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Commit message:
Uploaded |
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added:
tassel.sh tassel.xml |
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removed:
tassel/tassel.sh tassel/tassel.xml tassel/tool-data/tool_dependencies.xml |
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| diff -r d8a46ae7ee8a -r 0eebff4180d9 tassel.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tassel.sh Thu Nov 02 05:19:30 2017 -0400 |
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| @@ -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 |
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| diff -r d8a46ae7ee8a -r 0eebff4180d9 tassel.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tassel.xml Thu Nov 02 05:19:30 2017 -0400 |
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| @@ -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> |
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| diff -r d8a46ae7ee8a -r 0eebff4180d9 tassel/tassel.sh --- a/tassel/tassel.sh Fri Jul 03 04:37:26 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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 |
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| diff -r d8a46ae7ee8a -r 0eebff4180d9 tassel/tassel.xml --- a/tassel/tassel.xml Fri Jul 03 04:37:26 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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> |
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| diff -r d8a46ae7ee8a -r 0eebff4180d9 tassel/tool-data/tool_dependencies.xml --- 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 |
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| @@ -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> - - |