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comparison mapBed.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 ce3c7f062223
comparison
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33:87ee588b3d45 34:dde39ba9c031
1 <tool id="bedtools_map" name="bedtools MapBed" version="@WRAPPER_VERSION@.2"> 1 <tool id="bedtools_map" name="bedtools MapBed" version="@TOOL_VERSION@.2">
2 <description>apply a function to a column for each overlapping interval</description> 2 <description>apply a function to a column for each overlapping interval</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[
10 bedtools map 9 bedtools map
11 -a '${inputA}' 10 -a '${inputA}'
12 -b '${inputB}' 11 -b '${inputB}'
13 $strand 12 $strand
14 @C_AND_O_ARGUMENT@ 13 @C_AND_O_ARGUMENT@
15 -f $overlap 14 @OVERLAP@
15 #if str($overlapB):
16 -F $overlapB
17 #end if
16 $reciprocal 18 $reciprocal
17 $split 19 $split
18 $header 20 $header
19 @GENOME_FILE_MAPBED@ 21 @GENOME_FILE_MAPBED@
20 > '${output}' 22 > '${output}'
21 ]]> 23 ]]></command>
22 </command>
23 <inputs> 24 <inputs>
24 <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="File A (BAM/@STD_BEDTOOLS_INPUT_LABEL@)" /> 25 <param name="inputA" argument="-a" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="File A (BAM/@STD_BEDTOOLS_INPUT_LABEL@)" />
25 <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" label="File B (BAM/@STD_BEDTOOLS_INPUT_LABEL@)" /> 26 <param name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="File B (BAM/@STD_BEDTOOLS_INPUT_LABEL@)" />
26 <expand macro="overlap" /> 27 <expand macro="overlap" />
27 <param name="reciprocal" type="boolean" checked="false" truevalue="-r" falsevalue="" 28 <expand macro="overlap" name="overlapB" argument="-F" fracof="B"/>
29 <param name="reciprocal" argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="false"
28 label="Require reciprocal overlap" 30 label="Require reciprocal overlap"
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)" /> 31 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" />
30 <expand macro="strand2" /> 32 <expand macro="strand2" />
31 <expand macro="c_and_o_argument"> 33 <expand macro="c_and_o_argument">
32 <param name="col" argument="-c" type="data_column" data_ref="inputB" label="Specify the column(s) from the B file to map onto intervals in A" help="Multiple columns can be specified in a comma-delimited list" /> 34 <param name="col" argument="-c" type="data_column" data_ref="inputB" label="Specify the column(s) from the B file to map onto intervals in A" help="Multiple columns can be specified in a comma-delimited list" />
33 </expand> 35 </expand>
34 <expand macro="split" /> 36 <expand macro="split" />
35 <expand macro="print_header" /> 37 <expand macro="print_header" />
36 <conditional name="genome"> 38 <conditional name="genome">
37 <param name="genome_choose" argument="-g" type="select" 39 <param name="genome_choose" argument="-g" type="select"
38 label="Specify a genome file the defines the expected chromosome order in the input files." > 40 label="Specify a genome file the defines the expected chromosome order in the input files." >
39 <option value="" selected="true">No</option> 41 <option value="" selected="true">No</option>
40 <option value="-g">Yes</option> 42 <option value="-g">Yes</option>
41 </param> 43 </param>
42 <when value="-g"> 44 <when value="-g">
44 </when> 46 </when>
45 <when value="" /> 47 <when value="" />
46 </conditional> 48 </conditional>
47 </inputs> 49 </inputs>
48 <outputs> 50 <outputs>
49 <data format_source="inputA" name="output" metadata_source="inputA" label="Mapping of ${inputB.name} into ${inputA.name}" /> 51 <data name="output" format_source="inputA" metadata_source="inputA" label="Mapping of ${inputB.name} into ${inputA.name}" />
50 </outputs> 52 </outputs>
51 <tests> 53 <tests>
52 <test> 54 <test>
53 <param name="inputA" value="mapBed1.bed" ftype="bed" /> 55 <param name="inputA" value="mapBed1.bed" ftype="bed" />
54 <param name="inputB" value="mapBed2.bed" ftype="bed" /> 56 <param name="inputB" value="mapBed2.bed" ftype="bed" />
99 <param name="genome_file_opts_selector" value="hist" /> 101 <param name="genome_file_opts_selector" value="hist" />
100 <param name="genome" value="mm9.len" ftype="bed" /> 102 <param name="genome" value="mm9.len" ftype="bed" />
101 <output name="output" file="mapBed_result5.bed" ftype="bed" /> 103 <output name="output" file="mapBed_result5.bed" ftype="bed" />
102 </test> 104 </test>
103 </tests> 105 </tests>
104 <help> 106 <help><![CDATA[
105 <![CDATA[
106 **What it does** 107 **What it does**
107 108
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. 109 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.
109 110
110 .. image:: $PATH_TO_IMAGES/map-glyph.png 111 .. image:: $PATH_TO_IMAGES/map-glyph.png
116 .. class:: infomark 117 .. class:: infomark
117 118
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. 119 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.
119 120
120 @REFERENCES@ 121 @REFERENCES@
121 ]]> 122 ]]></help>
122 </help>
123 <expand macro="citations" /> 123 <expand macro="citations" />
124 </tool> 124 </tool>