# HG changeset patch
# User dereeper
# Date 1424931707 18000
# Node ID 4027928a1f4c4a9ba4eb2cf97bb272b638e65fb0
# Parent 1b672da89d00d20faafdb1f53410ac8dbaacca8f
Uploaded
diff -r 1b672da89d00 -r 4027928a1f4c tassel/tassel.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tassel/tassel.sh Thu Feb 26 01:21:47 2015 -0500
@@ -0,0 +1,41 @@
+#!/bin/bash
+
+analyseType=$1;
+out1=$2;
+out2=$3;
+out3=$4;
+log1=$5;
+galaxyOutDir=$6;
+
+
+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
diff -r 1b672da89d00 -r 4027928a1f4c tassel/tassel.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tassel/tassel.xml Thu Feb 26 01:21:47 2015 -0500
@@ -0,0 +1,153 @@
+
+ Software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
+
+ tassel
+
+ ./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
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+ analysis_opts['fonction_selector'] == "glm" or analysis_opts['fonction_selector'] == "mlm"
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+ analysis_opts['fonction_selector'] == "mlm"
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+.. 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/
+
+
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diff -r 1b672da89d00 -r 4027928a1f4c tassel/tool-data/tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tassel/tool-data/tool_dependencies.xml Thu Feb 26 01:21:47 2015 -0500
@@ -0,0 +1,8 @@
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