|
0
|
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 > $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 <expand macro="citations" />
|
|
|
66 </tool>
|
