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comparison makeWindowsBed.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 b28e0cfa7ba1
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33:87ee588b3d45 34:dde39ba9c031
1 <tool id="bedtools_makewindowsbed" name="bedtools MakeWindowsBed" version="@WRAPPER_VERSION@"> 1 <tool id="bedtools_makewindowsbed" name="bedtools MakeWindowsBed" version="@TOOL_VERSION@">
2 <description>make interval windows across a genome</description> 2 <description>make interval windows across a genome</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 makewindows
10 bedtools makewindows 10 #if $type.type_select == 'genome':
11 #if $type.type_select == 'genome': 11 @GENOME_FILE_MAKEWINDOWS@
12 @GENOME_FILE_MAKEWINDOWS@ 12 #else:
13 #else: 13 -b '$type.input'
14 -b '$type.input' 14 #end if
15 #end if 15 #if $action.action_select == 'windowsize':
16 #if $action.action_select == 'windowsize': 16 -w $action.windowsize
17 -w $action.windowsize 17 #if $action.step_size.step_size_select == 'yes':
18 #if $action.step_size.step_size_select == 'yes': 18 -s $action.step_size.step_size
19 -s $action.step_size.step_size 19 #end if
20 #end if 20 #else:
21 #else: 21 -n $action.number
22 -n $action.number 22 -s $action.step_size
23 -s $action.step_size 23 #end if
24 #end if 24 $sourcename
25 $sourcename 25 > '$output'
26 > '$output' 26 ]]></command>
27 ]]>
28 </command>
29 <inputs> 27 <inputs>
30 <conditional name="type"> 28 <conditional name="type">
31 <param name="type_select" type="select" label="Work with"> 29 <param name="type_select" type="select" label="Work with">
32 <option value="bed" selected="True">Bed File</option> 30 <option value="bed" selected="true">Bed File</option>
33 <option value="genome">Genome File</option> 31 <option value="genome">Genome File</option>
34 </param> 32 </param>
35 <when value="bed"> 33 <when value="bed">
36 <param name="input" format="@STD_BEDTOOLS_INPUTS@" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> 34 <param name="input" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
37 </when> 35 </when>
38 <when value="genome"> 36 <when value="genome">
39 <expand macro="input_conditional_genome_file" /> 37 <expand macro="input_conditional_genome_file" />
40 </when> 38 </when>
41 </conditional> 39 </conditional>
42 <conditional name="action"> 40 <conditional name="action">
43 <param name="action_select" type="select" label="Work with"> 41 <param name="action_select" type="select" label="Work with">
44 <option value="windowsize" selected="True">Set WindowSize</option> 42 <option value="windowsize" selected="true">Set WindowSize</option>
45 <option value="number">Give Number of Windows</option> 43 <option value="number">Give Number of Windows</option>
46 </param> 44 </param>
47 <when value="windowsize"> 45 <when value="windowsize">
48 <param name="windowsize" type="integer" value="1" 46 <param name="windowsize" argument="-w" type="integer" value="1"
49 label="Divide each input interval (either a chromosome or a BED interval) to fixed-sized windows" 47 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" /> 48 help="i.e. same number of nucleotide in each window" />
51 <conditional name="step_size"> 49 <conditional name="step_size">
52 <param name="step_size_select" type="select" 50 <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" 51 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)."> 52 help="Used to create 'sliding' windows. Defaults to window size (non-sliding windows).">
55 <option value="yes">Yes</option> 53 <option value="yes">Yes</option>
56 <option value="no" selected="True">No</option> 54 <option value="no" selected="true">No</option>
57 </param> 55 </param>
58 <when value="yes"> 56 <when value="yes">
59 <param name="step_size" type="integer" value="100" label="Specify it" /> 57 <param name="step_size" argument="-s" type="integer" value="100" label="Specify it" />
60 </when> 58 </when>
61 <when value="no" /> 59 <when value="no" />
62 </conditional> 60 </conditional>
63 </when> 61 </when>
64 <when value="number"> 62 <when value="number">
65 <param name="number" type="integer" value="1" 63 <param name="number" argument="-n" type="integer" value="1"
66 label="Divide each input interval (either a chromosome or a BED interval) to fixed number of windows" 64 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" /> 65 help="I.e. same number of windows, with varying window sizes" />
68 <param name="step_size" type="integer" value="100" label="Specify it" /> 66 <param name="step_size" argument="-s" type="integer" value="100" label="Specify it" />
69 </when> 67 </when>
70 </conditional> 68 </conditional>
71 <param name="sourcename" type="select" label="ID Naming Options"> 69 <param name="sourcename" type="select" label="ID Naming Options">
72 <option value="" selected="True">Default</option> 70 <option value="" selected="true">Default</option>
73 <option value="-i src">use the source interval's name</option> 71 <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> 72 <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> 73 <option value="-i srcwinnum">use the source interval's name with the window number.</option>
76 </param> 74 </param>
77 </inputs> 75 </inputs>
113 <param name="number" value="15" /> 111 <param name="number" value="15" />
114 <param name="step_size" value="100" /> 112 <param name="step_size" value="100" />
115 <output name="output" file="makeWindowBed_result4.bed" ftype="bed" /> 113 <output name="output" file="makeWindowBed_result4.bed" ftype="bed" />
116 </test> 114 </test>
117 </tests> 115 </tests>
118 <help> 116 <help><![CDATA[
119 <![CDATA[
120 **What it does** 117 **What it does**
121 118
122 Makes adjacent or sliding windows across a genome or BED file. 119 Makes adjacent or sliding windows across a genome or BED file.
123 120
124 @REFERENCES@ 121 @REFERENCES@
125 ]]> 122 ]]></help>
126 </help>
127 <expand macro="citations" /> 123 <expand macro="citations" />
128 </tool> 124 </tool>