Mercurial > repos > anton > vcfvcfintersect
annotate vcfvcfintersect.xml @ 1:3a799597bc67
Updated to new vcflib version
| author | Anton Nekrutenko <anton@bx.psu.edu> |
|---|---|
| date | Wed, 25 Jun 2014 15:44:06 -0400 |
| parents | 17216b2fae6e |
| children | b8ab4ef85a5b |
| rev | line source |
|---|---|
| 0 | 1 <tool id="vcfvcfintersect" name="VCF-VCFintersect:" version="0.0.1"> |
| 2 <requirements> | |
|
1
3a799597bc67
Updated to new vcflib version
Anton Nekrutenko <anton@bx.psu.edu>
parents:
0
diff
changeset
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3 <requirement type="package" version="86723982aa">vcflib</requirement> |
| 0 | 4 <!-- <requirement type="package" version="0.1.18">samtools</requirement> --> |
| 5 </requirements> | |
| 6 <description>Intersect two VCF datasets</description> | |
| 7 <command> | |
| 8 | |
| 9 #set $reference_fasta_filename = "localref.fa" | |
| 10 #if str( $reference_source.reference_source_selector ) == "history": | |
| 11 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && | |
| 12 #else: | |
| 13 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) | |
| 14 #end if | |
| 15 | |
| 16 #if $adv_options.adv_options_selector == True: | |
| 17 | |
| 18 vcfintersect "${adv_options.adv_options_input}" ${loci} ${invert} -r "${reference_fasta_filename}" -w "${window_size}" ${isect_union} "${vcf_input1}" "${vcf_input2}" > "${out_file1}" | |
| 19 | |
| 20 #else: | |
| 21 | |
| 22 vcfintersect ${loci} ${invert} -r "${reference_fasta_filename}" -w "${window_size}" ${isect_union} "${vcf_input1}" "${vcf_input2}" > "${out_file1}" | |
| 23 | |
| 24 #end if | |
| 25 | |
| 26 </command> | |
| 27 <inputs> | |
| 28 <!-- selecting refernce source --> | |
| 29 <param name="vcf_input1" type="data" format="vcf" label="The first VCF dataset" /> | |
| 30 <param name="vcf_input2" type="data" format="vcf" label="The second VCF dataset" help="The second dataset will be instersected with the first"/> | |
| 31 <conditional name="reference_source"> | |
| 32 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome" help="This tools needs to access reference genomes sequence specified by this option."> | |
| 33 <option value="cached">Locally cached</option> | |
| 34 <option value="history">History</option> | |
| 35 </param> | |
| 36 <when value="cached"> | |
| 37 <param name="ref_file" type="select" label="Select reference genome"> | |
| 38 <options from_data_table="fasta_indexes"> | |
| 39 <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>--> | |
| 40 </options> | |
| 41 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
| 42 </param> | |
| 43 </when> | |
| 44 <when value="history"> <!-- FIX ME!!!! --> | |
| 45 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> | |
| 46 </when> | |
| 47 </conditional> | |
| 48 <param name="isect_union" type="select" label="Union or intersection" help="-i or -u"> | |
| 49 <option value="-i">Intersect</option> | |
| 50 <option value="-u">Union</option> | |
| 51 </param> | |
| 52 <param name="invert" type="boolean" truevalue="-v" falsevalue="" label="Invert selection?" help="-v, --invert" /> | |
| 53 <param name="window_size" type="integer" value="30" label="compare records up to this many bp away (window size)" help="-w, --window-size" /> | |
| 54 <param name="loci" type="boolean" truevalue="-l" falsevalue="" label="output whole loci when one alternate allele matches" help="-l, --loci" /> | |
| 55 <conditional name="adv_options"> | |
| 56 <param name="adv_options_selector" type="boolean" truevalue="use_adv_controls" label="Advanced controls" help="Allows you to specify options that are not listed above"/> | |
| 57 <when value="use_adv_controls"> | |
| 58 <param name="adv_options_input" type="text" value="-t "vcfvcf-intersect-result"" label="Enter additional command line options described in the help section below" help="such as -m, -t, -V, -M, and -T" /> | |
| 59 <sanitizer> | |
| 60 <valid initial="string.printable"> | |
| 61 <remove value="'"/> | |
| 62 </valid> | |
| 63 <mapping initial="none"> | |
| 64 <add source="'" target="__sq__"/> | |
| 65 </mapping> | |
| 66 </sanitizer> | |
| 67 </when> | |
| 68 </conditional> | |
| 69 </inputs> | |
| 70 <outputs> | |
| 71 <data format="vcf" name="out_file1" /> | |
| 72 </outputs> | |
| 73 <stdio> | |
| 74 <exit_code range="1:" level="fatal" /> | |
| 75 </stdio> | |
| 76 <tests> | |
| 77 <test> | |
| 78 <param name="reference_source_selector" value="history" /> | |
| 79 <param name="vcf_input1" value="vcfvcfintersect-input1.vcf" /> | |
| 80 <param name="vcf_input2" value="vcfvcfintersect-input2.vcf" /> | |
| 81 <param name="isect_union" value="Intersect" /> | |
| 82 <param name="invert" value="False" /> | |
| 83 <param name="loci" value="False" /> | |
| 84 <patam name="adv_options" value="False" /> | |
| 85 <param name="window_size" value="30" /> | |
| 86 <param name="ref_file" value="vcflib-test-genome-phix.fa" /> | |
| 87 <output name="out_file1" file="vcfvcfintersect-test1.vcf"/> | |
| 88 </test> | |
| 89 <test> | |
| 90 <param name="reference_source_selector" value="history" /> | |
| 91 <param name="vcf_input1" value="vcfvcfintersect-input1.vcf" /> | |
| 92 <param name="vcf_input2" value="vcfvcfintersect-input2.vcf" /> | |
| 93 <param name="isect_union" value="Union" /> | |
| 94 <param name="invert" value="False" /> | |
| 95 <param name="loci" value="False" /> | |
| 96 <patam name="adv_options" value="False" /> | |
| 97 <param name="window_size" value="30" /> | |
| 98 <param name="ref_file" value="vcflib-test-genome-phix.fa" /> | |
| 99 <output name="out_file1" file="vcfvcfintersect-test2.vcf"/> | |
| 100 </test> | |
| 101 </tests> | |
| 102 <help> | |
| 103 | |
| 104 Computes intersections and unions for two VCF datasets. Unifies equivalent alleles within window-size bp. | |
| 105 | |
| 106 The options are:: | |
| 107 | |
| 108 -v, --invert invert the selection, printing only records which would | |
| 109 -i, --intersect-vcf FILE use this VCF for set intersection 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) | |
| 112 -r, --reference FILE FASTA reference file, required with -i and -u | |
| 113 -l, --loci output whole loci when one alternate allele matches | |
| 114 -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 | |
| 116 -V, --tag-value VAL use this value to indicate that the allele is passing | |
| 117 '.' will be used otherwise. default: 'PASS' | |
| 118 -M, --merge-from FROM-TAG | |
| 119 -T, --merge-to TO-TAG merge from FROM-TAG used in the -i file, setting TO-TAG | |
| 120 in the current file. | |
| 121 | |
| 122 ---- | |
| 123 | |
| 124 VCFVCFintersect is based on vcfintersect utility of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). | |
| 125 | |
| 126 </help> | |
| 127 </tool> |