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comparison vcfallelicprimitives.xml @ 2:0a69cff7946e draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 0b9b6512272b82637c2f1e831367e89aed77ae79
author devteam
date Thu, 15 Sep 2016 16:07:24 -0400
parents f49b23b41a12
children a8a4f94aa321
comparison
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1:f49b23b41a12 2:0a69cff7946e
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="vcfallelicprimitives" name="VcfAllelicPrimitives:" version="0.0.3"> 2 <tool id="vcfallelicprimitives" name="VcfAllelicPrimitives:" version="@WRAPPER_VERSION@.0">
3 <description>Split alleleic primitives (gaps or mismatches) into multiple VCF lines</description> 3 <description>Split alleleic primitives (gaps or mismatches) into multiple VCF lines</description>
4 <macros> 4 <macros>
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"/>
21 <param name="max_length" type="integer" value="200" label="Do not manipulate records in which either the ALT or REF is longer than (bp)" help="--max-length option"/> 21 <param name="max_length" type="integer" value="200" label="Do not manipulate records in which either the ALT or REF is longer than (bp)" help="--max-length option"/>
22 <param name="keep_info" type="boolean" truevalue="--keep-info" falsevalue="" checked="False" 22 <param name="keep_info" type="boolean" truevalue="--keep-info" falsevalue="" checked="False"
23 label="Maintain site and allele-level annotations when decomposing" 23 label="Maintain site and allele-level annotations when decomposing"
24 help="Note that in many cases, such as multisample VCFs, these won't be valid post-decomposition. For biallelic loci in single-sample VCFs, they should be usable with caution. (--keep-info)"/> 24 help="Note that in many cases, such as multisample VCFs, these won't be valid post-decomposition. For biallelic loci in single-sample VCFs, they should be usable with caution. (--keep-info)"/>
25 <param name="keep_geno" type="boolean" truevalue="--keep-geno" falsevalue="" checked="False" 25 <param name="keep_geno" type="boolean" truevalue="--keep-geno" falsevalue="" checked="False"
26 label="Maintain genotype-level annotations when decomposing" 26 label="Maintain genotype-level annotations when decomposing"