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comparison complementBed.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_complementbed" name="ComplementBed" 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 complementBed
11 -i "$input"
12 -g "$genome"
13 > "$output"
14 ]]>
15 </command>
16 <inputs>
17 <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/>
18 <expand macro="genome" />
19 </inputs>
20 <outputs>
21 <data format_source="input" name="output" metadata_source="input" label="Complemen of ${input.name}"/>
22 </outputs>
23 <tests>
24 <test>
25 <param name="input" value="a.bed" ftype="bed" />
26 <param name="genome" value="mm9_chr1.len" />
27 <output name="output" file="complementBed_result1.bed" ftype="bed" />
28 </test>
29 </tests>
30 <help>
31 <![CDATA[
32 **What it does**
33
34 bedtools complement returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file.
35
36 .. image:: $PATH_TO_IMAGES/complement-glyph.png
37
38 @REFERENCES@
39 ]]>
40 </help>
41 <expand macro="citations" />
42 </tool>