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comparison mapBed.xml @ 31:e19bebe96cd2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 39701b6cbb7a45ec45f1545648b73a6b8ed3e184
author iuc
date Tue, 20 Nov 2018 10:34:42 -0500
parents 95a3b2c25bd1
children 4f7a5ccd2ae9
comparison
equal deleted inserted replaced
30:db1841942d2b 31:e19bebe96cd2
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 $header
19 @GENOME_FILE_MAPBED@ 19 @GENOME_FILE_MAPBED@
20 > "${output}" 20 > '${output}'
21 ]]> 21 ]]>
22 </command> 22 </command>
23 <inputs> 23 <inputs>
24 <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="File A (BAM/@STD_BEDTOOLS_INPUT_LABEL@)" /> 24 <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" 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@)" /> 25 <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" label="File B (BAM/@STD_BEDTOOLS_INPUT_LABEL@)" />
27 <param name="reciprocal" type="boolean" checked="false" truevalue="-r" falsevalue="" 27 <param name="reciprocal" type="boolean" checked="false" truevalue="-r" falsevalue=""
28 label="Require reciprocal overlap" 28 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)" /> 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)" />
30 <expand macro="strand2" /> 30 <expand macro="strand2" />
31 <expand macro="c_and_o_argument"> 31 <expand macro="c_and_o_argument">
32 <param name="col" type="data_column" data_ref="inputA" label="Specify the column(s) that should be summarized" help="(-c)" /> 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" />
33 </expand> 33 </expand>
34 <expand macro="split" /> 34 <expand macro="split" />
35 <expand macro="print_header" /> 35 <expand macro="print_header" />
36 <conditional name="genome"> 36 <conditional name="genome">
37 <param name="genome_choose" argument="-g" type="select" 37 <param name="genome_choose" argument="-g" type="select"