Mercurial > repos > anton > vcfvcfintersect
comparison vcfvcfintersect.xml @ 5:89c1efc31618 draft default tip
Uploaded
| author | anton |
|---|---|
| date | Mon, 15 Sep 2014 14:54:08 -0400 |
| parents | b8ab4ef85a5b |
| children |
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| 4:b8ab4ef85a5b | 5:89c1efc31618 |
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| 1 <tool id="vcfvcfintersect" name="VCF-VCFintersect:" version="0.0.2"> | 1 <tool id="vcfvcfintersect" name="VCF-VCFintersect:" version="0.0.2"> |
| 2 <requirements> | 2 <requirements> |
| 3 <requirement type="package" version="86723982aa">vcflib</requirement> | 3 <requirement type="package" version="8a5602bf07">vcflib</requirement> |
| 4 <!-- <requirement type="package" version="0.1.18">samtools</requirement> --> | 4 <!-- <requirement type="package" version="0.1.18">samtools</requirement> --> |
| 5 </requirements> | 5 </requirements> |
| 6 <description>Intersect two VCF datasets</description> | 6 <description>Intersect two VCF datasets</description> |
| 7 <command> | 7 <command> |
| 8 | 8 |
| 76 <tests> | 76 <tests> |
| 77 <test> | 77 <test> |
| 78 <param name="reference_source_selector" value="history" /> | 78 <param name="reference_source_selector" value="history" /> |
| 79 <param name="vcf_input1" value="vcfvcfintersect-input1.vcf" /> | 79 <param name="vcf_input1" value="vcfvcfintersect-input1.vcf" /> |
| 80 <param name="vcf_input2" value="vcfvcfintersect-input2.vcf" /> | 80 <param name="vcf_input2" value="vcfvcfintersect-input2.vcf" /> |
| 81 <param name="isect_union" value="Intersect" /> | 81 <param name="isect_union" value="-i" /> |
| 82 <param name="invert" value="False" /> | 82 <param name="invert" value="False" /> |
| 83 <param name="loci" value="False" /> | 83 <param name="loci" value="False" /> |
| 84 <patam name="adv_options" value="False" /> | 84 <patam name="adv_options" value="False" /> |
| 85 <param name="window_size" value="30" /> | 85 <param name="window_size" value="30" /> |
| 86 <param name="ref_file" value="vcflib-test-genome-phix.fa" /> | 86 <param name="ref_file" value="vcflib-test-genome-phix.fa" /> |
| 88 </test> | 88 </test> |
| 89 <test> | 89 <test> |
| 90 <param name="reference_source_selector" value="history" /> | 90 <param name="reference_source_selector" value="history" /> |
| 91 <param name="vcf_input1" value="vcfvcfintersect-input1.vcf" /> | 91 <param name="vcf_input1" value="vcfvcfintersect-input1.vcf" /> |
| 92 <param name="vcf_input2" value="vcfvcfintersect-input2.vcf" /> | 92 <param name="vcf_input2" value="vcfvcfintersect-input2.vcf" /> |
| 93 <param name="isect_union" value="Union" /> | 93 <param name="isect_union" value="-u" /> |
| 94 <param name="invert" value="False" /> | 94 <param name="invert" value="False" /> |
| 95 <param name="loci" value="False" /> | 95 <param name="loci" value="False" /> |
| 96 <patam name="adv_options" value="False" /> | 96 <patam name="adv_options" value="False" /> |
| 97 <param name="window_size" value="30" /> | 97 <param name="window_size" value="30" /> |
| 98 <param name="ref_file" value="vcflib-test-genome-phix.fa" /> | 98 <param name="ref_file" value="vcflib-test-genome-phix.fa" /> |
| 107 | 107 |
| 108 -v, --invert invert the selection, printing only records which would | 108 -v, --invert invert the selection, printing only records which would |
| 109 -i, --intersect-vcf FILE use this VCF for set intersection generation | 109 -i, --intersect-vcf FILE use this VCF for set intersection generation |
| 110 -u, --union-vcf FILE use this VCF for set union generation | 110 -u, --union-vcf FILE use this VCF for set union generation |
| 111 -w, --window-size N compare records up to this many bp away (default 30) | 111 -w, --window-size N compare records up to this many bp away (default 30) |
| 112 -r, --reference FILE FASTA reference file, required with -i and -u | |
| 113 -l, --loci output whole loci when one alternate allele matches | 112 -l, --loci output whole loci when one alternate allele matches |
| 114 -m, --ref-match intersect on the basis of record REF string | 113 -m, --ref-match intersect on the basis of record REF string |
| 115 -t, --tag TAG attach TAG to each record's info field if it would intersect | 114 -t, --tag TAG attach TAG to each record's info field if it would intersect |
| 116 -V, --tag-value VAL use this value to indicate that the allele is passing | 115 -V, --tag-value VAL use this value to indicate that the allele is passing |
| 117 '.' will be used otherwise. default: 'PASS' | 116 '.' will be used otherwise. default: 'PASS' |