Mercurial > repos > iuc > bedtools
annotate annotateBed.xml @ 17:a2d4c30ba2f9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
author | iuc |
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date | Sun, 21 Jun 2015 22:49:46 -0400 |
parents | 0d3aa592ce27 |
children | 5efc48568d8d |
rev | line source |
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8 | 1 <tool id="bedtools_annotatebed" name="AnnotateBed" 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
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changeset
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2 <description>annotate coverage of features from multiple 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 bedtools annotate | |
11 -i "${inputA}" | |
12 #if $names.names_select == 'yes': | |
13 -files | |
14 #for $bed in $names.beds: | |
15 "${bed.input}" | |
16 #end for | |
17 | |
18 -names | |
19 #for $bed in $names.beds: | |
20 "${bed.inputName}" | |
21 #end for | |
22 #else: | |
23 #set files = '" "'.join( [ str( $file ) for $file in $names.beds ] ) | |
24 -files "${files}" | |
25 #end if | |
26 $strand | |
27 $counts | |
28 $both | |
29 > "${output}" | |
30 ]]> | |
31 </command> | |
32 <inputs> | |
33 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file" /> | |
34 <!-- Additional files, if the user needs more --> | |
35 <conditional name="names"> | |
36 <param name="names_select" type="select" label="Specify names for each file"> | |
37 <option value="no" selected="True">No</option> | |
38 <option value="yes">Yes</option> | |
39 </param> | |
40 <when value="yes"> | |
41 <repeat name="beds" title="Add BED files and names" > | |
42 <param name="input" format="bed" type="data" label="BED file" /> | |
43 <param name="inputName" type="text" label="Name of the file" /> | |
44 </repeat> | |
45 </when> | |
46 <when value="no"> | |
47 <param name="beds" format="bed" multiple="True" type="data" label="BED file" /> | |
48 </when> | |
49 </conditional> | |
50 <expand macro="strand2" /> | |
51 <param name="counts" type="boolean" checked="false" truevalue="-counts" falsevalue="" | |
52 label="Report the count of features followed by the % coverage for each annotation file" | |
53 help="Default is to report solely the fraction of -i covered by each file." /> | |
54 <param name="both" type="boolean" checked="false" truevalue="-both" falsevalue="" | |
55 label="Report the count of features followed by the % coverage for each annotation file" | |
56 help="Default is to report solely the fraction of the input file covered by each file." /> | |
57 </inputs> | |
58 <outputs> | |
59 <data format="bed" name="output" /> | |
60 </outputs> | |
61 <tests> | |
62 <test> | |
63 <param name="inputA" value="annotateBed1.bed" ftype="bed" /> | |
64 <param name="names_select" value="no" /> | |
65 <param name="beds" value="annotateBed2.bed,annotateBed3.bed,annotateBed4.bed" /> | |
66 <output name="output" file="annotateBed_result.bed" ftype="bed" /> | |
67 </test> | |
68 </tests> | |
69 <help> | |
70 <![CDATA[ | |
71 **What it does** | |
72 | |
73 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. | |
74 | |
75 @REFERENCES@ | |
76 ]]> | |
77 </help> | |
78 <expand macro="citations" /> | |
79 </tool> |