# HG changeset patch
# User gdroc
# Date 1473073783 14400
# Node ID dabf0a44251ac234f370e502d3def57a4e4da4cc
# Parent  75d479c7b38a6a16822edd6de054beaf7c4ff9c5
Uploaded

diff -r 75d479c7b38a -r dabf0a44251a rave.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rave.xml	Mon Sep 05 07:09:43 2016 -0400
@@ -0,0 +1,157 @@
+<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 southgreen@cirad.fr
+
+.. 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>
+