Mercurial > repos > gdroc > rave
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author | gdroc |
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date | Mon, 05 Sep 2016 04:55:54 -0400 |
parents | e49dcf006e1b |
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<tool id="rave" name="RAVE" version="1.0"> <description>- Rapid Allelic Variant Extractor</description> <!-- Required for the tool to work --> <!-- Wrapper compatible with Plink v1.90b3k --> <requirements> <requirement type="binary">perl</requirement> <requirement type="package" version="1.90">plink</requirement> </requirements> <stdio> <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> <exit_code range="1:" level="fatal" /> </stdio> <command interpreter="perl">./rave.pl --tool_directory $__tool_directory__ --bfile ${snpdb.fields.path} #if $filter_var.subpopulation == 'yes': --keep ${filter_var.population_select.fields.path} #end if #if $filter_individuals.individual == 'file': --keep ${filter_individuals.variety_file} #else if $filter_individuals.individual == 'list': --variety_list "${filter_individuals.variety_list}" #end if #if $filter_loc.location == 'file': --extract range ${filter_loc.location_file} #else if $filter_loc.location == 'list': --location_list "${filter_loc.location_list}" #end if #if $filter_locus.locus == 'file': --extract range ${filter_locus.locus_file} #else if $filter_locus.locus == 'list': --locus_list "${filter_locus.locus_list}" #end if --maf $maf --output_format $output_format --out $plink_output </command> <inputs> <param name="snpdb" type="select" label="Select SNP DB" help="If your genome of interest is not listed, contact us"> <options from_data_table="plink"> <filter type="sort_by" column="1"/> <validator type="no_options" message="No indexes are available for the selected input dataset"/> </options> </param> <param name="maf" type="float" value="0.01" label="Minor allele frequencies" help="--maf filters out all variants with minor allele frequency below the provided threshold (default 0.01)" /> <conditional name="filter_var"> <param name="subpopulation" type="select" label="Filter SNP based on subpopulation"> <option value="no">No</option> <option value="yes">Yes</option> </param> <when value="no"/> <when value="yes"> <param name="population_select" type="select" display="radio" label="Subpopulation"> <options from_data_table="subpopulation"> <filter type="sort_by" column="1"/> <validator type="no_options" message="No indexes are available for the selected input dataset"/> </options> </param> </when> </conditional> <conditional name="filter_individuals"> <param name="individual" type="select" label="Filter SNP based on individual (This parameter can be empty)"> <option value="file">Upload a file from your history</option> <option value="list">Cut & Paste your list</option> </param> <when value="file"> <param name="variety_file" format="txt" type="data" optional="true" label="Variety list from file" help="One range per line, whitespace-separated (i.e : B001 B001)"/> </when> <when value="list"> <param name="variety_list" type="text" area="True" size="5x15" label="Variety list from area" help="One range per line, whitespace-separated (i.e : B001 B001)"/> </when> </conditional> <conditional name="filter_loc"> <param name="location" type="select" label="Filter SNP based on genomic location (This parameter can be empty)"> <option value="file">Upload a file from your history</option> <option value="list">Cut & Paste your list</option> </param> <when value="file"> <param name="location_file" format="txt" type="data" optional="true" label="Range list from file" help="One range per line, whitespace-separated (i.e : 1 100000 120000 chr1)"/> </when> <when value="list"> <param name="location_list" type="text" area="True" size="5x15" label="Range list from area" help="One range per line, whitespace-separated (i.e : 1 100000 120000 chr1)"/> </when> </conditional> <conditional name="filter_locus"> <param name="locus" type="select" label="Filter SNP based on specific locus (This parameter can be empty)"> <option value="file">Upload a file from your history</option> <option value="list">Cut & Paste your list</option> </param> <when value="file"> <param name="locus_file" format="txt" type="data" optional="true" label="Locus file (MSU locus name)" help="One locus per line (i.e : LOC_Os01g13620)"/> </when> <when value="list"> <param name="locus_list" type="text" area="True" size="5x15" label="Locus list from area (MSU locus name)" help="One range per line (i.e : LOC_Os01g13620)"/> </when> </conditional> <param name="output_format" type="select" label="Select output format" help="--recode creates a new text fileset, after applying sample/variant filters and other operations."> <option value="vcf">VCF</option> <option value="bgz">VCF bgzip</option> <option value="structure">Structure</option> <option value="beagle">Beagle</option> <option value="fastphase">fastPHASE</option> </param> </inputs> <outputs> <data format="vcf" name="plink_output" label="${output_format} output" /> <change_format> <when input="output_format" value="structure" format="txt" /> <when input="output_format" value="beagle" format="bgzip" /> <when input="output_format" value="fastphase" format="bgzip" /> <when input="output_format" value="bgz" format="bgzip" /> </change_format> <!--output.recode.strct_in--> </outputs> <help> .. class:: infomark **Program encapsulated in Galaxy by South Green** .. class:: infomark ----- ========== Overview ========== **PLINK Overview** PLINK2 Majority of information in this page is derived from an excellent PLINK_ manual written by Shaun Purcell, Christopher Chang. .. _PLINK: https://www.cog-genomics.org/plink2 .. class:: infomark **Galaxy integration** Droc Gaetan (CIRAD), Ruiz Manuel (CIRAD). .. class:: infomark **Support** For any questions about Galaxy integration, please send an e-mail to southgreen@cirad.fr ------- </help> <citations> <citation type="doi">10.1186/s13742-015-0047-8</citation> <citation type="doi">10.1086/519795</citation> </citations> </tool>