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Commit message:
Deleted selected files |
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removed:
rave.xml |
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| diff -r 8ecefea7e0f7 -r 75d479c7b38a rave.xml --- a/rave.xml Mon Sep 05 05:02:34 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,154 +0,0 @@ -<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> - |