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comparison windowBed.xml @ 34:dde39ba9c031 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
author iuc
date Mon, 29 Apr 2019 05:55:48 -0400
parents 4f7a5ccd2ae9
children 3e38c9b3214f
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33:87ee588b3d45 34:dde39ba9c031
1 <tool id="bedtools_windowbed" name="bedtools WindowBed" version="@WRAPPER_VERSION@"> 1 <tool id="bedtools_windowbed" name="bedtools WindowBed" version="@TOOL_VERSION@">
2 <description>find overlapping intervals within a window around an interval</description> 2 <description>find overlapping intervals within a window around an interval</description>
3 <macros> 3 <macros>
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><![CDATA[
9 <![CDATA[ 9 bedtools window
10 bedtools window 10 #if $inputA.is_of_type('bam'):
11 #if $inputA.is_of_type('bam'): 11 -abam '$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 $bed
17 $bed 17 $strandB
18 $strandB 18 #if $addition.addition_select == 'window':
19 #if $addition.addition_select == 'window': 19 -w $addition.w
20 -w $addition.w 20 #elif $addition.addition_select == 'lr':
21 #elif $addition.addition_select == 'lr': 21 -l $addition.l
22 -l $addition.l 22 -r $addition.r
23 -r $addition.r 23 #end if
24 #end if 24 $original
25 $original 25 $number
26 $number 26 $nooverlaps
27 $nooverlaps 27 $header
28 $header 28 > '$output'
29 > '$output' 29 ]]></command>
30 ]]>
31 </command>
32 <inputs> 30 <inputs>
33 <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@/BAM file"/> 31 <param name="inputA" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@/BAM file"/>
34 <param format="@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> 32 <param name="inputB" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
35 <param name="bed" type="boolean" checked="false" truevalue="-bed" falsevalue="" 33 <param argument="-bed" type="boolean" truevalue="-bed" falsevalue="" checked="false"
36 label="When using BAM input, write output as BED. The default is to write output in BAM when using a bam file" 34 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)" />
38 <conditional name="addition"> 35 <conditional name="addition">
39 <param name="addition_select" type="select" label="Choose what you want to do"> 36 <param name="addition_select" type="select" label="Choose what you want to do">
40 <option value="window">Add Base pairs for **both** upstream and downstream of each entry in A when searching for overlaps in B</option> 37 <option value="window">Add Base pairs for **both** 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> 38 <option value="lr">Add Base pairs **separately** for upstream and downstream of each entry in A when searching for overlaps in B</option>
42 </param> 39 </param>
43 <when value="window"> 40 <when value="window">
44 <param name="w" type="integer" value="1000" label="Base pairs to add upstream and downstream" /> 41 <param argument="-w" type="integer" value="1000" label="Base pairs to add upstream and downstream" />
45 </when> 42 </when>
46 <when value="lr"> 43 <when value="lr">
47 <param name="l" type="integer" value="1000" 44 <param argument="-l" type="integer" value="1000"
48 label="Base pairs added upstream (left) of each entry in A when searching for overlaps in B" 45 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)" /> 46 help="Allows one to create assymetrical “windows”. Default is 1000bp." />
50 <param name="r" type="integer" value="1000" 47 <param argument="-r" type="integer" value="1000"
51 label="Base pairs added downstream (right) of each entry in A when searching for overlaps in B" 48 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)" /> 49 help="Allows one to create assymetrical “windows”. Default is 1000bp." />
53 </when> 50 </when>
54 </conditional> 51 </conditional>
55 <param name="strandB" type="select" label="Calculation based on strandedness?"> 52 <param name="strandB" type="select" label="Calculation based on strandedness?">
56 <option value="" selected="True">Report any hit in B</option> 53 <option value="" selected="true">Report any hit in B</option>
57 <option value="-sm">Only report hits in B that overlap A on the **same** strand</option> 54 <option value="-sm">Only report hits in B that overlap A on the **same** strand</option>
58 <option value="-Sm">Only report hits in B that overlap A on the **opposite** strand</option> 55 <option value="-Sm">Only report hits in B that overlap A on the **opposite** strand</option>
59 </param> 56 </param>
60 <param name="original" type="boolean" checked="false" truevalue="-u" falsevalue="" 57 <param name="original" argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="false"
61 label="Write original A entry once if any overlaps found in B" 58 label="Write original A entry once if any overlaps found in B"
62 help="In other words, just report the fact at least one overlap was found in B. (-u)" /> 59 help="In other words, just report the fact at least one overlap was found in B" />
63 <param name="number" type="boolean" checked="false" truevalue="-c" falsevalue="" 60 <param name="number" argument="-c" type="boolean" truevalue="-c" falsevalue="" checked="false"
64 label="For each entry in A, report the number of hits in B" 61 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)" /> 62 help="Reports 0 for A entries that have no overlap with B" />
66 <param name="nooverlaps" type="boolean" checked="false" truevalue="-v" falsevalue="" 63 <param name="nooverlaps" argument="-v" type="boolean" truevalue="-v" falsevalue="" checked="false"
67 label="Only report those entries in A that have no overlaps with B" help="(-v)" /> 64 label="Only report those entries in A that have no overlaps with B" />
68 <expand macro="print_header" /> 65 <expand macro="print_header" />
69 </inputs> 66 </inputs>
70 <outputs> 67 <outputs>
71 <data format_source="inputA" name="output" metadata_source="inputA" label=""/> 68 <data name="output" format_source="inputA" metadata_source="inputA" />
72 </outputs> 69 </outputs>
73 <tests> 70 <tests>
74 <test> 71 <test>
75 <param name="inputA" value="windowBedA.bed" ftype="bed" /> 72 <param name="inputA" value="windowBedA.bed" ftype="bed" />
76 <param name="inputB" value="windowBedB.bed" ftype="bed" /> 73 <param name="inputB" value="windowBedB.bed" ftype="bed" />
90 <param name="l" value="200" /> 87 <param name="l" value="200" />
91 <param name="r" value="20000" /> 88 <param name="r" value="20000" />
92 <output name="output" file="windowBed_result2.bed" ftype="bed" /> 89 <output name="output" file="windowBed_result2.bed" ftype="bed" />
93 </test> 90 </test>
94 </tests> 91 </tests>
95 <help> 92 <help><![CDATA[
96 <![CDATA[
97 **What it does** 93 **What it does**
98 94
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. 95 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.
100 96
101 .. image:: $PATH_TO_IMAGES/window-glyph.png 97 .. image:: $PATH_TO_IMAGES/window-glyph.png
102 98
103 @REFERENCES@ 99 @REFERENCES@
104 ]]> 100 ]]></help>
105 </help>
106 <expand macro="citations" /> 101 <expand macro="citations" />
107 </tool> 102 </tool>