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comparison windowBed.xml @ 0:4fb5ea02b441 draft

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author iuc
date Tue, 15 Jul 2014 14:42:23 -0400
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-1:000000000000 0:4fb5ea02b441
1 <tool id="bedtools_windowbed" name="WindowBed" 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 window
10 #if $inputA.ext == "bam":
11 -abam $inputA
12 #else:
13 -a $inputA
14 #end if
15 -b $inputB
16 $ubam
17 $bed
18 $strandB
19 #if $addition.addition_select == 'b':
20 -w $addition.b
21 #elif $addition.addition_select == 'lr':
22 -l $addition.l
23 -r $addition.r
24 #end if
25 $original
26 $number
27 $nooverlaps
28 $header
29 &gt; $output
30 </command>
31 <inputs>
32 <param format="bed,bam,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF/BAM file"/>
33 <param format="bed,gff,vcf,gff3" name="inputB" type="data" label="BED/VCF/GFF file"/>
34 <param name="ubam" type="boolean" checked="false" truevalue="-ubam" falsevalue="" label="Write uncompressed BAM output" />
35 <param name="bed" type="boolean" checked="false" truevalue="bed" falsevalue="" label="When using BAM input, write output as BED. The default is to write output in BAM when using a bam file" />
36 <conditional name="addition">
37 <param name="addition_select" type="select" label="Choose what you want to do">
38 <option value="huhn" selected="True">Do not change added base pairs</option>
39 <option value="b">Add Base pairs for **both** upstream and downstream of each entry in A when searching for overlaps in B</option>
40 <option value="lr">Add Base pairs **separately** for upstream and downstream of each entry in A when searching for overlaps in B</option>
41 </param>
42 <when value="b">
43 <param name="b" label="Give Value" type="integer" value="1000" />
44 </when>
45 <when value="lr">
46 <param name="l" label="Base pairs added upstream (left of) of each entry in A when searching for overlaps in B. Allows one to create assymetrical “windows”. Default is 1000bp" type="integer" value="1000" />
47 <param name="r" label="Base pairs added downstream (right of) of each entry in A when searching for overlaps in B. Allows one to create assymetrical “windows”. Default is 1000bp" type="integer" value="1000" />
48 </when>
49 </conditional>
50 <param name="strandB" type="select" label="Calculation based on strandedness?">
51 <option value="" selected="True">Report any hit in B</option>
52 <option value="-sm">Only report hits in B that overlap A on the **same** strand</option>
53 <option value="-Sm">Only report hits in B that overlap A on the **opposite** strand</option>
54 </param>
55 <param name="original" type="boolean" checked="false" truevalue="-u" falsevalue="" label="Write original A entry once if any overlaps found in B. In other words, just report the fact at least one overlap was found in B" />
56 <param name="number" type="boolean" checked="false" truevalue="-c" falsevalue="" label="For each entry in A, report the number of hits in B while restricting to -f. Reports 0 for A entries that have no overlap with B" />
57 <param name="nooverlaps" type="boolean" checked="false" truevalue="-v" falsevalue="" label="Only report those entries in A that have no overlaps with B" />
58 <param name="header" type="boolean" checked="false" truevalue="-header" falsevalue="" label="Print the header from the A file prior to results" />
59
60 </inputs>
61 <outputs>
62 <data format_source="inputA" name="output" metadata_source="inputA" label=""/>
63 </outputs>
64 <help>
65
66 **What it does**
67
68 Similar to bedtools intersect, window searches for overlapping features in A and B. However, window adds a specified number (1000, by default) of base pairs upstream and downstream of each feature in A. In effect, this allows features in B that are “near” features in A to be detected.
69
70 .. image:: $PATH_TO_IMAGES/window-glyph.png
71
72 @REFERENCES@
73 </help>
74 </tool>