607c0576c6ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
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1
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changeset
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2 <description>tag BAM alignments based on overlaps with interval files</description> |
| 0 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <command> | |
| 1 | 9 <![CDATA[ |
| 10 #set files = '" "'.join( [ str( $file ) for $file in $inputB ] ) | |
| 0 | 11 bedtools tag |
| 1 | 12 -i "${inputA}" |
| 13 -files "${files}" | |
| 0 | 14 -f $overlap |
| 15 $strand | |
| 1 | 16 -tag "${tag}" |
| 0 | 17 $field |
| 1 | 18 > "${output}" |
| 19 ]]> | |
| 0 | 20 </command> |
| 21 <inputs> | |
| 1 | 22 <param name="inputA" format="bam" type="data" label="BAM file"/> |
| 23 <param name="inputB" format="bed,gff,vcf" multiple="True" type="data" label="BED/VCF/GFF file" /> | |
| 0 | 24 <expand macro="strand2" /> |
| 25 <expand macro="overlap" /> | |
| 1 | 26 <param name="tag" type="text" value="YB" label="Specify the tag to use" /> |
| 27 <param name="field" type="select" label="Field from the annotation files to populate tags?"> | |
| 28 <option value="-labels" selected="True">Labels</option> | |
| 0 | 29 <option value="-scores">Scores</option> |
| 30 <option value="-names">Names</option> | |
| 31 <option value="-labels -intervals">Intervals</option> | |
| 32 </param> | |
| 33 </inputs> | |
| 34 <outputs> | |
| 1 | 35 <data format="bam" name="output"/> |
| 0 | 36 </outputs> |
| 1 | 37 <tests> |
| 38 <test> | |
| 39 <param name="inputA" value="srma_in3.bam" ftype="bam" /> | |
| 40 <param name="inputB" value="tagBed1.bed" ftype="bed" /> | |
| 41 <param name="field" value="-names" /> | |
| 42 <output name="output" file="tagBed_result1.bam" ftype="bam" /> | |
| 43 </test> | |
| 44 </tests> | |
| 0 | 45 <help> |
| 1 | 46 <![CDATA[ |
| 0 | 47 **What it does** |
| 48 | |
| 49 Annotates a BAM file based on overlaps with multiple BED/GFF/VCF files on the intervals in an input bam file | |
| 50 | |
| 51 @REFERENCES@ | |
| 1 | 52 ]]> |
| 0 | 53 </help> |
| 54 <expand macro="citations" /> | |
| 55 </tool> |