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comparison bedpeToBam.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 a2d4c30ba2f9
children ac2040a5e6ff
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31:cb98f29aa1dc 32:b0d5e752c0c5
1 <tool id="bedtools_bedpetobam" name="BEDPE to BAM" version="@WRAPPER_VERSION@.0"> 1 <tool id="bedtools_bedpetobam" name="BEDPE to BAM" version="@WRAPPER_VERSION@.1">
2 <description>converter</description> 2 <description>converter</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" />
8 <command> 8 <command>
9 <![CDATA[ 9 <![CDATA[
10 bedtools bedpetobam 10 bedtools bedpetobam
11 -mapq $mapq 11 -mapq $mapq
12 -i '$input' 12 -i '$input'
13 -g $genome 13 -g @GENOME_FILE@
14 > '$output' 14 > '$output'
15 ]]> 15 ]]>
16 </command> 16 </command>
17 <inputs> 17 <inputs>
18 <param name="input" format="bed,gff,vcf" type="data" label="BED/VCF/GFF file"/> 18 <param name="input" format="bed,gff,vcf" type="data" label="BED/VCF/GFF file"/>
19 <expand macro="genome" /> 19 <expand macro="input_conditional_genome_file" />
20 <param name="mapq" type="integer" value="255" 20 <param name="mapq" type="integer" value="255"
21 label="Set a mapping quality (SAM MAPQ field) value for all BED entries" 21 label="Set a mapping quality (SAM MAPQ field) value for all BED entries"
22 help="(-mapq)" /> 22 help="(-mapq)" />
23 </inputs> 23 </inputs>
24 <outputs> 24 <outputs>
25 <data format="bam" name="output" metadata_source="input"/> 25 <data format="bam" name="output" metadata_source="input"/>
26 </outputs> 26 </outputs>
27 <tests> 27 <tests>
28 <test> 28 <test>
29 <param name="input" value="bedpeToBamBed1.bed" ftype="bed" /> 29 <param name="input" value="bedpeToBamBed1.bed" ftype="bed" />
30 <param name="genome_file_opts_selector" value="hist" />
30 <param name="genome" value="mm9.len"/> 31 <param name="genome" value="mm9.len"/>
31 <output name="output" file="bedpeToBam_result1.bam" lines_diff="72" ftype="bam" /> 32 <output name="output" file="bedpeToBam_result1.bam" lines_diff="72" ftype="bam" />
32 </test> 33 </test>
33 </tests> 34 </tests>
34 <help> 35 <help>