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comparison multiIntersectBed.xml @ 8:0d3aa592ce27 draft

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author iuc
date Tue, 28 Apr 2015 22:56:34 -0400
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7:76db45de75c6 8:0d3aa592ce27
1 <tool id="bedtools_multiintersectbed" name="Intersect multiple sorted BED files" version="@WRAPPER_VERSION@.0">
2 <description></description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="stdio" />
8 <command>
9 <![CDATA[
10 bedtools multiinter
11 $header
12 $cluster
13 -filler "${filler}"
14 #if $zero.value == True:
15 -empty
16 -g $genome
17 #end if
18
19 #if str($tag.tag_select) == "tag":
20 #set files = '" "'.join( [ str( $file ) for $file in $tag.inputs ] )
21 -i "${files}"
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
31 #end if
32
33 > '$output'
34 ]]>
35 </command>
36 <inputs>
37 <conditional name="tag">
38 <param name="tag_select" type="select" label="Sample name">
39 <option value="tag" selected="true">Use input's tag</option>
40 <option value="custom">Enter custom name per file</option>
41 </param>
42 <when value="tag">
43 <param name="inputs" format="bed" type="data" multiple="True" label="BED files" />
44 </when>
45 <when value="custom">
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>
50 </when>
51 </conditional>
52 <expand macro="genome" />
53 <param name="cluster" type="boolean" checked="false" truevalue="-cluster" falsevalue=""
54 label="Invoke Ryan Layers's clustering algorithm"
55 help="(-cluster)" />
56 <param name="zero" type="boolean" checked="true"
57 label="Report regions that are not covered by any of the files"
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" />
59 <param name="filler" type="text" value="N/A"
60 label="Text to use for no-coverage value"
61 help="Can be 0.0, N/A, - or any other value. (-filler)" />
62 <expand macro="print_header" />
63
64 </inputs>
65 <outputs>
66 <data format="bed" name="output" />
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>
90 <help>
91 <![CDATA[
92 **What it does**
93
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.
95
96
97 .. class:: warningmark
98
99 This tool requires that each BED file is reference-sorted (chrom, then start).
100
101
102 .. class:: infomark
103
104 The output file will contain five fixed columns, plus additional columns for each BED file:
105
106 * 1. Chromosome name (or 'genome' for whole-genome coverage).
107 * 2. The zero-based start position of the interval.
108 * 3. The one-based end position of the interval.
109 * 4. The number of input files that had at least one feature overlapping this interval.
110 * 5. A list of input files or labels that had at least one feature overlapping this interval.
111 * 6. For each input file, an indication (1 = Yes, 0 = No) of whether or not the file had at least one feature overlapping this interval.
112
113 ------
114
115 **Example input**::
116
117 # a.bed
118 chr1 6 12bed
119 chr1 10 20
120 chr1 22 27
121 chr1 24 30
122
123 # b.bed
124 chr1 12 32
125 chr1 14 30
126
127 # c.bed
128 chr1 8 15
129 chr1 10 14
130 chr1 32 34
131
132
133 ------
134
135 **Example without a header and without reporting intervals with zero coverage**::
136
137
138 chr1 6 8 1 1 1 0 0
139 chr1 8 12 2 1,3 1 0 1
140 chr1 12 15 3 1,2,3 1 1 1
141 chr1 15 20 2 1,2 1 1 0
142 chr1 20 22 1 2 0 1 0
143 chr1 22 30 2 1,2 1 1 0
144 chr1 30 32 1 2 0 1 0
145 chr1 32 34 1 3 0 0 1
146
147
148 **Example adding a header line**::
149
150
151 chrom start end num list a.bed b.bed c.bed
152 chr1 6 8 1 1 1 0 0
153 chr1 8 12 2 1,3 1 0 1
154 chr1 12 15 3 1,2,3 1 1 1
155 chr1 15 20 2 1,2 1 1 0
156 chr1 20 22 1 2 0 1 0
157 chr1 22 30 2 1,2 1 1 0
158 chr1 30 32 1 2 0 1 0
159 chr1 32 34 1 3 0 0 1
160
161
162 **Example adding a header line and custom file labels**::
163
164
165 chrom start end num list joe bob sue
166 chr1 6 8 1 joe 1 0 0
167 chr1 8 12 2 joe,sue 1 0 1
168 chr1 12 15 3 joe,bob,sue 1 1 1
169 chr1 15 20 2 joe,bob 1 1 0
170 chr1 20 22 1 bob 0 1 0
171 chr1 22 30 2 joe,bob 1 1 0
172 chr1 30 32 1 bob 0 1 0
173 chr1 32 34 1 sue 0 0 1
174
175
176 @REFERENCES@
177 ]]>
178 </help>
179 <expand macro="citations" />
180 </tool>