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comparison multiIntersectBed.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
comparison
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33:87ee588b3d45 34:dde39ba9c031
1 <tool id="bedtools_multiintersectbed" name="bedtools Multiple Intersect" version="@WRAPPER_VERSION@"> 1 <tool id="bedtools_multiintersectbed" name="bedtools Multiple Intersect" version="@TOOL_VERSION@+galaxy1">
2 <description>identifies common intervals among multiple interval files</description> 2 <description>identifies common intervals among multiple interval files</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 multiinter
10 bedtools multiinter 10 $header
11 $header 11 $cluster
12 $cluster 12 -filler '${filler}'
13 -filler "${filler}" 13 $empty.empty_selector
14 $empty.empty_selector 14 @GENOME_FILE_UNION@
15 @GENOME_FILE_UNION@
16 15
17 #if str($tag.tag_select) == "tag": 16 #if str($tag.tag_select) == "tag":
18 #set files = '" "'.join( [ str( $file ) for $file in $tag.inputs ] ) 17 -i
19 -i "${files}" 18 #for $file in $tag.inputs
20 #else: 19 '$file'
21 -i 20 #end for
22 #for $file in $tag.beds: 21 #else:
23 "${file.input}" 22 -i
24 #end for 23 #for $file in $tag.beds:
25 -names 24 '${file.input}'
26 #for $file in $tag.beds: 25 #end for
27 "{$file.custom_name}" 26 -names
28 #end for 27 #for $file in $tag.beds:
29 #end if 28 '{$file.custom_name}'
30 29 #end for
31 > '$output' 30 #end if
32 ]]> 31 > '$output'
33 </command> 32 ]]></command>
34 <inputs> 33 <inputs>
35 <conditional name="tag"> 34 <conditional name="tag">
36 <param name="tag_select" type="select" label="Sample name"> 35 <param name="tag_select" type="select" label="Sample name">
37 <option value="tag" selected="true">Use input's tag</option> 36 <option value="tag" selected="true">Use input's tag</option>
38 <option value="custom">Enter custom name per file</option> 37 <option value="custom">Enter custom name per file</option>
39 </param> 38 </param>
40 <when value="tag"> 39 <when value="tag">
41 <param name="inputs" format="@STD_BEDTOOLS_INPUTS@" type="data" multiple="True" label="@STD_BEDTOOLS_INPUT_LABEL@ files" /> 40 <param name="inputs" type="data" format="@STD_BEDTOOLS_INPUTS@" multiple="true" label="@STD_BEDTOOLS_INPUT_LABEL@ files" />
42 </when> 41 </when>
43 <when value="custom"> 42 <when value="custom">
44 <repeat name="beds" title="Add BED files" min="2" > 43 <repeat name="beds" title="Add BED files" min="2" >
45 <param name="input" format="@STD_BEDTOOLS_INPUTS@" type="data" multiple="True" label="@STD_BEDTOOLS_INPUT_LABEL@ file" /> 44 <param name="input" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
46 <param name="custom_name" type="text" area="false" label="Custom sample name" /> 45 <param name="custom_name" type="text" area="false" label="Custom sample name" />
47 </repeat> 46 </repeat>
48 </when> 47 </when>
49 </conditional> 48 </conditional>
50 <param name="cluster" type="boolean" checked="false" truevalue="-cluster" falsevalue="" 49 <param argument="-cluster" type="boolean" truevalue="-cluster" falsevalue="" checked="false"
51 label="Invoke Ryan Layers's clustering algorithm" 50 label="Invoke Ryan Layers's clustering algorithm" />
52 help="(-cluster)" />
53 <conditional name="empty"> 51 <conditional name="empty">
54 <param name="empty_selector" argument="-empty" type="select" label="Report empty regions" help="Include regions that have zero coverage in all BedGraph datasets"> 52 <param name="empty_selector" argument="-empty" type="select" label="Report empty regions" help="Include regions that have zero coverage in all BedGraph datasets">
55 <option value="-empty">Yes</option> 53 <option value="-empty">Yes</option>
56 <option value="">No</option> 54 <option value="">No</option>
57 </param> 55 </param>
58 <when value="-empty"> 56 <when value="-empty">
59 <expand macro="input_conditional_genome_file" /> 57 <expand macro="input_conditional_genome_file" />
60 </when> 58 </when>
61 <when value="" /> 59 <when value="" />
62 </conditional> 60 </conditional>
63 <param name="filler" type="text" value="N/A" 61 <param argument="-filler" type="text" value="N/A"
64 label="Text to use for no-coverage value" 62 label="Text to use for no-coverage value"
65 help="Can be 0.0, N/A, - or any other value. (-filler)" /> 63 help="Can be 0.0, N/A, - or any other value" />
66 <expand macro="print_header" /> 64 <expand macro="print_header" />
67
68 </inputs> 65 </inputs>
69 <outputs> 66 <outputs>
70 <data format="bed" name="output" /> 67 <data name="output" format="bed" />
71 </outputs> 68 </outputs>
72 <tests> 69 <tests>
73 <test> 70 <test>
74 <param name="tag_select" value="tag" /> 71 <param name="tag_select" value="tag" />
75 <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" /> 72 <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" />
90 <param name="genome_file_opts_selector" value="hist" /> 87 <param name="genome_file_opts_selector" value="hist" />
91 <param name="genome" value="multiIntersectBed1.len" /> 88 <param name="genome" value="multiIntersectBed1.len" />
92 <output name="output" file="multiIntersectBed_result3.bed" ftype="bed" /> 89 <output name="output" file="multiIntersectBed_result3.bed" ftype="bed" />
93 </test> 90 </test>
94 </tests> 91 </tests>
95 <help> 92 <help><![CDATA[
96 <![CDATA[
97 **What it does** 93 **What it does**
98 94
99 This tool identifies common intervals among multiple, sorted BED files. Intervals can be common among 0 to N of the N input BED files. 95 This tool identifies common intervals among multiple, sorted BED files. Intervals can be common among 0 to N of the N input BED files.
100 96
101 97
177 chr1 30 32 1 bob 0 1 0 173 chr1 30 32 1 bob 0 1 0
178 chr1 32 34 1 sue 0 0 1 174 chr1 32 34 1 sue 0 0 1
179 175
180 176
181 @REFERENCES@ 177 @REFERENCES@
182 ]]> 178 ]]></help>
183 </help>
184 <expand macro="citations" /> 179 <expand macro="citations" />
185 </tool> 180 </tool>