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comparison fisherBed.xml @ 1:82aac94b06c3 draft

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author iuc
date Thu, 08 Jan 2015 14:25:51 -0500
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0:b8348686a0b9 1:82aac94b06c3
1 <tool id="bedtools_fisher" name="FisherBed" 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 bedtools fisher
11 $strand
12 $split
13 -a $inputA
14 -b $inputB
15 -f $overlap
16 -g $genome
17 $reciprocal
18 $m
19 > $output
20 ]]>
21 </command>
22 <inputs>
23 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
24 <param format="bed,gff,vcf,gff3" name="inputB" type="data" label="BED/VCF/GFF file"/>
25 <expand macro="genome" />
26 <expand macro="strand2" />
27 <expand macro="split" />
28 <expand macro="overlap" />
29 <expand macro="reciprocal" />
30 <param name="m" type="boolean" checked="False" truevalue="-m" falsevalue=""
31 label="Merge overlapping intervals before looking at overlap" help="(-m)" />
32 </inputs>
33 <outputs>
34 <data name="output" metadata_source="inputA" format_source="inputA" label="Fisher Test on ${inputA.name} and ${inputB.name}"/>
35 </outputs>
36 <tests>
37 <test>
38 <param name="inputA" value="fisherBed1.bed" ftype="bed" />
39 <param name="inputB" value="fisherBed2.bed" ftype="bed" />
40 <param name="genome" value="fisherBed.len" ftype="tabular" />
41 <output name="output" file="fisherBed_result1.bed" ftype="bed" />
42 </test>
43 </tests>
44 <help>
45 <![CDATA[
46 **What it does**
47
48 Perform fisher’s exact test on the number of overlaps/unique intervals between 2 files.
49
50 @REFERENCES@
51 ]]>
52 </help>
53 <expand macro="citations" />
54 </tool>