Mercurial > repos > iuc > bedtools
annotate tagBed.xml @ 17:a2d4c30ba2f9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
| author | iuc |
|---|---|
| date | Sun, 21 Jun 2015 22:49:46 -0400 |
| parents | 0d3aa592ce27 |
| children | d279800f4ff9 |
| rev | line source |
|---|---|
| 8 | 1 <tool id="bedtools_tagbed" name="TagBed" version="@WRAPPER_VERSION@.0"> |
|
17
a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
8
diff
changeset
|
2 <description>tag BAM alignments based on overlaps with interval files</description> |
| 8 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <command> | |
| 9 <![CDATA[ | |
| 10 #set files = '" "'.join( [ str( $file ) for $file in $inputB ] ) | |
| 11 bedtools tag | |
| 12 -i "${inputA}" | |
| 13 -files "${files}" | |
| 14 -f $overlap | |
| 15 $strand | |
| 16 -tag "${tag}" | |
| 17 $field | |
| 18 > "${output}" | |
| 19 ]]> | |
| 20 </command> | |
| 21 <inputs> | |
| 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" /> | |
| 24 <expand macro="strand2" /> | |
| 25 <expand macro="overlap" /> | |
| 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> | |
| 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> | |
| 35 <data format="bam" name="output"/> | |
| 36 </outputs> | |
| 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> | |
| 45 <help> | |
| 46 <![CDATA[ | |
| 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@ | |
| 52 ]]> | |
| 53 </help> | |
| 54 <expand macro="citations" /> | |
| 55 </tool> |