Mercurial > repos > devteam > vcfallelicprimitives
comparison vcfallelicprimitives.xml @ 0:3f4fefbc52c8 draft
Uploaded
| author | devteam |
|---|---|
| date | Thu, 19 Mar 2015 12:23:24 -0400 |
| parents | |
| children | f49b23b41a12 |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:3f4fefbc52c8 |
|---|---|
| 1 <?xml version="1.0" encoding="utf-8"?> | |
| 2 <tool id="vcfallelicprimitives" name="VcfAllelicPrimitives:" version="0.0.3"> | |
| 3 <description>Split alleleic primitives (gaps or mismatches) into multiple VCF lines</description> | |
| 4 <macros> | |
| 5 <import>macros.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="requirements"></expand> | |
| 8 <expand macro="stdio" /> | |
| 9 <command> | |
| 10 cat "${input}" | vcfallelicprimitives | |
| 11 ${m_option} | |
| 12 -t "${t_option}" | |
| 13 -L "${max_length}" | |
| 14 $keep_info | |
| 15 $keep_geno > "${out_file1}" | |
| 16 </command> | |
| 17 <inputs> | |
| 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"/> | |
| 20 <param name="t_option" size="20" 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" size="4" 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" | |
| 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)"/> | |
| 25 <param name="keep_geno" type="boolean" truevalue="--keep-geno" falsevalue="" checked="False" | |
| 26 label="Maintain genotype-level annotations when decomposing" | |
| 27 help="Similar caution should be used for this as for --keep-info. (--keep-geno)"/> | |
| 28 </inputs> | |
| 29 <outputs> | |
| 30 <data format="vcf" name="out_file1" label="${tool.name} on ${on_string}" /> | |
| 31 </outputs> | |
| 32 <tests> | |
| 33 <test> | |
| 34 <param name="input" value="vcflib.vcf"/> | |
| 35 <output name="out_file1" file="vcfallelicprimitives-test1.vcf"/> | |
| 36 </test> | |
| 37 </tests> | |
| 38 <help> | |
| 39 | |
| 40 If multiple alleleic primitives (gaps or mismatches) are specified in a single VCF record, this tools splits the record into multiple lines, but drops all INFO fields. | |
| 41 "Pure" MNPs are split into multiple SNPs unless the -m flag is provided. | |
| 42 Genotypes are phased where complex alleles have been decomposed, provided genotypes in the input. | |
| 43 | |
| 44 The options are:: | |
| 45 | |
| 46 -m, --use-mnps Retain MNPs as separate events (default: false). | |
| 47 -t, --tag-parsed FLAG Tag records which are split apart of a complex allele with this flag. | |
| 48 -L, --max-length LEN Do not manipulate records in which either the ALT or | |
| 49 REF is longer than LEN (default: 200). | |
| 50 -k, --keep-info Maintain site and allele-level annotations when decomposing. | |
| 51 Note that in many cases, such as multisample VCFs, these won't | |
| 52 be valid post-decomposition. For biallelic loci in single-sample | |
| 53 VCFs, they should be usable with caution. | |
| 54 -g, --keep-geno Maintain genotype-level annotations when decomposing. Similar | |
| 55 caution should be used for this as for --keep-info. | |
| 56 | |
| 57 ---- | |
| 58 | |
| 59 Vcfallelicprimitives @IS_PART_OF_VCFLIB@ | |
| 60 </help> | |
| 61 <expand macro="citations" /> | |
| 62 </tool> |