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comparison subtractBed.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_subtractbed" name="SubtractBed" 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 subtract
11 $strand
12 -a $inputA
13 -b $inputB
14 -f $overlap
15 $removeIfOverlap
16 > $output
17 ]]>
18 </command>
19 <inputs>
20 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
21 <param format="bed,gff,vcf,gff3" name="inputB" type="data" label="BED/VCF/GFF file"/>
22 <expand macro="strand2" />
23 <expand macro="overlap" />
24 <param name="removeIfOverlap" type="select" label="Calculation based on strandedness?">
25 <option value="" selected="True">Dont Remove entire feature on overlap</option>
26 <option value="-A">Remove entire feature if any overlap. That is, by default, only subtract the portion of A that overlaps B. Here, if any overlap is found (or -f amount), the entire feature is removed</option>
27 <option value="-N">Same as -A except when used with -f, the amount is the sum of all features (not any single feature)</option>
28 </param>
29 </inputs>
30 <outputs>
31 <data format_source="inputA" name="output" metadata_source="inputA"/>
32 </outputs>
33 <tests>
34 <test>
35 <param name="inputA" value="subtractBed1.bed" ftype="bed" />
36 <param name="inputB" value="subtractBed2.bed" ftype="bed" />
37 <output name="output" file="subtractBed_result1.bed" ftype="bed" />
38 </test>
39 <test>
40 <param name="inputA" value="subtractBed1.bed" ftype="bed" />
41 <param name="inputB" value="subtractBed2.bed" ftype="bed" />
42 <param name="overlap" value="0.80" />
43 <output name="output" file="subtractBed_result2.bed" ftype="bed" />
44 </test>
45 <test>
46 <param name="inputA" value="subtractBed1.bed" ftype="bed" />
47 <param name="inputB" value="subtractBed2.bed" ftype="bed" />
48 <param name="removeIfOverlap" value="-A" />
49 <output name="output" file="subtractBed_result3.bed" ftype="bed" />
50 </test>
51 </tests>
52 <help>
53 <![CDATA[
54 **What it does**
55
56 bedtools subtract searches for features in B that overlap A. If an overlapping feature is found in B, the overlapping portion is removed from A and the remaining portion of A is reported. If a feature in B overlaps all of a feature in A, the A feature will not be reported.
57
58 .. image:: $PATH_TO_IMAGES/subtract-glyph.png
59
60 @REFERENCES@
61 ]]>
62 </help>
63 <expand macro="citations" />
64 </tool>