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changeset 3:0eebff4180d9 draft

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Uploaded
author dereeper
date Thu, 02 Nov 2017 05:19:30 -0400
parents d8a46ae7ee8a
children 652aafd88060
files tassel.sh tassel.xml tassel/tassel.sh tassel/tassel.xml tassel/tool-data/tool_dependencies.xml
diffstat 5 files changed, 200 insertions(+), 208 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tassel.sh	Thu Nov 02 05:19:30 2017 -0400
@@ -0,0 +1,47 @@
+#!/bin/bash
+
+analyseType=$1;
+out1=$2;
+out2=$3;
+out3=$4;
+log1=$5;
+galaxyOutDir=$6;
+
+version=$(java -version 2>&1 | grep version)
+if [[ ! $version =~ 1.8 ]]; then
+    echo "Java found: $version. Tassel 5.0 requires java 1.8..." >&2
+    exit 1
+fi
+
+mkdir $galaxyOutDir
+
+# Suppression des 6 premiers arguments de la liste des arguments $@
+shift; shift; shift; shift; shift; shift;
+
+
+if [[ $analyseType == glm ]] 
+then
+ run_pipeline.pl $* >> $log1 2>&1
+ mv "$galaxyOutDir/TASSELGLM1.txt" $out1
+ mv "$galaxyOutDir/TASSELGLM2.txt" $out2
+fi
+
+if [[ $analyseType == mlm ]] 
+then
+ run_pipeline.pl $* >> $log1 2>&1
+ mv "$galaxyOutDir/TASSELMLM1.txt" $out1
+ mv "$galaxyOutDir/TASSELMLM2.txt" $out2
+ mv "$galaxyOutDir/TASSELMLM3.txt" $out3
+fi
+
+if [[ $analyseType == ld ]] 
+then
+ run_pipeline.pl $* >> $log1 2>&1
+fi
+
+
+if [[ $analyseType == ck ]]
+then
+ run_pipeline.pl $* >> $log1 2>&1
+ mv "$galaxyOutDir/kinship.txt" $out1
+fi
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tassel.xml	Thu Nov 02 05:19:30 2017 -0400
@@ -0,0 +1,153 @@
+<tool id="Tassel" name="Tassel" version="5.0">
+	<description> Software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium. </description>
+	<requirements>
+                <requirement type="package" version="5.0">tassel</requirement>
+        </requirements>
+	<command interpreter="bash">./tassel.sh $analysis_opts.fonction_selector $output1 $output2 $output3 $log tmpdir$$/
+#if $analysis_opts.fonction_selector == "mlm":
+ -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq
+ -fork2 -r $analysis_opts.trait
+ #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
+  -fork3 -q $analysis_opts.add_structure_file.structure -excludeLastTrait
+ #end if
+ -fork4 -k $analysis_opts.kinship
+ -combineA -input1 -input2 
+ #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
+  -input3
+ #end if
+ -intersect -combineB -inputA -input4 -mlm -mlmVarCompEst $analysis_opts.mlmVarCompEst -mlmCompressionLevel $analysis_opts.mlmCompressionLevel -export tmpdir$$/TASSELMLM -runfork1 -runfork2 
+ #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
+  -runfork3
+ #end if
+ -runfork4
+ 
+#else if $analysis_opts.fonction_selector == "glm":
+ -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq
+ -fork2 -r $analysis_opts.trait
+ #if $analysis_opts.add_file.additional_file_selector == "yes":
+  -fork3 -q $analysis_opts.add_file.structure -excludeLastTrait
+ #end if
+ -combineA -input1 -input2 
+ #if $analysis_opts.add_file.additional_file_selector == "yes":
+  -input3
+ #end if
+ -intersect -glm -export tmpdir$$/TASSELGLM -runfork1 -runfork2
+ #if $analysis_opts.add_file.additional_file_selector == "yes":
+  -runfork3
+ #end if 
+#else if $analysis_opts.fonction_selector == "ld":
+ -fork1 -h $hapmap
+ -ld -ldType All -ldd png -ldplotsize 3000 -o $output1 -runfork1
+#else if $analysis_opts.fonction_selector == "ck":
+ -fork1 -h $hapmap
+ -ck -export tmpdir$$/kinship -runfork1
+#end if
+	</command>
+	<inputs>
+		<param format="txt" name="hapmap" type="data" label="HapMap file"/>
+		<conditional name="analysis_opts">
+			<param name="fonction_selector" type="select" label="Type of analysis">
+				<option value="mlm" selected="True">MLM</option>
+				<option value="glm">GLM</option>
+				<option value="ld">Linkage Disequilibrium</option>
+				<option value="ck">Kinship</option>
+			</param>
+			<when value="glm">
+                		<param format="txt" name="trait" type="data" label="Trait file"/>
+				<conditional name="add_file">
+					<param name="additional_file_selector" type="select" label="Add structure file">
+        	                	        <option value="no" selected="True">no</option>
+                	                	<option value="yes">yes</option>
+	                	        </param>
+					<when value="yes">
+						<param format="txt" name="structure" type="data" label="Structure file"/>
+					</when>
+				</conditional>
+			</when>
+			<when value="mlm">
+                		<param format="txt" name="trait" type="data" label="Trait file"/>
+		                <param format="txt" name="kinship" type="data" label="Kinship file"/>
