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comparison makeWindowsBed.xml @ 10:71af3ebbbb7a draft

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author iuc
date Wed, 29 Apr 2015 12:06:53 -0400
parents 315929597efb
children a2d4c30ba2f9
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9:21f1d1c5467b 10:71af3ebbbb7a
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 <![CDATA[
10 bedtools makewindows
11 #if $type.type_select == 'genome':
12 -g $type.genome
13 #else:
14 -b $type.input
15 #end if
16 #if $action.action_select == 'windowsize':
17 -w $action.windowsize
18 #if $action.step_size.step_size_select == 'yes':
19 -s $action.step_size.step_size
20 #end if
21 #else:
22 -n $action.number
23 -s $action.step_size
24 #end if
25 $sourcename
26 > $output
27 ]]>
28 </command>
29 <inputs>
30 <conditional name="type">
31 <param name="type_select" type="select" label="Work with">
32 <option value="bed" selected="True">Bed File</option>
33 <option value="genome">Genome File</option>
34 </param>
35 <when value="bed">
36 <param name="input" format="bed,vcf,gff,gff3" type="data" label="BED/VCF/GFF file"/>
37 </when>
38 <when value="genome">
39 <expand macro="genome" />
40 </when>
41 </conditional>
42 <conditional name="action">
43 <param name="action_select" type="select" label="Work with">
44 <option value="windowsize" selected="True">Set WindowSize</option>
45 <option value="number">Give Number of Windows</option>
46 </param>
47 <when value="windowsize">
48 <param name="windowsize" type="integer" value="1"
49 label="Divide each input interval (either a chromosome or a BED interval) to fixed-sized windows"
50 help="i.e. same number of nucleotide in each window" />
51 <conditional name="step_size">
52 <param name="step_size_select" type="select"
53 label="Specify Step size? i.e. how many base pairs to step before creating a new window"
54 help="Used to create 'sliding' windows. Defaults to window size (non-sliding windows).">
55 <option value="yes">Yes</option>
56 <option value="no" selected="True">No</option>
57 </param>
58 <when value="yes">
59 <param name="step_size" type="integer" value="100" label="Specify it" />
60 </when>
61 <when value="no" />
62 </conditional>
63 </when>
64 <when value="number">
65 <param name="number" type="integer" value="1"
66 label="Divide each input interval (either a chromosome or a BED interval) to fixed number of windows"
67 help="i.e. same number of windows, with varying window sizes" />
68 <param name="step_size" type="integer" value="100" label="Specify it" />
69 </when>
70 </conditional>
71 <param name="sourcename" type="select" label="ID Naming Options">
72 <option value="" selected="True">Default</option>
73 <option value="-i src">use the source interval's name</option>
74 <option value="-i winnum">use the window number as the ID (e.g. 1,2,3,4...)</option>
75 <option value="-i srcwinnum">use the source interval's name with the window number.</option>
76 </param>
77 </inputs>
78 <outputs>
79 <data name="output" format="bed" />
80 </outputs>
81 <tests>
82 <test>
83 <param name="type_select" value="genome" />
84 <param name="genome" value="mm9_chr1.len" ftype="tabular" />
85 <param name="action_select" value="windowsize" />
86 <param name="windowsize" value="1000000" />
87 <output name="output" file="makeWindowBed_result1.bed" ftype="bed" />
88 </test>
89 <test>
90 <param name="type_select" value="genome" />
91 <param name="genome" value="mm9_chr1.len" ftype="tabular" />
92 <param name="action_select" value="windowsize" />
93 <param name="windowsize" value="1000000" />
94 <param name="step_size_select" value="yes" />
95 <param name="step_size" value="50000" />
96 <output name="output" file="makeWindowBed_result2.bed" ftype="bed" />
97 </test>
98 <test>
99 <param name="type_select" value="genome" />
100 <param name="genome" value="mm9_chr1.len" ftype="tabular" />
101 <param name="action_select" value="number" />
102 <param name="number" value="100" />
103 <param name="step_size" value="10000" />
104 <output name="output" file="makeWindowBed_result3.bed" ftype="bed" />
105 </test>
106 <test>
107 <param name="type_select" value="bed" />
108 <param name="input" value="makeWindowBed1.bed" ftype="bed" />
109 <param name="action_select" value="number" />
110 <param name="number" value="15" />
111 <param name="step_size" value="100" />
112 <output name="output" file="makeWindowBed_result4.bed" ftype="bed" />
113 </test>
114 </tests>
115 <help>
116 <![CDATA[
117 **What it does**
118
119 Makes adjacent or sliding windows across a genome or BED file.
120
121 @REFERENCES@
122 ]]>
123 </help>
124 <expand macro="citations" />
125 </tool>