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comparison vcf2tsv.xml @ 1:70e8edde1030 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
author devteam
date Thu, 15 Sep 2016 16:04:12 -0400
parents 687e82ed082c
children eee41a27d68a
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0:687e82ed082c 1:70e8edde1030
1 <tool id="vcf2tsv" name="VCFtoTab-delimited:" version="0.0.3"> 1 <tool id="vcf2tsv" name="VCFtoTab-delimited:" version="@WRAPPER_VERSION@.0">
2 <description>Convert VCF data into TAB-delimited format</description> 2 <description>Convert VCF data into TAB-delimited format</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"></expand> 6 <expand macro="requirements"/>
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command>vcf2tsv ${g_option} -n "${null_filler}" "${input}" > "${out_file1}"</command> 8 <command>vcf2tsv ${g_option} -n '${null_filler}' '${input}' > '${out_file1}'</command>
9 <inputs> 9 <inputs>
10 <param format="vcf" name="input" type="data" label="Select VCF dataset to convert"/> 10 <param format="vcf" name="input" type="data" label="Select VCF dataset to convert"/>
11 <param name="g_option" type="boolean" checked="true" truevalue="-g" falsevalue="" label="Report data per sample" help="-g option"/> 11 <param name="g_option" type="boolean" checked="true" truevalue="-g" falsevalue="" label="Report data per sample" help="-g option"/>
12 <param name="null_filler" type="select" label="Fill empty fields with" help="-n option" > 12 <param name="null_filler" type="select" label="Fill empty fields with" help="-n option" >
13 <option value="">Nothing</option> 13 <option value="">Nothing</option>
32 <param name="input" value="vcflib.vcf"/> 32 <param name="input" value="vcflib.vcf"/>
33 <output name="out_file1" file="vcf2tsv-test2.tab"/> 33 <output name="out_file1" file="vcf2tsv-test2.tab"/>
34 </test> 34 </test>
35 </tests> 35 </tests>
36 <help> 36 <help>
37
38 Converts VCF dataset to tab-delimited format, using null string to replace empty values in the table. 37 Converts VCF dataset to tab-delimited format, using null string to replace empty values in the table.
39 Specifying "**Report data per sample**" (-g) will output one line per sample with genotype information. 38 Specifying "**Report data per sample**" (-g) will output one line per sample with genotype information.
40 39
41 ---- 40 ----
42 41
43 Vcf2Tsv @IS_PART_OF_VCFLIB@ 42 Vcf2Tsv @IS_PART_OF_VCFLIB@
44 </help> 43 </help>
45 <expand macro="citations" /> 44 <expand macro="citations" />
46 </tool> 45 </tool>