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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect commit 36e9065027cc7bf721e9d203208477ee88906c57"
author | iuc |
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date | Thu, 23 Jan 2020 08:11:02 -0500 |
parents | 6f6bf10618d7 |
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<tool id="vcfvcfintersect" name="VCF-VCFintersect:" version="@WRAPPER_VERSION@+galaxy0"> <description>Intersect two VCF datasets</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio" /> <command><![CDATA[ #set $reference_fasta_filename = "localref.fa" #if str( $reference_source.reference_source_selector ) == "history": ln -s '${reference_source.ref_file}' '${reference_fasta_filename}' && #else: #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) #end if #if $adv_options.adv_options_selector == "use_adv_controls": vcfintersect '${adv_options.adv_options_input}' ${loci} ${invert} -r '${reference_fasta_filename}' -w "${window_size}" ${isect_union} '${vcf_input1}' '${vcf_input2}' > '${out_file1}' #else: vcfintersect ${loci} ${invert} -r '${reference_fasta_filename}' -w "${window_size}" ${isect_union} '${vcf_input1}' '${vcf_input2}' > '${out_file1}' #end if ]]></command> <inputs> <!-- selecting refernce source --> <param name="vcf_input1" type="data" format="vcf" label="The first VCF dataset" /> <param name="vcf_input2" type="data" format="vcf" label="The second VCF dataset" help="The second dataset will be instersected with the first"/> <conditional name="reference_source"> <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."> <option value="cached">Locally cached</option> <option value="history">History</option> </param> <when value="cached"> <param name="ref_file" type="select" label="Select reference genome"> <options from_data_table="fasta_indexes"> <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>--> </options> <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> </param> </when> <when value="history"> <!-- FIX ME!!!! --> <param name="ref_file" type="data" format="fasta" label="Using reference file" /> </when> </conditional> <param name="isect_union" type="select" label="Union or intersection" help="-i or -u"> <option value="-i">Intersect</option> <option value="-u">Union</option> </param> <param name="invert" type="boolean" truevalue="-v" falsevalue="" label="Invert selection?" help="-v, --invert" /> <param name="window_size" type="integer" value="30" label="compare records up to this many bp away (window size)" help="-w, --window-size" /> <param name="loci" type="boolean" truevalue="-l" falsevalue="" label="output whole loci when one alternate allele matches" help="-l, --loci" /> <conditional name="adv_options"> <param name="adv_options_selector" type="select" label="Advanced controls" help="Allows you to specify options that are not listed above"> <option value="no">Don't use advanced options</option> <option value="use_adv_controls">Use advanced options</option> </param> <when value="no" /> <when value="use_adv_controls"> <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"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> </valid> <mapping initial="none"> <add source="'" target="__sq__"/> </mapping> </sanitizer> </param> </when> </conditional> </inputs> <outputs> <data format="vcf" name="out_file1" /> </outputs> <tests> <test> <param name="vcf_input1" value="vcfvcfintersect-input1.vcf" /> <param name="vcf_input2" value="vcfvcfintersect-input2.vcf" /> <param name="reference_source_selector" value="history" /> <param name="ref_file" value="vcflib-test-genome-phix.fa" /> <param name="isect_union" value="-i" /> <param name="invert" value="False" /> <param name="loci" value="False" /> <param name="adv_options_selector" value="no" /> <param name="window_size" value="30" /> <output name="out_file1" file="vcfvcfintersect-test1.vcf"/> </test> <test> <param name="reference_source_selector" value="history" /> <param name="vcf_input1" value="vcfvcfintersect-input1.vcf" /> <param name="vcf_input2" value="vcfvcfintersect-input2.vcf" /> <param name="isect_union" value="-u" /> <param name="invert" value="False" /> <param name="loci" value="False" /> <param name="adv_options_selector" value="no" /> <param name="window_size" value="30" /> <param name="ref_file" value="vcflib-test-genome-phix.fa" /> <output name="out_file1" file="vcfvcfintersect-test2.vcf"/> </test> </tests> <help> Computes intersections and unions for two VCF datasets. Unifies equivalent alleles within window-size bp. The options are:: -v, --invert invert the selection, printing only records which would -i, --intersect-vcf FILE use this VCF for set intersection generation -u, --union-vcf FILE use this VCF for set union generation -w, --window-size N compare records up to this many bp away (default 30) -l, --loci output whole loci when one alternate allele matches -m, --ref-match intersect on the basis of record REF string -t, --tag TAG attach TAG to each record's info field if it would intersect -V, --tag-value VAL use this value to indicate that the allele is passing '.' will be used otherwise. default: 'PASS' -M, --merge-from FROM-TAG -T, --merge-to TO-TAG merge from FROM-TAG used in the -i file, setting TO-TAG in the current file. ---- VCFVCFintersect is based on vcfintersect utility of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). </help> <expand macro="citations" /> </tool>