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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687 |
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modified:
macros.xml vcfvcfintersect.xml |
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| diff -r d3f4f86a18d4 -r c7314b925161 macros.xml --- a/macros.xml Wed Nov 11 13:01:47 2015 -0500 +++ b/macros.xml Thu Sep 15 13:30:27 2016 -0400 |
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| @@ -1,7 +1,7 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="8a5602bf07">vcflib</requirement> + <requirement type="package" version="1.0.0_rc1">vcflib</requirement> <yield/> </requirements> </xml> @@ -10,6 +10,7 @@ <exit_code range="1:" level="fatal" /> </stdio> </xml> + <token name="@WRAPPER_VERSION@">1.0.0_rc1</token> <xml name="citations"> <citations> <citation type="bibtex"> |
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| diff -r d3f4f86a18d4 -r c7314b925161 vcfvcfintersect.xml --- a/vcfvcfintersect.xml Wed Nov 11 13:01:47 2015 -0500 +++ b/vcfvcfintersect.xml Thu Sep 15 13:30:27 2016 -0400 |
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| b'@@ -1,124 +1,127 @@\n-<tool id="vcfvcfintersect" name="VCF-VCFintersect:" version="0.0.3">\r\n- <description>Intersect two VCF datasets</description>\r\n- <macros>\r\n- <import>macros.xml</import>\r\n- </macros>\r\n- <expand macro="requirements"></expand>\r\n- <expand macro="stdio"></expand>\r\n- <command>\r\n-\r\n- #set $reference_fasta_filename = "localref.fa"\r\n- #if str( $reference_source.reference_source_selector ) == "history":\r\n- ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&\r\n- #else:\r\n- #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )\r\n- #end if\r\n- \r\n- #if $adv_options.adv_options_selector == True:\r\n- \r\n- vcfintersect "${adv_options.adv_options_input}" ${loci} ${invert} -r "${reference_fasta_filename}" -w "${window_size}" ${isect_union} "${vcf_input1}" "${vcf_input2}" > "${out_file1}"\r\n-\r\n- #else:\r\n-\r\n- vcfintersect ${loci} ${invert} -r "${reference_fasta_filename}" -w "${window_size}" ${isect_union} "${vcf_input1}" "${vcf_input2}" > "${out_file1}" \r\n-\r\n- #end if\r\n-\r\n- </command>\r\n- <inputs>\r\n- <!-- selecting refernce source -->\r\n- <param name="vcf_input1" type="data" format="vcf" label="The first VCF dataset" />\r\n- <param name="vcf_input2" type="data" format="vcf" label="The second VCF dataset" help="The second dataset will be instersected with the first"/>\r\n- <conditional name="reference_source">\r\n- <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.">\r\n-\t<option value="cached">Locally cached</option>\r\n-\t<option value="history">History</option>\r\n- </param>\r\n- <when value="cached">\r\n-\t<param name="ref_file" type="select" label="Select reference genome">\r\n-\t <options from_data_table="fasta_indexes">\r\n-\t <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->\r\n-\t </options>\r\n-\t <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>\r\n-\t</param>\r\n- </when>\r\n- <when value="history"> <!-- FIX ME!!!! -->\r\n-\t<param name="ref_file" type="data" format="fasta" label="Using reference file" />\r\n- </when>\r\n- </conditional>\r\n- <param name="isect_union" type="select" label="Union or intersection" help="-i or -u">\r\n- <option value="-i">Intersect</option>\r\n- <option value="-u">Union</option>\r\n- </param>\r\n- <param name="invert" type="boolean" truevalue="-v" falsevalue="" label="Invert selection?" help="-v, --invert" />\r\n- <param name="window_size" type="integer" value="30" label="compare records up to this many bp away (window size)" help="-w, --window-size" />\r\n- <param name="loci" type="boolean" truevalue="-l" falsevalue="" label="output whole loci when one alternate allele matches" help="-l, --loci" />\r\n- <conditional name="adv_options">\r\n- <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"/> \r\n- <when