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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 ${plinkdb.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="plinkdb" type="select" label="Select plink DB" help="If your dataset 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 &amp; 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 &amp; 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 &amp; 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>

==========
 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
  
**Input formats**

Plink binary file (bed/bim/fam)
 
Example : Plink binary for High Density Rice Array (HDRA, 700k SNPs, McCouch SR et al. Nat Commun 7, 10532)

See Plink genotype data bundle available at https://ricediversity.org/data/

-----

.. 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 [e-mail]

.. class:: infomark

**Program encapsulated in Galaxy by South Green**

	</help>
    <citations>
		<citation type="doi">10.1186/s13742-015-0047-8</citation>
    	<citation type="doi">10.1086/519795</citation>
  	</citations>
</tool>