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comparison windowBed.xml @ 4:315929597efb draft

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author iuc
date Wed, 07 Jan 2015 12:45:05 -0500
parents 7511823bdea1
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3:190a747ddaa8 4:315929597efb
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command> 8 <command>
9 <![CDATA[
9 bedtools window 10 bedtools window
10 #if $inputA.ext == "bam": 11 #if $inputA.ext == "bam":
11 -abam $inputA 12 -abam $inputA
12 #else: 13 #else:
13 -a $inputA 14 -a $inputA
14 #end if 15 #end if
15 -b $inputB 16 -b $inputB
16 $ubam
17 $bed 17 $bed
18 $strandB 18 $strandB
19 #if $addition.addition_select == 'b': 19 #if $addition.addition_select == 'window':
20 -w $addition.b 20 -w $addition.w
21 #elif $addition.addition_select == 'lr': 21 #elif $addition.addition_select == 'lr':
22 -l $addition.l 22 -l $addition.l
23 -r $addition.r 23 -r $addition.r
24 #end if 24 #end if
25 $original 25 $original
26 $number 26 $number
27 $nooverlaps 27 $nooverlaps
28 $header 28 $header
29 &gt; $output 29 > $output
30 ]]>
30 </command> 31 </command>
31 <inputs> 32 <inputs>
32 <param format="bed,bam,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF/BAM file"/> 33 <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 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=""
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 label="When using BAM input, write output as BED. The default is to write output in BAM when using a bam file"
37 help="(-bed)" />
36 <conditional name="addition"> 38 <conditional name="addition">
37 <param name="addition_select" type="select" label="Choose what you want to do"> 39 <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> 40 <option value="window">Add Base pairs for **both** upstream and downstream of each entry in A when searching for overlaps in B</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 <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 </param>
42 <when value="b"> 43 <when value="window">
43 <param name="b" label="Give Value" type="integer" value="1000" /> 44 <param name="w" type="integer" value="1000" label="Base pairs to add upstream and downstream" />
44 </when> 45 </when>
45 <when value="lr"> 46 <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="l" 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 label="Base pairs added upstream (left) of each entry in A when searching for overlaps in B"
49 help="Allows one to create assymetrical “windows”. Default is 1000bp. (-l)" />
50 <param name="r" type="integer" value="1000"
51 label="Base pairs added downstream (right) of each entry in A when searching for overlaps in B"
52 help="Allows one to create assymetrical “windows”. Default is 1000bp. (-r)" />
48 </when> 53 </when>
49 </conditional> 54 </conditional>
50 <param name="strandB" type="select" label="Calculation based on strandedness?"> 55 <param name="strandB" type="select" label="Calculation based on strandedness?">
51 <option value="" selected="True">Report any hit in B</option> 56 <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> 57 <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> 58 <option value="-Sm">Only report hits in B that overlap A on the **opposite** strand</option>
54 </param> 59 </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" /> 60 <param name="original" type="boolean" checked="false" truevalue="-u" falsevalue=""
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" /> 61 label="Write original A entry once if any overlaps found in 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" /> 62 help="In other words, just report the fact at least one overlap was found in B. (-u)" />
58 <param name="header" type="boolean" checked="false" truevalue="-header" falsevalue="" label="Print the header from the A file prior to results" /> 63 <param name="number" type="boolean" checked="false" truevalue="-c" falsevalue=""
59 64 label="For each entry in A, report the number of hits in B"
65 help="Reports 0 for A entries that have no overlap with B (-c)" />
66 <param name="nooverlaps" type="boolean" checked="false" truevalue="-v" falsevalue=""
67 label="Only report those entries in A that have no overlaps with B" help="(-v)" />
68 <expand macro="print_header" />
60 </inputs> 69 </inputs>
61 <outputs> 70 <outputs>
62 <data format_source="inputA" name="output" metadata_source="inputA" label=""/> 71 <data format_source="inputA" name="output" metadata_source="inputA" label=""/>
63 </outputs> 72 </outputs>
73 <tests>
74 <test>
75 <param name="inputA" value="windowBedA.bed" ftype="bed" />
76 <param name="inputB" value="windowBedB.bed" ftype="bed" />
77 <output name="output" file="windowBed_result1.bed" ftype="bed" />
78 </test>
79 <test>
80 <param name="inputA" value="windowBedA.bed" ftype="bed" />
81 <param name="inputB" value="windowBedB.bed" ftype="bed" />
82 <param name="addition_select" value="window" />
83 <param name="w" value="5000" />
84 <output name="output" file="windowBed_result2.bed" ftype="bed" />
85 </test>
86 <test>
87 <param name="inputA" value="windowBedA.bed" ftype="bed" />
88 <param name="inputB" value="windowBedB.bed" ftype="bed" />
89 <param name="addition_select" value="lr" />
90 <param name="l" value="200" />
91 <param name="r" value="20000" />
92 <output name="output" file="windowBed_result2.bed" ftype="bed" />
93 </test>
94 </tests>
64 <help> 95 <help>
65 96 <![CDATA[
66 **What it does** 97 **What it does**
67 98
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. 99 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.
69 100
70 .. image:: $PATH_TO_IMAGES/window-glyph.png 101 .. image:: $PATH_TO_IMAGES/window-glyph.png
71 102
72 @REFERENCES@ 103 @REFERENCES@
104 ]]>
73 </help> 105 </help>
74 <expand macro="citations" /> 106 <expand macro="citations" />
75 </tool> 107 </tool>