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comparison mapBed.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
comparison
equal deleted inserted replaced
31:cb98f29aa1dc 32:b0d5e752c0c5
1 <tool id="bedtools_map" name="MapBed" version="@WRAPPER_VERSION@.0"> 1 <tool id="bedtools_map" name="MapBed" version="@WRAPPER_VERSION@.1">
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>
9 <![CDATA[ 9 <![CDATA[
10 bedtools map 10 bedtools map
11 -a "${inputA}" 11 -a '${inputA}'
12 -b "${inputB}" 12 -b '${inputB}'
13 $strand 13 $strand
14 @C_AND_O_ARGUMENT@ 14 @C_AND_O_ARGUMENT@
15 -f $overlap 15 -f $overlap
16 $reciprocal 16 $reciprocal
17 $split 17 $split
18 $header 18 $header
19 #if $genome.genome_choose == "-g" : 19 @GENOME_FILE_MAPBED@
20 -g $genome.genome
21 #end if
22 > "${output}" 20 > "${output}"
23 ]]> 21 ]]>
24 </command> 22 </command>
25 <inputs> 23 <inputs>
26 <param format="bam,bed,vcf,gff,gff3" name="inputA" type="data" label="File A (BAM/BED/VCF/GFF)" /> 24 <param format="bam,bed,vcf,gff,gff3" name="inputA" type="data" label="File A (BAM/BED/VCF/GFF)" />
34 <param name="col" type="data_column" data_ref="inputA" label="Specify the column(s) that should be summarized" help="(-c)" /> 32 <param name="col" type="data_column" data_ref="inputA" label="Specify the column(s) that should be summarized" help="(-c)" />
35 </expand> 33 </expand>
36 <expand macro="split" /> 34 <expand macro="split" />
37 <expand macro="print_header" /> 35 <expand macro="print_header" />
38 <conditional name="genome"> 36 <conditional name="genome">
39 <param name="genome_choose" type="boolean" checked="false" truevalue="-g" falsevalue="" 37 <param name="genome_choose" argument="-g" type="select"
40 label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage." help="(-g)" /> 38 label="Specify a genome file the defines the expected chromosome order in the input files." >
39 <option value="" selected="true">No</option>
40 <option value="-g">Yes</option>
41 </param>
41 <when value="-g"> 42 <when value="-g">
42 <expand macro="genome" /> 43 <expand macro="input_conditional_genome_file" />
43 </when> 44 </when>
44 <when value="" /> 45 <when value="" />
45 </conditional> 46 </conditional>
46 </inputs> 47 </inputs>
47 <outputs> 48 <outputs>
48 <data format_source="inputA" name="output" metadata_source="inputA" label="Mapping of ${inputB.name} into ${inputA.name}"/> 49 <data format_source="inputA" name="output" metadata_source="inputA" label="Mapping of ${inputB.name} into ${inputA.name}" />
49 </outputs> 50 </outputs>
50 <tests> 51 <tests>
51 <test> 52 <test>
52 <param name="inputA" value="mapBed1.bed" ftype="bed" /> 53 <param name="inputA" value="mapBed1.bed" ftype="bed" />
53 <param name="inputB" value="mapBed2.bed" ftype="bed" /> 54 <param name="inputB" value="mapBed2.bed" ftype="bed" />
84 <param name="operation" value="collapse" /> 85 <param name="operation" value="collapse" />
85 </repeat> 86 </repeat>
86 <param name="strand" value="-s" /> 87 <param name="strand" value="-s" />
87 <output name="output" file="mapBed_result4.bed" ftype="bed" /> 88 <output name="output" file="mapBed_result4.bed" ftype="bed" />
88 </test> 89 </test>
90 <test>
91 <param name="inputA" value="mapBed3.bed" ftype="bed" />
92 <param name="inputB" value="mapBed4.bed" ftype="bed" />
93 <repeat name="c_and_o_argument_repeat">
94 <param name="col" value="5" />
95 <param name="operation" value="collapse" />
96 </repeat>
97 <param name="strand" value="-s" />
98 <param name="genome_choose" value="-g" />
99 <param name="genome_file_opts_selector" value="hist" />
100 <param name="genome" value="mm9.len" ftype="bed" />
101 <output name="output" file="mapBed_result5.bed" ftype="bed" />
102 </test>
89 </tests> 103 </tests>
90 <help> 104 <help>
91 <![CDATA[ 105 <![CDATA[
92 **What it does** 106 **What it does**
93 107