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comparison annotateBed.xml @ 0:4fb5ea02b441 draft

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author iuc
date Tue, 15 Jul 2014 14:42:23 -0400
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1 <tool id="bedtools_annotatebed" name="AnnotateBed" 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 annotate
10 -i $inputA
11 -files
12 #for $bed in $names.beds:
13 $bed.input
14 #end for
15
16 #if $names.names_select == 'yes':
17 -names
18 #for $bed in $names.beds:
19 $bed.inputName
20 #end for
21 #end if
22 $strand
23 $counts
24 $both
25 &gt; $output
26 </command>
27 <inputs>
28 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file" />
29 <!-- Additional files, if the user needs more -->
30 <conditional name="names">
31 <param name="names_select" type="select" label="Specify names for each file">
32 <option value="no" selected="True">No</option>
33 <option value="yes">Yes</option>
34 </param>
35 <when value="yes">
36 <repeat name="beds" title="Add BED files and names" >
37 <param name="input" format="bed" type="data" label="BED file" />
38 <param name="inputName" type="text" label="Name of the file" />
39 </repeat>
40 </when>
41 <when value="no">
42 <repeat name="beds" title="Add BED files" >
43 <param name="input" format="bed" type="data" label="BED file" />
44 </repeat>
45 </when>
46 </conditional>
47
48 <expand macro="strand2" />
49 <param name="counts" type="boolean" checked="false" truevalue="-counts" falsevalue="" label="Report the count of features followed by the % coverage for each annotation file. Default is to report solely the fraction of -i covered by each file." />
50 <param name="both" type="boolean" checked="false" truevalue="-both" falsevalue="" label="Report the count of features followed by the % coverage for each annotation file. Default is to report solely the fraction of the input file covered by each file." />
51 </inputs>
52
53 <outputs>
54 <data format="bed" name="output" label="" />
55 </outputs>
56 <help>
57
58 **What it does**
59
60 bedtools annotate, well, annotates one BED/VCF/GFF file with the coverage and number of overlaps observed from multiple other BED/VCF/GFF files. In this way, it allows one to ask to what degree one feature coincides with multiple other feature types with a single command.
61
62 @REFERENCES@
63
64 </help>
65 </tool>