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comparison multiIntersectBed.xml @ 4:315929597efb draft

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author iuc
date Wed, 07 Jan 2015 12:45:05 -0500
parents 7511823bdea1
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3:190a747ddaa8 4:315929597efb
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>
9 multiIntersectBed 9 <![CDATA[
10 bedtools multiinter
10 $header 11 $header
12 $cluster
13 -filler "${filler}"
11 #if $zero.value == True: 14 #if $zero.value == True:
12 -empty 15 -empty
13 -g ${chromInfo} 16 -g $genome
14 #end if
15
16 -i '$input1'
17 '$input2'
18 #for $q in $beds
19 '${q.input}'
20 #end for
21
22 -names
23 #if $name1.choice == "tag":
24 '${input1.name}'
25 #else
26 '${name1.custom_name}'
27 #end if 17 #end if
28 18
29 #if $name2.choice == "tag": 19 #if str($tag.tag_select) == "tag":
30 '${input2.name}' 20 #set files = '" "'.join( [ str( $file ) for $file in $tag.inputs ] )
31 #else 21 -i "${files}"
32 '${name2.custom_name}' 22 #else:
23 -i
24 #for $file in $tag.beds:
25 "${file.input}"
26 #end for
27 -names
28 #for $file in $tag.beds:
29 "{$file.custom_name}"
30 #end for
33 #end if 31 #end if
34 32
35 #for $q in $beds 33 > '$output'
36 #if $q.name.choice == "tag": 34 ]]>
37 '${q.input.name}'
38 #else
39 '${q.input.custom_name}'
40 #end if
41 #end for
42 &gt; '$output'
43 </command> 35 </command>
44
45 <inputs> 36 <inputs>
46 <!-- Make it easy for the user, first two input files are always shown --> 37 <conditional name="tag">
47 <!-- INPUT 1 --> 38 <param name="tag_select" type="select" label="Sample name">
48 <param name="input1" format="bed" type="data" label="First sorted BED file" />
49
50 <conditional name="name1">
51 <param name="choice" type="select" label="Sample name">
52 <option value="tag" selected="true">Use input's tag</option> 39 <option value="tag" selected="true">Use input's tag</option>
53 <option value="custom">Enter custom table name</option> 40 <option value="custom">Enter custom name per file</option>
54 </param> 41 </param>
55 <when value="tag"> 42 <when value="tag">
43 <param name="inputs" format="bed" type="data" multiple="True" label="BED files" />
56 </when> 44 </when>
57 <when value="custom"> 45 <when value="custom">
58 <param name="custom_name" type="text" area="false" label="Custom sample name"/> 46 <repeat name="beds" title="Add BED files" min="2" >
47 <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"/>
49 </repeat>
59 </when> 50 </when>
60 </conditional> 51 </conditional>
61 52 <expand macro="genome" />
62 <!-- INPUT 2 --> 53 <param name="cluster" type="boolean" checked="false" truevalue="-cluster" falsevalue=""
63 <param name="input2" format="bed" type="data" label="Second sorted BED file" /> 54 label="Invoke Ryan Layers's clustering algorithm"
64 55 help="(-cluster)" />
65 <conditional name="name2"> 56 <param name="zero" type="boolean" checked="true"
66 <param name="choice" type="select" label="Sample name"> 57 label="Report regions that are not covered by any of the files"
67 <option value="tag" selected="true">Use input's tag</option> 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" />
68 <option value="custom">Enter custom table name</option> 59 <param name="filler" type="text" value="N/A"
69 </param> 60 label="Text to use for no-coverage value"
70 <when value="tag"> 61 help="Can be 0.0, N/A, - or any other value. (-filler)" />
71 </when> 62 <expand macro="print_header" />
72 <when value="custom">
73 <param name="custom_name" type="text" area="false" label="Custom sample name"/>
74 </when>
75 </conditional>
76
77 <!-- Additional files, if the user needs more -->
78 <repeat name="beds" title="Add'l sorted BED files" >
79 <param name="input" format="bed" type="data" label="BED file" />
80
81 <conditional name="name">
82 <param name="choice" type="select" label="Sample name">
83 <option value="tag" selected="true">Use input's tag</option>
84 <option value="custom">Enter custom table name</option>
85 </param>
86 <when value="tag">
87 </when>
88 <when value="custom">
89 <param name="custom_name" type="text" area="false" label="Custom sample name"/>
90 </when>
91 </conditional>
92 </repeat>
93
94 <param name="header" type="boolean" checked="true" truevalue="-header" falsevalue="" label="Print header line" help="The first line will include the name of each sample." />
95
96 <param name="zero" type="boolean" checked="true" label="Report regions that are not covered by any of the files" help="If set, regions that are not overlapped by any file will also be reported. Requires a valid organism key for all input datasets" />
97 63
98 </inputs> 64 </inputs>
99
100 <outputs> 65 <outputs>
101 <data format="tabular" name="output" metadata_source="input1" label="Common intervals identified from among ${input1.name}, ${input2.name} and so on." /> 66 <data format="bed" name="output" />
102 </outputs> 67 </outputs>
68 <tests>
69 <test>
70 <param name="tag_select" value="tag"/>
71 <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" />
72 <param name="zero" value="False"/>
73 <output name="output" file="multiIntersectBed_result1.bed" ftype="bed" />
74 </test>
75 <test>
76 <param name="tag_select" value="tag"/>
77 <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" />
78 <param name="header" value="True"/>
79 <param name="zero" value="False"/>
80 <output name="output" file="multiIntersectBed_result2.bed" lines_diff="2" ftype="bed" />
81 </test>
82 <test>
83 <param name="tag_select" value="tag"/>
84 <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" />
85 <param name="zero" value="True"/>
86 <param name="genome" value="multiIntersectBed1.len"/>
87 <output name="output" file="multiIntersectBed_result3.bed" ftype="bed" />
88 </test>
89 </tests>
103 <help> 90 <help>
104 91 <![CDATA[
105 **What it does** 92 **What it does**
106 93
107 This tool identifies common intervals among multiple, sorted BED files. Intervals can be common among 0 to N of the N input BED files. The pictorial and raw data examples below illustrate the behavior of this tool more clearly. 94 This tool identifies common intervals among multiple, sorted BED files. Intervals can be common among 0 to N of the N input BED files.
108
109
110 .. image:: http://people.virginia.edu/~arq5x/files/bedtools-galaxy/mbi.png
111 95
112 96
113 .. class:: warningmark 97 .. class:: warningmark
114 98
115 This tool requires that each BED file is reference-sorted (chrom, then start). 99 This tool requires that each BED file is reference-sorted (chrom, then start).
129 ------ 113 ------
130 114
131 **Example input**:: 115 **Example input**::
132 116
133 # a.bed 117 # a.bed
134 chr1 6 12 118 chr1 6 12bed
135 chr1 10 20 119 chr1 10 20
136 chr1 22 27 120 chr1 22 27
137 chr1 24 30 121 chr1 24 30
138 122
139 # b.bed 123 # b.bed
188 chr1 30 32 1 bob 0 1 0 172 chr1 30 32 1 bob 0 1 0
189 chr1 32 34 1 sue 0 0 1 173 chr1 32 34 1 sue 0 0 1
190 174
191 175
192 @REFERENCES@ 176 @REFERENCES@
193 177 ]]>
194 </help> 178 </help>
195 <expand macro="citations" /> 179 <expand macro="citations" />
196 </tool> 180 </tool>