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comparison tagBed.xml @ 1:82aac94b06c3 draft

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author iuc
date Thu, 08 Jan 2015 14:25:51 -0500
parents b8348686a0b9
children 607c0576c6ab
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0:b8348686a0b9 1:82aac94b06c3
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command> 8 <command>
9 <![CDATA[
10 #set files = '" "'.join( [ str( $file ) for $file in $inputB ] )
9 bedtools tag 11 bedtools tag
10 -i $inputA 12 -i "${inputA}"
11 -files 13 -files "${files}"
12 #for $bed in beds:
13 $bed.input
14 #end for
15 -f $overlap 14 -f $overlap
16 $strand 15 $strand
17 -tag $tag 16 -tag "${tag}"
18 $field 17 $field
19 &gt; $output 18 > "${output}"
19 ]]>
20 </command> 20 </command>
21 <inputs> 21 <inputs>
22 <param format="bam" name="inputA" type="data" label="BAM file"/> 22 <param name="inputA" format="bam" type="data" label="BAM file"/>
23 23 <param name="inputB" format="bed,gff,vcf" multiple="True" type="data" label="BED/VCF/GFF file" />
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" /> 24 <expand macro="strand2" />
28 <expand macro="overlap" /> 25 <expand macro="overlap" />
29 26 <param name="tag" type="text" value="YB" label="Specify the tag to use" />
30 <param name="tag" type="text" value="YB" label="Dictate what the tag should be." /> 27 <param name="field" type="select" label="Field from the annotation files to populate tags?">
31 <param name="field" type="select" label="Use which field from the annotation files to populate tags?"> 28 <option value="-labels" selected="True">Labels</option>
32 <option value="-labels" selected="True">labels</option>
33 <option value="-scores">Scores</option> 29 <option value="-scores">Scores</option>
34 <option value="-names">Names</option> 30 <option value="-names">Names</option>
35 <option value="-labels -intervals">Intervals</option> 31 <option value="-labels -intervals">Intervals</option>
36 </param> 32 </param>
37 </inputs> 33 </inputs>
38 <outputs> 34 <outputs>
39 <data format="bed" name="output" label="" /> 35 <data format="bam" name="output"/>
40 </outputs> 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>
41 <help> 45 <help>
42 46 <![CDATA[
43 **What it does** 47 **What it does**
44 48
45 Annotates a BAM file based on overlaps with multiple BED/GFF/VCF files on the intervals in an input bam file 49 Annotates a BAM file based on overlaps with multiple BED/GFF/VCF files on the intervals in an input bam file
46 50
47 @REFERENCES@ 51 @REFERENCES@
48 52 ]]>
49 </help> 53 </help>
50 <expand macro="citations" /> 54 <expand macro="citations" />
51 </tool> 55 </tool>