Mercurial > repos > iuc > bedtools

annotate makeWindowsBed.xml @ 64:f6c88d2e9ae5 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
64
f6c88d2e9ae5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
iuc
parents: 59
diff changeset
1 <tool id="bedtools_makewindowsbed" name="bedtools MakeWindowsBed" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
17
a2d4c30ba2f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 4
diff changeset
2 <description>make interval windows across a genome</description>
4
315929597efb Uploaded
iuc
parents:
diff changeset
3 <macros>
315929597efb Uploaded
iuc
parents:
diff changeset
4 <import>macros.xml</import>
315929597efb Uploaded
iuc
parents:
diff changeset
5 </macros>
59
539958feb49c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b"
iuc
parents: 57
diff changeset
6 <expand macro="bio_tools" />
4
315929597efb Uploaded
iuc
parents:
diff changeset
7 <expand macro="requirements" />
315929597efb Uploaded
iuc
parents:
diff changeset
8 <expand macro="stdio" />
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
9 <command><![CDATA[
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
10 bedtools makewindows
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
11 #if $type.type_select == 'genome':
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
12 @GENOME_FILE_MAKEWINDOWS@
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
13 #else:
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
14 -b '$type.input'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
15 #end if
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
16 #if $action.action_select == 'windowsize':
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
17 -w $action.windowsize
64
f6c88d2e9ae5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
iuc
parents: 59
diff changeset
18 #if $action.step_size != '':
f6c88d2e9ae5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
iuc
parents: 59
diff changeset
19 -s $action.step_size
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
20 #end if
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
21 #else:
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
22 -n $action.number
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
23 #end if
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
24 $sourcename
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
25 > '$output'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
26 ]]></command>
4
315929597efb Uploaded
iuc
parents:
diff changeset
27 <inputs>
315929597efb Uploaded
iuc
parents:
diff changeset
28 <conditional name="type">
315929597efb Uploaded
iuc
parents:
diff changeset
29 <param name="type_select" type="select" label="Work with">
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
30 <option value="bed" selected="true">Bed File</option>
4
315929597efb Uploaded
iuc
parents:
diff changeset
31 <option value="genome">Genome File</option>
315929597efb Uploaded
iuc
parents:
diff changeset
32 </param>
315929597efb Uploaded
iuc
parents:
diff changeset
33 <when value="bed">
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
34 <param name="input" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
4
315929597efb Uploaded
iuc
parents:
diff changeset
35 </when>
315929597efb Uploaded
iuc
parents:
diff changeset
36 <when value="genome">
32
b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
iuc
parents: 26
diff changeset
37 <expand macro="input_conditional_genome_file" />
4
315929597efb Uploaded
iuc
parents:
diff changeset
38 </when>
315929597efb Uploaded
iuc
parents:
diff changeset
39 </conditional>
315929597efb Uploaded
iuc
parents:
diff changeset
40 <conditional name="action">
315929597efb Uploaded
iuc
parents:
diff changeset
41 <param name="action_select" type="select" label="Work with">
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
42 <option value="windowsize" selected="true">Set WindowSize</option>
4
315929597efb Uploaded
iuc
parents:
diff changeset
43 <option value="number">Give Number of Windows</option>
315929597efb Uploaded
iuc
parents:
diff changeset
44 </param>
315929597efb Uploaded
iuc
parents:
diff changeset
45 <when value="windowsize">
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
46 <param name="windowsize" argument="-w" type="integer" value="1"
4
315929597efb Uploaded
iuc
parents:
diff changeset
47 label="Divide each input interval (either a chromosome or a BED interval) to fixed-sized windows"
315929597efb Uploaded
iuc
parents:
diff changeset
48 help="i.e. same number of nucleotide in each window" />
64
f6c88d2e9ae5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
iuc
parents: 59
diff changeset
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)."/>
4
315929597efb Uploaded
iuc
parents:
diff changeset
50 </when>
315929597efb Uploaded
iuc
parents:
diff changeset
51 <when value="number">
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
52 <param name="number" argument="-n" type="integer" value="1"
4
315929597efb Uploaded
iuc
parents:
diff changeset
53 label="Divide each input interval (either a chromosome or a BED interval) to fixed number of windows"
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
54 help="I.e. same number of windows, with varying window sizes" />
4
315929597efb Uploaded
iuc
parents:
diff changeset
55 </when>
315929597efb Uploaded
iuc
parents:
diff changeset
56 </conditional>
315929597efb Uploaded
iuc
parents:
diff changeset
57 <param name="sourcename" type="select" label="ID Naming Options">
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
58 <option value="" selected="true">Default</option>
4
315929597efb Uploaded
iuc
parents:
diff changeset
