Mercurial > repos > devteam > vcfallelicprimitives
comparison vcfallelicprimitives.xml @ 1:c58ebedf1159 draft
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 16:05:20 -0400 |
| parents | bbf46057ef48 |
| children | 3c6eefd09af1 |
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| 0:bbf46057ef48 | 1:c58ebedf1159 |
|---|---|
| 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" |