Mercurial > repos > iuc > bedtools

annotate makeWindowsBed.xml @ 52:9a9f1a7abf54 draft

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 fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
author iuc
date Fri, 06 Sep 2019 14:28:37 -0400
parents df28283b3778
children 7a06bb42dbb1
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
1 <tool id="bedtools_makewindowsbed" name="bedtools MakeWindowsBed" version="@TOOL_VERSION@">
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>
315929597efb Uploaded
iuc
parents:
diff changeset
6 <expand macro="requirements" />
315929597efb Uploaded
iuc
parents:
diff changeset
7 <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
8 <command><![CDATA[
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
9 bedtools makewindows
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
10 #if $type.type_select == 'genome':
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
11 @GENOME_FILE_MAKEWINDOWS@
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
12 #else:
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
13 -b '$type.input'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
14 #end if
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
15 #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
16 -w $action.windowsize
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
17 #if $action.step_size.step_size_select == 'yes':
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
18 -s $action.step_size.step_size
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
19 #end if
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
20 #else:
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
21 -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
22 #end if
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
23 $sourcename
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
24 > '$output'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
25 ]]></command>
4
315929597efb Uploaded
iuc
parents:
diff changeset
26 <inputs>
315929597efb Uploaded
iuc
parents:
diff changeset
27 <conditional name="type">
315929597efb Uploaded
iuc
parents:
diff changeset
28 <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
29 <option value="bed" selected="true">Bed File</option>
4
315929597efb Uploaded
iuc
parents:
diff changeset
30 <option value="genome">Genome File</option>
315929597efb Uploaded
iuc
parents:
diff changeset
31 </param>
315929597efb Uploaded
iuc
parents:
diff changeset
32 <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
33 <param name="input" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
4
315929597efb Uploaded
iuc
parents:
diff changeset
34 </when>
315929597efb Uploaded
iuc
parents:
diff changeset
35 <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
36 <expand macro="input_conditional_genome_file" />
4
315929597efb Uploaded
iuc
parents:
diff changeset
37 </when>
315929597efb Uploaded
iuc
parents:
diff changeset
38 </conditional>
315929597efb Uploaded
iuc
parents:
diff changeset
39 <conditional name="action">
315929597efb Uploaded
iuc
parents:
diff changeset
40 <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
41 <option value="windowsize" selected="true">Set WindowSize</option>
4
315929597efb Uploaded
iuc
parents:
diff changeset
42 <option value="number">Give Number of Windows</option>
315929597efb Uploaded
iuc
parents:
diff changeset
43 </param>
315929597efb Uploaded
iuc
parents:
diff changeset
44 <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
45 <param name="windowsize" argument="-w" type="integer" value="1"
4
315929597efb Uploaded
iuc
parents:
diff changeset
46 label="Divide each input interval (either a chromosome or a BED interval) to fixed-sized windows"
315929597efb Uploaded
iuc
parents:
diff changeset
47 help="i.e. same number of nucleotide in each window" />
315929597efb Uploaded
iuc
parents:
diff changeset
48 <conditional name="step_size">
315929597efb Uploaded
iuc
parents:
diff changeset
49 <param name="step_size_select" type="select"
315929597efb Uploaded
iuc
parents:
diff changeset
50 label="Specify Step size? i.e. how many base pairs to step before creating a new window"
315929597efb Uploaded
iuc
parents:
diff changeset
51 help="Used to create 'sliding' windows. Defaults to window size (non-sliding windows).">
315929597efb Uploaded
iuc
parents:
diff changeset
52 <option value="yes">Yes</option>
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
53 <option value="no" selected="true">No</option>
4
315929597efb Uploaded
iuc
parents:
diff changeset
54 </param>
315929597efb Uploaded
iuc
parents:
diff changeset
55 <when value="yes">
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
56 <param name="step_size" argument="-s" type="integer" value="100" label="Specify it" />
4
315929597efb Uploaded
iuc
parents:
diff changeset
57 </when>
315929597efb Uploaded
iuc
parents:
diff changeset
58 <when value="no" />
315929597efb Uploaded
iuc
parents:
diff changeset
59 </conditional>
315929597efb Uploaded
iuc
parents:
diff changeset
60 </when>
315929597efb Uploaded
iuc
parents:
diff changeset
61 <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