59 <option value="-i src">use the source interval's name</option>
315929597efb Uploaded
iuc
parents:
diff changeset
60 <option value="-i winnum">use the window number as the ID (e.g. 1,2,3,4...)</option>
315929597efb Uploaded
iuc
parents:
diff changeset
61 <option value="-i srcwinnum">use the source interval's name with the window number.</option>
315929597efb Uploaded
iuc
parents:
diff changeset
62 </param>
315929597efb Uploaded
iuc
parents:
diff changeset
63 </inputs>
315929597efb Uploaded
iuc
parents:
diff changeset
64 <outputs>
315929597efb Uploaded
iuc
parents:
diff changeset
65 <data name="output" format="bed" />
315929597efb Uploaded
iuc
parents:
diff changeset
66 </outputs>
315929597efb Uploaded
iuc
parents:
diff changeset
67 <tests>
315929597efb Uploaded
iuc
parents:
diff changeset
68 <test>
64
f6c88d2e9ae5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
iuc
parents: 59
diff changeset
69 <param name="type|type_select" value="genome" />
f6c88d2e9ae5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
iuc
parents: 59
diff changeset
70 <param name="type|genome_file_opts|genome_file_opts_selector" value="hist" />
f6c88d2e9ae5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
iuc
parents: 59
diff changeset
71 <param name="type|genome_file_opts|genome" value="mm9_chr1.len" ftype="tabular" />
f6c88d2e9ae5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
iuc
parents: 59
diff changeset
72 <param name="action|action_select" value="windowsize" />
f6c88d2e9ae5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
iuc
parents: 59
diff changeset
73 <param name="action|windowsize" value="1000000" />
4
315929597efb Uploaded
iuc
parents:
diff changeset
74 <output name="output" file="makeWindowBed_result1.bed" ftype="bed" />
315929597efb Uploaded
iuc
parents:
diff changeset
75 </test>
315929597efb Uploaded
iuc
parents:
diff changeset
76 <test>
64
f6c88d2e9ae5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
iuc
parents: 59
diff changeset
77 <param name="type|type_select" value="genome" />
f6c88d2e9ae5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
iuc
parents: 59
diff changeset
78 <param name="type|genome_file_opts|genome_file_opts_selector" value="hist" />
f6c88d2e9ae5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
iuc
parents: 59
diff changeset
79 <param name="type|genome_file_opts|genome" value="mm9_chr1.len" ftype="tabular" />
f6c88d2e9ae5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
iuc
parents: 59
diff changeset
80 <param name="action|action_select" value="windowsize" />
f6c88d2e9ae5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
iuc
parents: 59
diff changeset
81 <param name="action|windowsize" value="1000000" />
f6c88d2e9ae5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
iuc
parents: 59
diff changeset
82 <param name="action|step_size" value="50000" />
4
315929597efb Uploaded
iuc
parents:
diff changeset
83 <output name="output" file="makeWindowBed_result2.bed" ftype="bed" />
315929597efb Uploaded
iuc
parents:
diff changeset
84 </test>
315929597efb Uploaded
iuc
parents:
diff changeset
85 <test>
64
f6c88d2e9ae5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
iuc
parents: 59
diff changeset
86 <param name="type|type_select" value="genome" />
f6c88d2e9ae5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
iuc
parents: 59
diff changeset
87 <param name="type|genome_file_opts|genome_file_opts_selector" value="hist" />
f6c88d2e9ae5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
iuc
parents: 59
diff changeset
88 <param name="type|genome_file_opts|genome" value="mm9_chr1.len" ftype="tabular" />
f6c88d2e9ae5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
iuc
parents: 59
diff changeset
89 <param name="action|action_select" value="number" />
f6c88d2e9ae5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
iuc
parents: 59
diff changeset
90 <param name="action|number" value="100" />
4
315929597efb Uploaded
iuc
parents:
diff changeset
91 <output name="output" file="makeWindowBed_result3.bed" ftype="bed" />
315929597efb Uploaded
iuc
parents:
diff changeset
92 </test>
315929597efb Uploaded
iuc
parents:
diff changeset
93 <test>
64
f6c88d2e9ae5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
iuc
parents: 59
diff changeset
94 <param name="type|type_select" value="bed" />
f6c88d2e9ae5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
iuc
parents: 59
diff changeset
95 <param name="type|input" value="makeWindowBed1.bed" ftype="bed" />
f6c88d2e9ae5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
iuc
parents: 59
diff changeset
96 <param name="action|action_select" value="number" />
f6c88d2e9ae5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
iuc
parents: 59
diff changeset
97 <param name="action|number" value="15" />
4
315929597efb Uploaded
iuc
parents:
diff changeset
98 <output name="output" file="makeWindowBed_result4.bed" ftype="bed" />
315929597efb Uploaded
iuc
parents:
diff changeset
99 </test>
315929597efb Uploaded
iuc
parents:
diff changeset
100 </tests>
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
101 <help><![CDATA[
4
315929597efb Uploaded
iuc
parents:
diff changeset
102 **What it does**
315929597efb Uploaded
iuc
parents:
diff changeset
103
315929597efb Uploaded
iuc
parents:
diff changeset
104 Makes adjacent or sliding windows across a genome or BED file.
315929597efb Uploaded
iuc
parents:
diff changeset
105
315929597efb Uploaded
iuc
parents:
diff changeset
106 @REFERENCES@
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
107 ]]></help>
4
315929597efb Uploaded
iuc
parents:
diff changeset
108 <expand macro="citations" />
315929597efb Uploaded
iuc
parents:
diff changeset
109 </tool>