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comparison makewindowsBed.xml @ 0:4fb5ea02b441 draft

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author iuc
date Tue, 15 Jul 2014 14:42:23 -0400
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1 <tool id="bedtools_makewindowsbed" name="MakeWindowsBed" 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 makewindows
10 #if $type.type_select == 'genome':
11 -g $type.genome
12 #else:
13 -i $type.inputA
14 #end if
15 #if $action.action_select == 'windowsize':
16 -w $action.windowsize
17 #if $action.step_size.step_size_select == 'yes':
18 -s $action.step_size.step_size
19 #end if
20 #else:
21 -n $action.number
22 #end if
23 $sourcename
24 &gt; $output
25 </command>
26 <inputs>
27 <conditional name="type">
28 <param name="type_select" type="select" label="Work with">
29 <option value="bed" selected="True">Bed File</option>
30 <option value="genome">Genome File</option>
31 </param>
32 <when value="bed">
33 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
34 </when>
35 <when value="genome">
36 <expand macro="genome" />
37 </when>
38 </conditional>
39 <conditional name="action">
40 <param name="action_select" type="select" label="Work with">
41 <option value="windowsize" selected="True">Set WindowSize</option>
42 <option value="number">Give Number of Windows</option>
43 </param>
44 <when value="windowsize">
45 <param name="windowsize" type="integer" value="1" label="Divide each input interval (either a chromosome or a BED interval) to fixed-sized windows (i.e. same number of nucleotide in each window)." />
46 <conditional name="step_size">
47 <param name="step_size_select" type="select" label="Specify Step size? i.e. how many base pairs to step before creating a new window. Used to create 'sliding' windows. Defaults to window size (non-sliding windows).">
48 <option value="yes">Yes</option>
49 <option value="no" selected="True">No</option>
50 </param>
51 <when value="yes">
52 <param name="step_size" type="integer" value="100" label="Specify it" />
53 </when>
54 </conditional>
55 </when>
56 <when value="number">
57 <param name="number" type="integer" value="1" label="Divide each input interval (either a chromosome or a BED interval) to fixed number of windows (i.e. same number of windows, with varying window sizes)." />
58 </when>
59 </conditional>
60 <param name="sourcename" type="select" label="ID Naming Options">
61 <option value="" selected="True">Default</option>
62 <option value="-i src">use the source interval's name</option>
63 <option value="-i winnum">use the window number as the ID (e.g. 1,2,3,4...)</option>
64 <option value="-i srcwinnum">use the source interval's name with the window number.</option>
65 </param>
66 </inputs>
67 <outputs>
68 <data format_source="inputA" name="output" metadata_source="inputA" label=""/>
69 </outputs>
70 <help>
71
72 **What it does**
73
74 Makes adjacent or sliding windows across a genome or BED file.
75
76 @REFERENCES@
77 </help>
78 </tool>