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comparison tagBed.xml @ 10:71af3ebbbb7a draft

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author iuc
date Wed, 29 Apr 2015 12:06:53 -0400
parents 0d3aa592ce27
children a2d4c30ba2f9
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9:21f1d1c5467b 10:71af3ebbbb7a
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 <![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>