Mercurial > repos > devteam > vcfallelicprimitives
annotate vcfallelicprimitives.xml @ 4:57a16b310fe8 draft default tip
"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 |
| children |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0" encoding="utf-8"?> |
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a8a4f94aa321
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
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2
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changeset
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2 <tool id="vcfallelicprimitives" name="VcfAllelicPrimitives:" version="@WRAPPER_VERSION@+galaxy0"> |
| 0 | 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> | |
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57a16b310fe8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 36e9065027cc7bf721e9d203208477ee88906c57"
iuc
parents:
3
diff
changeset
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10 cat '${input}' | vcfallelicprimitives |
| 0 | 11 ${m_option} |
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57a16b310fe8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 36e9065027cc7bf721e9d203208477ee88906c57"
iuc
parents:
3
diff
changeset
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12 -t '${t_option}' |
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0a69cff7946e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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1
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changeset
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13 -L "${max_length}" |
| 0 | 14 $keep_info |
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57a16b310fe8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 36e9065027cc7bf721e9d203208477ee88906c57"
iuc
parents:
3
diff
changeset
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15 $keep_geno > '${out_file1}' |
| 0 | 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"/> | |
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f49b23b41a12
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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0
diff
changeset
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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"/> |
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2
0a69cff7946e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents:
1
diff
changeset
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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"/> |
| 0 | 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> |