value="use_adv_controls">\r\n-\t<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" />\r\n-\t<sanitizer>\r\n-\t <valid initial="string.printable">\r\n-\t <remove value="'"/>\r\n-\t </valid>\r\n-\t <mapping initial="none">\r\n-\t <add source="'" target="__sq__"/>\r\n-\t </mapping>\r\n-\t</sanitizer>\r\n- </when>\r\n- </conditional>\r\n- </inputs>\r\n- <outputs>\r\n- <data format="vcf" name="out_file1" />\r\n- </outputs>\r\n- <tests>\r\n- <test>\r\n- <param name="reference_source_selector" value="history" />\r\n- <param name="vcf_input1" value="vcfvcfintersect-input1.vcf" />\r\n- <param name="vcf_input2" value="vcfvcfintersect-input2.vc'..b'ize)" help="-w, --window-size" />\n+ <param name="loci" type="boolean" truevalue="-l" falsevalue=""\n+ label="output whole loci when one alternate allele matches" help="-l, --loci" />\n+ <conditional name="adv_options">\n+ <param name="adv_options_selector" type="select" label="Advanced controls" help="Allows you to specify options that are not listed above">\n+ <option value="no">Don\'t use advanced options</option>\n+ <option value="use_adv_controls">Use advanced options</option>\n+ </param>\n+ <when value="no" />\n+ <when value="use_adv_controls">\n+ <param name="adv_options_input" type="text" value="-t "vcfvcf-intersect-result""\n+ label="Enter additional command line options described in the help section below"\n+ help="such as -m, -t, -V, -M, and -T" />\n+ <sanitizer>\n+ <valid initial="string.printable">\n+ <remove value="'"/>\n+ </valid>\n+ <mapping initial="none">\n+ <add source="'" target="__sq__"/>\n+ </mapping>\n+ </sanitizer>\n+ </when>\n+ </conditional>\n+ </inputs>\n+ <outputs>\n+ <data format="vcf" name="out_file1" />\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="vcf_input1" value="vcfvcfintersect-input1.vcf" />\n+ <param name="vcf_input2" value="vcfvcfintersect-input2.vcf" />\n+ <param name="reference_source_selector" value="history" />\n+ <param name="ref_file" value="vcflib-test-genome-phix.fa" />\n+ <param name="isect_union" value="-i" />\n+ <param name="invert" value="False" />\n+ <param name="loci" value="False" />\n+ <patam name="adv_options_selector" value="no" />\n+ <param name="window_size" value="30" />\n+ <output name="out_file1" file="vcfvcfintersect-test1.vcf"/>\n+ </test>\n+ <test>\n+ <param name="reference_source_selector" value="history" />\n+ <param name="vcf_input1" value="vcfvcfintersect-input1.vcf" />\n+ <param name="vcf_input2" value="vcfvcfintersect-input2.vcf" />\n+ <param name="isect_union" value="-u" />\n+ <param name="invert" value="False" />\n+ <param name="loci" value="False" />\n+ <patam name="adv_options_selector" value="no" />\n+ <param name="window_size" value="30" />\n+ <param name="ref_file" value="vcflib-test-genome-phix.fa" />\n+ <output name="out_file1" file="vcfvcfintersect-test2.vcf"/>\n+ </test>\n+ </tests>\n+ <help>\n+Computes intersections and unions for two VCF datasets. Unifies equivalent alleles within window-size bp.\n+\n+The options are::\n+\n+ -v, --invert invert the selection, printing only records which would\n+ -i, --intersect-vcf FILE use this VCF for set intersection generation\n+ -u, --union-vcf FILE use this VCF for set union generation\n+ -w, --window-size N compare records up to this many bp away (default 30)\n+ -l, --loci output whole loci when one alternate allele matches\n+ -m, --ref-match intersect on the basis of record REF string\n+ -t, --tag TAG attach TAG to each record\'s info field if it would intersect\n+ -V, --tag-value VAL use this value to indicate that the allele is passing\n+ \'.\' will be used otherwise. default: \'PASS\'\n+ -M, --merge-from FROM-TAG\n+ -T, --merge-to TO-TAG merge from FROM-TAG used in the -i file, setting TO-TAG\n+ in the current file.\n+\n+----\n+\n+VCFVCFintersect is based on vcfintersect utility of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).\n+ </help>\n+ <expand macro="citations" />\n+</tool>\n' |