annotate mapBed.xml @ 23:13400f3c3ec5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6418f2e58def1a81b3aa7c04cb5dc33decea1a96
author iuc
date Fri, 09 Feb 2018 09:00:06 -0500
parents a8eabd2838f6
children 95a3b2c25bd1
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
19
a8eabd2838f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
iuc
parents: 17
diff changeset
1 <tool id="bedtools_map" name="MapBed" version="@WRAPPER_VERSION@.0">
4
607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents: 3
diff changeset
2 <description>apply a function to a column for each overlapping interval</description>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
3 <macros>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
4 <import>macros.xml</import>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
5 </macros>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
6 <expand macro="requirements" />
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
7 <expand macro="stdio" />
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
8 <command>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
9 <![CDATA[
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
10 bedtools map
17
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
11 -a '${inputA}'
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
12 -b '${inputB}'
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
13 $strand
2
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
14 @C_AND_O_ARGUMENT@
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
15 -f $overlap
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
16 $reciprocal
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
17 $split
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
18 $header
17
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
19 @GENOME_FILE_MAPBED@
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
20 > "${output}"
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
21 ]]>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
22 </command>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
23 <inputs>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
24 <param format="bam,bed,vcf,gff,gff3" name="inputA" type="data" label="File A (BAM/BED/VCF/GFF)" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
25 <param format="bam,bed,gff,vcf,gff3" name="inputB" type="data" label="File B (BAM/BED/VCF/GFF)" />
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
26 <expand macro="overlap" />
11
7308cc546a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 4
diff changeset
27 <param name="reciprocal" type="boolean" checked="false" truevalue="-r" falsevalue=""
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
28 label="Require reciprocal overlap"
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
29 help="If set, the overlap between the BAM alignment and the BED interval must affect the above fraction of both the alignment and the BED interval. (-r)" />
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
30 <expand macro="strand2" />
3
2cd7e321d259 Uploaded
iuc
parents: 2
diff changeset
31 <expand macro="c_and_o_argument">
2cd7e321d259 Uploaded
iuc
parents: 2
diff changeset
32 <param name="col" type="data_column" data_ref="inputA" label="Specify the column(s) that should be summarized" help="(-c)" />
2cd7e321d259 Uploaded
iuc
parents: 2
diff changeset
33 </expand>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
34 <expand macro="split" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
35 <expand macro="print_header" />
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
36 <conditional name="genome">
17
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
37 <param name="genome_choose" argument="-g" type="select"
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
38 label="Specify a genome file the defines the expected chromosome order in the input files." >
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
39 <option value="" selected="true">No</option>
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
40 <option value="-g">Yes</option>
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
41 </param>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
42 <when value="-g">
17
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
43 <expand macro="input_conditional_genome_file" />
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
44 </when>
4
607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents: 3
diff changeset
45 <when value="" />
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
46 </conditional>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
47 </inputs>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
48 <outputs>
17
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
49 <data format_source="inputA" name="output" metadata_source="inputA" label="Mapping of ${inputB.name} into ${inputA.name}" />
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
50 </outputs>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
51 <tests>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
52 <test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
53 <param name="inputA" value="mapBed1.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
54 <param name="inputB" value="mapBed2.bed" ftype="bed" />
2
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
55 <repeat name="c_and_o_argument_repeat">
3
2cd7e321d259 Uploaded
iuc
parents: 2
diff changeset
56 <param name="col" value="5" />
2
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
57 <param name="operation" value="mean" />
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
58 </repeat>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
59 <output name="output" file="mapBed_result1.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
60 </test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
61 <test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
62 <param name="inputA" value="mapBed1.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
63 <param name="inputB" value="mapBed2.bed" ftype="bed" />
2
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
64 <repeat name="c_and_o_argument_repeat">
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
65 <param name="col" value="5" />
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
66 <param name="operation" value="collapse" />
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
67 </repeat>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
68 <output name="output" file="mapBed_result2.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
69 </test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
70 <test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
71 <param name="inputA" value="mapBed1.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
72 <param name="inputB" value="mapBed2.bed" ftype="bed" />
2
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
73 <repeat name="c_and_o_argument_repeat">
3
2cd7e321d259 Uploaded
iuc
parents: 2
diff changeset
74 <param name="col" value="5" />
2
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
75 <param name="operation" value="collapse" />
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
76 </repeat>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
77 <param name="strand" value="-S" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
78 <output name="output" file="mapBed_result3.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
79 </test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
80 <test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
81 <param name="inputA" value="mapBed1.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
82 <param name="inputB" value="mapBed2.bed" ftype="bed" />
2
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
83 <repeat name="c_and_o_argument_repeat">
3
2cd7e321d259 Uploaded
iuc
parents: 2
diff changeset
84 <param name="col" value="5" />
2
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
85 <param name="operation" value="collapse" />
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
86 </repeat>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
87 <param name="strand" value="-s" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
88 <output name="output" file="mapBed_result4.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
89 </test>
17
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
90 <test>
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
91 <param name="inputA" value="mapBed3.bed" ftype="bed" />
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
92 <param name="inputB" value="mapBed4.bed" ftype="bed" />
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
93 <repeat name="c_and_o_argument_repeat">
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
94 <param name="col" value="5" />
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
95 <param name="operation" value="collapse" />
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
96 </repeat>
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
97 <param name="strand" value="-s" />
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
98 <param name="genome_choose" value="-g" />
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
99 <param name="genome_file_opts_selector" value="hist" />
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
100 <param name="genome" value="mm9.len" ftype="bed" />
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
101 <output name="output" file="mapBed_result5.bed" ftype="bed" />
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
102 </test>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
103 </tests>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
104 <help>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
105 <![CDATA[
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
106 **What it does**
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
107
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
108 bedtools map allows one to map overlapping features in a B file onto features in an A file and apply statistics and/or summary operations on those features.
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
109
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
110 .. image:: $PATH_TO_IMAGES/map-glyph.png
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
111
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
112 .. class:: infomark
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
113
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
114 bedtools map requires each input file to be sorted by genome coordinate. For BED files, this can be done with sort -k1,1 -k2,2n. Other sorting criteria are allowed if a genome file (-g) is provides that specifies the expected chromosome order.
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
115
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
116 .. class:: infomark
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
117
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
118 The map tool is substantially faster in versions 2.19.0 and later. The plot below demonstrates the increased speed when, for example, counting the number of exome alignments that align to each exon. The bedtools times are compared to the bedops bedmap utility as a point of reference.
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
119
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
120 @REFERENCES@
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
121 ]]>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
122 </help>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
123 <expand macro="citations" />
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
124 </tool>