+				<conditional name="add_structure_file">
+					<param name="additional_file_selector" type="select" label="Add structure file">
+        	                	        <option value="no" selected="True">no</option>
+                	                	<option value="yes">yes</option>
+	                	        </param>
+					<when value="yes">
+						<param format="txt" name="structure" type="data" label="Structure file"/>
+					</when>
+				</conditional>
+				<param name="mlmVarCompEst" type="select" label="Variance Component Estimation">
+					<option value="P3D" selected="True">P3D</option>
+					<option value="EachMarker">EachMarker</option>
+				</param>
+				<param name="mlmCompressionLevel" type="select" label="Compression Level">
+					<option value="Optimum" selected="True">Optimum</option>
+					<option value="Custom">Custom</option>
+					<option value="None">None</option>
+				</param>
+                        </when>
+			<when value="ld"></when>
+			<when value="ck"></when>
+		</conditional>
+		<param type="text" name="filterAlignMinFreq" label="Filter minimal frequency allele" value="0.05"/>
+	</inputs>
+	<outputs>
+		<data format="txt" name="output1" label="Tassel output">
+			<change_format>
+				<when input="analysis_opts['fonction_selector']" value="ld" format="png"/>
+			</change_format>
+		</data>
+		
+		<data format="txt" name="output2" label="Allele effects">
+			<filter>analysis_opts['fonction_selector'] == "glm" or analysis_opts['fonction_selector'] == "mlm"</filter>
+		</data>
+		
+		<data format="txt" name="output3" label="Compression file">
+			<filter>analysis_opts['fonction_selector'] == "mlm"</filter>
+		</data>
+		
+		<data format="txt" name="log" label="Log file"/>
+	</outputs>
+	<help>
+
+.. class:: infomark
+
+**Program encapsulated in Galaxy by Southgreen**
+
+.. class:: infomark
+
+**Tassel**
+
+-----
+
+==========
+ Authors:
+==========
+
+**Terry Casstevens**
+
+-----
+
+==========
+ Overview
+==========
+
+Software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
+
+-----
+
+For further informations, please visite the website of TASSEL_.
+
+
+.. _TASSEL: http://www.maizegenetics.net/tassel/
+
+	</help>
+<!--
+<tests>
+  <test>
+      <param name="input" value="genotyping_file.inp" />
+      <output name="output" file="phase_output" />
+   </test>
+</tests>
+-->
+</tool>
--- a/tassel/tassel.sh	Fri Jul 03 04:37:26 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,47 +0,0 @@
-#!/bin/bash
-
-analyseType=$1;
-out1=$2;
-out2=$3;
-out3=$4;
-log1=$5;
-galaxyOutDir=$6;
-
-version=$(java -version 2>&1 | grep version)
-if [[ ! $version =~ 1.8 ]]; then
-    echo "Java found: $version. Tassel 5.0 requires java 1.8..." >&2
-    exit 1
-fi
-
-mkdir $galaxyOutDir
-
-# Suppression des 6 premiers arguments de la liste des arguments $@
-shift; shift; shift; shift; shift; shift;
-
-
-if [[ $analyseType == glm ]] 
-then
- run_pipeline.pl $* >> $log1 2>&1
- mv "$galaxyOutDir/TASSELGLM1.txt" $out1
- mv "$galaxyOutDir/TASSELGLM2.txt" $out2
-fi
-
-if [[ $analyseType == mlm ]] 
-then
- run_pipeline.pl $* >> $log1 2>&1
- mv "$galaxyOutDir/TASSELMLM1.txt" $out1
- mv "$galaxyOutDir/TASSELMLM2.txt" $out2
- mv "$galaxyOutDir/TASSELMLM3.txt" $out3
-fi
-
-if [[ $analyseType == ld ]] 
-then
- run_pipeline.pl $* >> $log1 2>&1
-fi
-
-
-if [[ $analyseType == ck ]]
-then
- run_pipeline.pl $* >> $log1 2>&1
- mv "$galaxyOutDir/kinship.txt" $out1
-fi
--- a/tassel/tassel.xml	Fri Jul 03 04:37:26 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,153 +0,0 @@
-<tool id="Tassel" name="Tassel" version="5.0">
-	<description> Software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium. </description>
-	<requirements>
-                <requirement type="package" version="5.0">tassel</requirement>
-        </requirements>
-	<command interpreter="bash">./tassel.sh $analysis_opts.fonction_selector $output1 $output2 $output3 $log tmpdir$$/
-#if $analysis_opts.fonction_selector == "mlm":
- -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq
- -fork2 -r $analysis_opts.trait
- #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
-  -fork3 -q $analysis_opts.add_structure_file.structure -excludeLastTrait
- #end if
- -fork4 -k $analysis_opts.kinship
- -combineA -input1 -input2 
- #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
-  -input3
- #end if
- -intersect -combineB -inputA -input4 -mlm -mlmVarCompEst $analysis_opts.mlmVarCompEst -mlmCompressionLevel $analysis_opts.mlmCompressionLevel -export tmpdir$$/TASSELMLM -runfork1 -runfork2 
- #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
-  -runfork3
- #end if
- -runfork4
- 
