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rave.xml |
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| diff -r a20b69e02f94 -r e49dcf006e1b rave.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rave.xml Mon Sep 05 04:55:34 2016 -0400 |
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| @@ -0,0 +1,154 @@ +<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> + |