Mercurial > repos > gdroc > rave

changeset 14:75d479c7b38a draft

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Deleted selected files
author gdroc
date Mon, 05 Sep 2016 07:09:30 -0400
parents 8ecefea7e0f7
children dabf0a44251a
files rave.xml
diffstat 1 files changed, 0 insertions(+), 154 deletions(-) [+]
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line diff
--- a/rave.xml	Mon Sep 05 05:02:34 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -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 &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>
-  
-  .. 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>
-