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comparison multiIntersectBed.xml @ 32:b0d5e752c0c5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
author iuc
date Tue, 05 Sep 2017 09:51:56 -0400
parents c0fbce5dc84a
children ac2040a5e6ff
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31:cb98f29aa1dc 32:b0d5e752c0c5
1 <tool id="bedtools_multiintersectbed" name="Multiple Intersect" version="@WRAPPER_VERSION@.0"> 1 <tool id="bedtools_multiintersectbed" name="Multiple Intersect" version="@WRAPPER_VERSION@.1">
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" />
9 <![CDATA[ 9 <![CDATA[
10 bedtools multiinter 10 bedtools multiinter
11 $header 11 $header
12 $cluster 12 $cluster
13 -filler "${filler}" 13 -filler "${filler}"
14 #if $zero.value == True: 14 $empty.empty_selector
15 -empty 15 @GENOME_FILE_UNION@
16 -g $genome
17 #end if
18 16
19 #if str($tag.tag_select) == "tag": 17 #if str($tag.tag_select) == "tag":
20 #set files = '" "'.join( [ str( $file ) for $file in $tag.inputs ] ) 18 #set files = '" "'.join( [ str( $file ) for $file in $tag.inputs ] )
21 -i "${files}" 19 -i "${files}"
22 #else: 20 #else:
43 <param name="inputs" format="bed" type="data" multiple="True" label="BED files" /> 41 <param name="inputs" format="bed" type="data" multiple="True" label="BED files" />
44 </when> 42 </when>
45 <when value="custom"> 43 <when value="custom">
46 <repeat name="beds" title="Add BED files" min="2" > 44 <repeat name="beds" title="Add BED files" min="2" >
47 <param name="input" format="bed" type="data" multiple="True" label="BED file" /> 45 <param name="input" format="bed" type="data" multiple="True" label="BED file" />
48 <param name="custom_name" type="text" area="false" label="Custom sample name"/> 46 <param name="custom_name" type="text" area="false" label="Custom sample name" />
49 </repeat> 47 </repeat>
50 </when> 48 </when>
51 </conditional> 49 </conditional>
52 <expand macro="genome" />
53 <param name="cluster" type="boolean" checked="false" truevalue="-cluster" falsevalue="" 50 <param name="cluster" type="boolean" checked="false" truevalue="-cluster" falsevalue=""
54 label="Invoke Ryan Layers's clustering algorithm" 51 label="Invoke Ryan Layers's clustering algorithm"
55 help="(-cluster)" /> 52 help="(-cluster)" />
56 <param name="zero" type="boolean" checked="true" 53 <conditional name="empty">
57 label="Report regions that are not covered by any of the files" 54 <param name="empty_selector" argument="-empty" type="select" label="Report empty regions" help="Include regions that have zero coverage in all BedGraph datasets">
58 help="If set, regions that are not overlapped by any file will also be reported. Requires a valid organism key for all input datasets" /> 55 <option value="-empty">Yes</option>
56 <option value="">No</option>
57 </param>
58 <when value="-empty">
59 <expand macro="input_conditional_genome_file" />
60 </when>
61 <when value="" />
62 </conditional>
59 <param name="filler" type="text" value="N/A" 63 <param name="filler" type="text" value="N/A"
60 label="Text to use for no-coverage value" 64 label="Text to use for no-coverage value"
61 help="Can be 0.0, N/A, - or any other value. (-filler)" /> 65 help="Can be 0.0, N/A, - or any other value. (-filler)" />
62 <expand macro="print_header" /> 66 <expand macro="print_header" />
63 67
65 <outputs> 69 <outputs>
66 <data format="bed" name="output" /> 70 <data format="bed" name="output" />
67 </outputs> 71 </outputs>
68 <tests> 72 <tests>
69 <test> 73 <test>
70 <param name="tag_select" value="tag"/> 74 <param name="tag_select" value="tag" />
71 <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" /> 75 <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" />
72 <param name="zero" value="False"/> 76 <param name="empty_selector" value="" />
73 <output name="output" file="multiIntersectBed_result1.bed" ftype="bed" /> 77 <output name="output" file="multiIntersectBed_result1.bed" ftype="bed" />
74 </test> 78 </test>
75 <test> 79 <test>
76 <param name="tag_select" value="tag"/> 80 <param name="tag_select" value="tag" />
77 <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" /> 81 <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" />
78 <param name="header" value="True"/> 82 <param name="header" value="True" />
79 <param name="zero" value="False"/> 83 <param name="empty_selector" value="" />
80 <output name="output" file="multiIntersectBed_result2.bed" lines_diff="2" ftype="bed" /> 84 <output name="output" file="multiIntersectBed_result2.bed" lines_diff="2" ftype="bed" />
81 </test> 85 </test>
82 <test> 86 <test>
83 <param name="tag_select" value="tag"/> 87 <param name="tag_select" value="tag" />
84 <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" /> 88 <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" />
85 <param name="zero" value="True"/> 89 <param name="empty_selector" value="-empty" />
86 <param name="genome" value="multiIntersectBed1.len"/> 90 <param name="genome_file_opts_selector" value="hist" />
91 <param name="genome" value="multiIntersectBed1.len" />
87 <output name="output" file="multiIntersectBed_result3.bed" ftype="bed" /> 92 <output name="output" file="multiIntersectBed_result3.bed" ftype="bed" />
88 </test> 93 </test>
89 </tests> 94 </tests>
90 <help> 95 <help>
91 <![CDATA[ 96 <![CDATA[