62 <param name="number" argument="-n" type="integer" value="1"
4
315929597efb Uploaded
iuc
parents:
diff changeset
63 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
64 help="I.e. same number of windows, with varying window sizes" />
4
315929597efb Uploaded
iuc
parents:
diff changeset
65 </when>
315929597efb Uploaded
iuc
parents:
diff changeset
66 </conditional>
315929597efb Uploaded
iuc
parents:
diff changeset
67 <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
68 <option value="" selected="true">Default</option>
4
315929597efb Uploaded
iuc
parents:
diff changeset
69 <option value="-i src">use the source interval's name</option>
315929597efb Uploaded
iuc
parents:
diff changeset
70 <option value="-i winnum">use the window number as the ID (e.g. 1,2,3,4...)</option>
315929597efb Uploaded
iuc
parents:
diff changeset
71 <option value="-i srcwinnum">use the source interval's name with the window number.</option>
315929597efb Uploaded
iuc
parents:
diff changeset
72 </param>
315929597efb Uploaded
iuc
parents:
diff changeset
73 </inputs>
315929597efb Uploaded
iuc
parents:
diff changeset
74 <outputs>
315929597efb Uploaded
iuc
parents:
diff changeset
75 <data name="output" format="bed" />
315929597efb Uploaded
iuc
parents:
diff changeset
76 </outputs>
315929597efb Uploaded
iuc
parents:
diff changeset
77 <tests>
315929597efb Uploaded
iuc
parents:
diff changeset
78 <test>
315929597efb Uploaded
iuc
parents:
diff changeset
79 <param name="type_select" 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
80 <param name="genome_file_opts_selector" value="hist" />
4
315929597efb Uploaded
iuc
parents:
diff changeset
81 <param name="genome" value="mm9_chr1.len" ftype="tabular" />
315929597efb Uploaded
iuc
parents:
diff changeset
82 <param name="action_select" value="windowsize" />
315929597efb Uploaded
iuc
parents:
diff changeset
83 <param name="windowsize" value="1000000" />
315929597efb Uploaded
iuc
parents:
diff changeset
84 <output name="output" file="makeWindowBed_result1.bed" ftype="bed" />
315929597efb Uploaded
iuc
parents:
diff changeset
85 </test>
315929597efb Uploaded
iuc
parents:
diff changeset
86 <test>
315929597efb Uploaded
iuc
parents:
diff changeset
87 <param name="type_select" 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
88 <param name="genome_file_opts_selector" value="hist" />
4
315929597efb Uploaded
iuc
parents:
diff changeset
89 <param name="genome" value="mm9_chr1.len" ftype="tabular" />
315929597efb Uploaded
iuc
parents:
diff changeset
90 <param name="action_select" value="windowsize" />
315929597efb Uploaded
iuc
parents:
diff changeset
91 <param name="windowsize" value="1000000" />
315929597efb Uploaded
iuc
parents:
diff changeset
92 <param name="step_size_select" value="yes" />
315929597efb Uploaded
iuc
parents:
diff changeset
93 <param name="step_size" value="50000" />
315929597efb Uploaded
iuc
parents:
diff changeset
94 <output name="output" file="makeWindowBed_result2.bed" ftype="bed" />
315929597efb Uploaded
iuc
parents:
diff changeset
95 </test>
315929597efb Uploaded
iuc
parents:
diff changeset
96 <test>
315929597efb Uploaded
iuc
parents:
diff changeset
97 <param name="type_select" 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
98 <param name="genome_file_opts_selector" value="hist" />
4
315929597efb Uploaded
iuc
parents:
diff changeset
99 <param name="genome" value="mm9_chr1.len" ftype="tabular" />
315929597efb Uploaded
iuc
parents:
diff changeset
100 <param name="action_select" value="number" />
315929597efb Uploaded
iuc
parents:
diff changeset
101 <param name="number" value="100" />
315929597efb Uploaded
iuc
parents:
diff changeset
102 <output name="output" file="makeWindowBed_result3.bed" ftype="bed" />
315929597efb Uploaded
iuc
parents:
diff changeset
103 </test>
315929597efb Uploaded
iuc
parents:
diff changeset
104 <test>
315929597efb Uploaded
iuc
parents:
diff changeset
105 <param name="type_select" value="bed" />
315929597efb Uploaded
iuc
parents:
diff changeset
106 <param name="input" value="makeWindowBed1.bed" ftype="bed" />
315929597efb Uploaded
iuc
parents:
diff changeset
107 <param name="action_select" value="number" />
315929597efb Uploaded
iuc
parents:
diff changeset
108 <param name="number" value="15" />
315929597efb Uploaded
iuc
parents:
diff changeset
109 <output name="output" file="makeWindowBed_result4.bed" ftype="bed" />
315929597efb Uploaded
iuc
parents:
diff changeset
110 </test>
315929597efb Uploaded
iuc
parents:
diff changeset
111 </tests>
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
112 <help><![CDATA[
4
315929597efb Uploaded
iuc
parents:
diff changeset
113 **What it does**
315929597efb Uploaded
iuc
parents:
diff changeset
114
315929597efb Uploaded
iuc
parents:
diff changeset
115 Makes adjacent or sliding windows across a genome or BED file.
315929597efb Uploaded
iuc
parents:
diff changeset
116
315929597efb Uploaded
iuc
parents:
diff changeset
117 @REFERENCES@
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
118 ]]></help>
4
315929597efb Uploaded
iuc
parents:
diff changeset
119 <expand macro="citations" />
315929597efb Uploaded
iuc
parents:
diff changeset
120 </tool>