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comparison mapBed.xml @ 43:07e8b80f278c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
author iuc
date Fri, 01 Apr 2022 19:02:51 +0000
parents 7ab85ac5f64b
children
comparison
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42:841fb4dc3ab3 43:07e8b80f278c
1 <tool id="bedtools_map" name="bedtools MapBed" version="@TOOL_VERSION@.2" profile="@PROFILE@"> 1 <tool id="bedtools_map" name="bedtools MapBed" version="@TOOL_VERSION@.3" profile="@PROFILE@">
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="bio_tools" /> 6 <expand macro="bio_tools" />
17 -F $overlapB 17 -F $overlapB
18 #end if 18 #end if
19 $reciprocal 19 $reciprocal
20 $split 20 $split
21 $header 21 $header
22 @GENOME_FILE_MAPBED@ 22 @GENOME_FILE@
23 > '${output}' 23 > '${output}'
24 ]]></command> 24 ]]></command>
25 <inputs> 25 <inputs>
26 <param name="inputA" argument="-a" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="File A (BAM/@STD_BEDTOOLS_INPUT_LABEL@)" /> 26 <param name="inputA" argument="-a" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="File A (BAM/@STD_BEDTOOLS_INPUT_LABEL@)" />
27 <param name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="File B (BAM/@STD_BEDTOOLS_INPUT_LABEL@)" /> 27 <param name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="File B (BAM/@STD_BEDTOOLS_INPUT_LABEL@)" />
34 <expand macro="c_and_o_argument"> 34 <expand macro="c_and_o_argument">
35 <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" /> 35 <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" />
36 </expand> 36 </expand>
37 <expand macro="split" /> 37 <expand macro="split" />
38 <expand macro="print_header" /> 38 <expand macro="print_header" />
39 <expand macro="input_optional_genome_file" /> 39 <expand macro="input_conditional_genome_file" optional="true"/>
40 </inputs> 40 </inputs>
41 <outputs> 41 <outputs>
42 <data name="output" format_source="inputA" metadata_source="inputA" label="Mapping of ${inputB.name} into ${inputA.name}" /> 42 <data name="output" format_source="inputA" metadata_source="inputA" label="Mapping of ${inputB.name} into ${inputA.name}" />
43 </outputs> 43 </outputs>
44 <tests> 44 <tests>
86 <repeat name="c_and_o_argument_repeat"> 86 <repeat name="c_and_o_argument_repeat">
87 <param name="col" value="5" /> 87 <param name="col" value="5" />
88 <param name="operation" value="collapse" /> 88 <param name="operation" value="collapse" />
89 </repeat> 89 </repeat>
90 <param name="strand" value="-s" /> 90 <param name="strand" value="-s" />
91 <param name="genome_choose" value="-g" /> 91 <conditional name="genome_file_opts">
92 <param name="genome_file_opts_selector" value="hist" /> 92 <param name="genome_file_opts_selector" value="hist" />
93 <param name="genome" value="mm9.len" ftype="bed" /> 93 <param name="genome" value="mm9.len" ftype="bed" />
94 </conditional>
95 <output name="output" file="mapBed_result5.bed" ftype="bed" />
96 </test>
97 <test>
98 <param name="inputA" value="mapBed3.bed" ftype="bed" />
99 <param name="inputB" value="mapBed4.bed" ftype="bed" />
100 <repeat name="c_and_o_argument_repeat">
101 <param name="col" value="5" />
102 <param name="operation" value="collapse" />
103 </repeat>
104 <param name="strand" value="-s" />
105 <conditional name="genome_file_opts">
106 <param name="genome_file_opts_selector" value="loc" />
107 <param name="genome" value="mm9"/>
108 </conditional>
94 <output name="output" file="mapBed_result5.bed" ftype="bed" /> 109 <output name="output" file="mapBed_result5.bed" ftype="bed" />
95 </test> 110 </test>
96 </tests> 111 </tests>
97 <help><![CDATA[ 112 <help><![CDATA[
98 **What it does** 113 **What it does**