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comparison makeWindowsBed.xml @ 64:f6c88d2e9ae5 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
author iuc
date Fri, 21 Feb 2025 21:38:34 +0000
parents 539958feb49c
children
comparison
equal deleted inserted replaced
63:7411007544bf 64:f6c88d2e9ae5
1 <tool id="bedtools_makewindowsbed" name="bedtools MakeWindowsBed" version="@TOOL_VERSION@" profile="@PROFILE@"> 1 <tool id="bedtools_makewindowsbed" name="bedtools MakeWindowsBed" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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="bio_tools" /> 6 <expand macro="bio_tools" />
13 #else: 13 #else:
14 -b '$type.input' 14 -b '$type.input'
15 #end if 15 #end if
16 #if $action.action_select == 'windowsize': 16 #if $action.action_select == 'windowsize':
17 -w $action.windowsize 17 -w $action.windowsize
18 #if $action.step_size.step_size_select == 'yes': 18 #if $action.step_size != '':
19 -s $action.step_size.step_size 19 -s $action.step_size
20 #end if 20 #end if
21 #else: 21 #else:
22 -n $action.number 22 -n $action.number
23 #end if 23 #end if
24 $sourcename 24 $sourcename
44 </param> 44 </param>
45 <when value="windowsize"> 45 <when value="windowsize">
46 <param name="windowsize" argument="-w" type="integer" value="1" 46 <param name="windowsize" argument="-w" type="integer" value="1"
47 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"
48 help="i.e. same number of nucleotide in each window" /> 48 help="i.e. same number of nucleotide in each window" />
49 <conditional name="step_size"> 49 <param name="step_size" argument="-s" type="integer" value="" optional="true" label="Step size" help="How many base pairs to step before creating a new window. Used to create 'sliding' windows. Defaults to window size (non-sliding windows)."/>
50 <param name="step_size_select" type="select"
51 label="Specify Step size? i.e. how many base pairs to step before creating a new window"
52 help="Used to create 'sliding' windows. Defaults to window size (non-sliding windows).">
53 <option value="yes">Yes</option>
54 <option value="no" selected="true">No</option>
55 </param>
56 <when value="yes">
57 <param name="step_size" argument="-s" type="integer" value="100" label="Specify it" />
58 </when>
59 <when value="no" />
60 </conditional>
61 </when> 50 </when>
62 <when value="number"> 51 <when value="number">
63 <param name="number" argument="-n" type="integer" value="1" 52 <param name="number" argument="-n" type="integer" value="1"
64 label="Divide each input interval (either a chromosome or a BED interval) to fixed number of windows" 53 label="Divide each input interval (either a chromosome or a BED interval) to fixed number of windows"
65 help="I.e. same number of windows, with varying window sizes" /> 54 help="I.e. same number of windows, with varying window sizes" />
75 <outputs> 64 <outputs>
76 <data name="output" format="bed" /> 65 <data name="output" format="bed" />
77 </outputs> 66 </outputs>
78 <tests> 67 <tests>
79 <test> 68 <test>
80 <param name="type_select" value="genome" /> 69 <param name="type|type_select" value="genome" />
81 <param name="genome_file_opts_selector" value="hist" /> 70 <param name="type|genome_file_opts|genome_file_opts_selector" value="hist" />
82 <param name="genome" value="mm9_chr1.len" ftype="tabular" /> 71 <param name="type|genome_file_opts|genome" value="mm9_chr1.len" ftype="tabular" />
83 <param name="action_select" value="windowsize" /> 72 <param name="action|action_select" value="windowsize" />
84 <param name="windowsize" value="1000000" /> 73 <param name="action|windowsize" value="1000000" />
85 <output name="output" file="makeWindowBed_result1.bed" ftype="bed" /> 74 <output name="output" file="makeWindowBed_result1.bed" ftype="bed" />
86 </test> 75 </test>
87 <test> 76 <test>
88 <param name="type_select" value="genome" /> 77 <param name="type|type_select" value="genome" />
89 <param name="genome_file_opts_selector" value="hist" /> 78 <param name="type|genome_file_opts|genome_file_opts_selector" value="hist" />
90 <param name="genome" value="mm9_chr1.len" ftype="tabular" /> 79 <param name="type|genome_file_opts|genome" value="mm9_chr1.len" ftype="tabular" />
91 <param name="action_select" value="windowsize" /> 80 <param name="action|action_select" value="windowsize" />
92 <param name="windowsize" value="1000000" /> 81 <param name="action|windowsize" value="1000000" />
93 <param name="step_size_select" value="yes" /> 82 <param name="action|step_size" value="50000" />
94 <param name="step_size" value="50000" />
95 <output name="output" file="makeWindowBed_result2.bed" ftype="bed" /> 83 <output name="output" file="makeWindowBed_result2.bed" ftype="bed" />
96 </test> 84 </test>
97 <test> 85 <test>
98 <param name="type_select" value="genome" /> 86 <param name="type|type_select" value="genome" />
99 <param name="genome_file_opts_selector" value="hist" /> 87 <param name="type|genome_file_opts|genome_file_opts_selector" value="hist" />
100 <param name="genome" value="mm9_chr1.len" ftype="tabular" /> 88 <param name="type|genome_file_opts|genome" value="mm9_chr1.len" ftype="tabular" />
101 <param name="action_select" value="number" /> 89 <param name="action|action_select" value="number" />
102 <param name="number" value="100" /> 90 <param name="action|number" value="100" />
103 <output name="output" file="makeWindowBed_result3.bed" ftype="bed" /> 91 <output name="output" file="makeWindowBed_result3.bed" ftype="bed" />
104 </test> 92 </test>
105 <test> 93 <test>
106 <param name="type_select" value="bed" /> 94 <param name="type|type_select" value="bed" />
107 <param name="input" value="makeWindowBed1.bed" ftype="bed" /> 95 <param name="type|input" value="makeWindowBed1.bed" ftype="bed" />
108 <param name="action_select" value="number" /> 96 <param name="action|action_select" value="number" />
109 <param name="number" value="15" /> 97 <param name="action|number" value="15" />
110 <output name="output" file="makeWindowBed_result4.bed" ftype="bed" /> 98 <output name="output" file="makeWindowBed_result4.bed" ftype="bed" />
111 </test> 99 </test>
112 </tests> 100 </tests>
113 <help><![CDATA[ 101 <help><![CDATA[
114 **What it does** 102 **What it does**