Mercurial > repos > devteam > vcfallelicprimitives

comparison vcfallelicprimitives.xml @ 4:57a16b310fe8 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 36e9065027cc7bf721e9d203208477ee88906c57"
author iuc
date Thu, 23 Jan 2020 08:02:42 -0500
parents a8a4f94aa321
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3:a8a4f94aa321 4:57a16b310fe8
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"></expand> 7 <expand macro="requirements"></expand>
8 <expand macro="stdio" /> 8 <expand macro="stdio" />
9 <command> 9 <command>
10 cat "${input}" | vcfallelicprimitives 10 cat '${input}' | vcfallelicprimitives
11 ${m_option} 11 ${m_option}
12 -t "${t_option}" 12 -t '${t_option}'
13 -L "${max_length}" 13 -L "${max_length}"
14 $keep_info 14 $keep_info
15 $keep_geno > "${out_file1}" 15 $keep_geno > '${out_file1}'
16 </command> 16 </command>
17 <inputs> 17 <inputs>
18 <param format="vcf" name="input" type="data" label="Select VCF dataset"/> 18 <param format="vcf" name="input" type="data" label="Select VCF dataset"/>
19 <param name="m_option" type="boolean" checked="false" truevalue="--use-mnps" falsevalue="" label="Retain MNPs as separate events" help="--use-mnps option"/> 19 <param name="m_option" type="boolean" checked="false" truevalue="--use-mnps" falsevalue="" label="Retain MNPs as separate events" help="--use-mnps option"/>
20 <param name="t_option" type="text" value="Split primitives" label="Tag records which are split apart of a complex allele with this flag. " help="--tag-parsed option"/> 20 <param name="t_option" type="text" value="Split primitives" label="Tag records which are split apart of a complex allele with this flag. " help="--tag-parsed option"/>