-#else if $analysis_opts.fonction_selector == "glm":
- -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq
- -fork2 -r $analysis_opts.trait
- #if $analysis_opts.add_file.additional_file_selector == "yes":
-  -fork3 -q $analysis_opts.add_file.structure -excludeLastTrait
- #end if
- -combineA -input1 -input2 
- #if $analysis_opts.add_file.additional_file_selector == "yes":
-  -input3
- #end if
- -intersect -glm -export tmpdir$$/TASSELGLM -runfork1 -runfork2
- #if $analysis_opts.add_file.additional_file_selector == "yes":
-  -runfork3
- #end if 
-#else if $analysis_opts.fonction_selector == "ld":
- -fork1 -h $hapmap
- -ld -ldType All -ldd png -ldplotsize 3000 -o $output1 -runfork1
-#else if $analysis_opts.fonction_selector == "ck":
- -fork1 -h $hapmap
- -ck -export tmpdir$$/kinship -runfork1
-#end if
-	</command>
-	<inputs>
-		<param format="txt" name="hapmap" type="data" label="HapMap file"/>
-		<conditional name="analysis_opts">
-			<param name="fonction_selector" type="select" label="Type of analysis">
-				<option value="mlm" selected="True">MLM</option>
-				<option value="glm">GLM</option>
-				<option value="ld">Linkage Disequilibrium</option>
-				<option value="ck">Kinship</option>
-			</param>
-			<when value="glm">
-                		<param format="txt" name="trait" type="data" label="Trait file"/>
-				<conditional name="add_file">
-					<param name="additional_file_selector" type="select" label="Add structure file">
-        	                	        <option value="no" selected="True">no</option>
-                	                	<option value="yes">yes</option>
-	                	        </param>
-					<when value="yes">
-						<param format="txt" name="structure" type="data" label="Structure file"/>
-					</when>
-				</conditional>
-			</when>
-			<when value="mlm">
-                		<param format="txt" name="trait" type="data" label="Trait file"/>
-		                <param format="txt" name="kinship" type="data" label="Kinship file"/>
-				<conditional name="add_structure_file">
-					<param name="additional_file_selector" type="select" label="Add structure file">
-        	                	        <option value="no" selected="True">no</option>
-                	                	<option value="yes">yes</option>
-	                	        </param>
-					<when value="yes">
-						<param format="txt" name="structure" type="data" label="Structure file"/>
-					</when>
-				</conditional>
-				<param name="mlmVarCompEst" type="select" label="Variance Component Estimation">
-					<option value="P3D" selected="True">P3D</option>
-					<option value="EachMarker">EachMarker</option>
-				</param>
-				<param name="mlmCompressionLevel" type="select" label="Compression Level">
-					<option value="Optimum" selected="True">Optimum</option>
-					<option value="Custom">Custom</option>
-					<option value="None">None</option>
-				</param>
-                        </when>
-			<when value="ld"></when>
-			<when value="ck"></when>
-		</conditional>
-		<param type="text" name="filterAlignMinFreq" label="Filter minimal frequency allele" value="0.05"/>
-	</inputs>
-	<outputs>
-		<data format="txt" name="output1" label="Tassel output">
-			<change_format>
-				<when input="analysis_opts['fonction_selector']" value="ld" format="png"/>
-			</change_format>
-		</data>
-		
-		<data format="txt" name="output2" label="Allele effects">
-			<filter>analysis_opts['fonction_selector'] == "glm" or analysis_opts['fonction_selector'] == "mlm"</filter>
-		</data>
-		
-		<data format="txt" name="output3" label="Compression file">
-			<filter>analysis_opts['fonction_selector'] == "mlm"</filter>
-		</data>
-		
-		<data format="txt" name="log" label="Log file"/>
-	</outputs>
-	<help>
-
-.. class:: infomark
-
-**Program encapsulated in Galaxy by Southgreen**
-
-.. class:: infomark
-
-**Tassel**
-
------
-
-==========
- Authors:
-==========
-
-**Terry Casstevens**
-
------
-
-==========
- Overview
-==========
-
-Software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
-
------
-
-For further informations, please visite the website of TASSEL_.
-
-
-.. _TASSEL: http://www.maizegenetics.net/tassel/
-
-	</help>
-<!--
-<tests>
-  <test>
-      <param name="input" value="genotyping_file.inp" />
-      <output name="output" file="phase_output" />
-   </test>
-</tests>
--->
-</tool>
--- a/tassel/tool-data/tool_dependencies.xml	Fri Jul 03 04:37:26 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="tassel" version="5.0">
-        <repository changeset_revision="097d4c366e0d" name="package_tassel_5_0" owner="dereeper" toolshed="https://toolshed.g2.bx.psu.edu/" />
-    </package>
-</tool_dependency>
-
-