| Previous changeset 0:14045c80a222 (2020-06-26) Next changeset 2:ccca6ad98f78 (2020-09-14) |
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galaxy/wrappers/ExprHeatmapClustering.xml |
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| diff -r 14045c80a222 -r 0b09345fa632 galaxy/wrappers/ExprHeatmapClustering.xml --- a/galaxy/wrappers/ExprHeatmapClustering.xml Fri Jun 26 09:38:23 2020 -0400 +++ b/galaxy/wrappers/ExprHeatmapClustering.xml Mon Sep 14 13:16:28 2020 +0000 |
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| @@ -1,4 +1,4 @@ -<tool name="GIANT-Heatmap and Hierarchical clustering" id="giant_hierarchical_clustering" version="0.5.1"> +<tool name="GIANT-Heatmap and Hierarchical clustering" id="giant_hierarchical_clustering" version="0.5.2"> <description>Run hierarchical clustering and plot heatmap from expression data and/or differential expression analysis</description> <requirements> <requirement type="package" version="4.8.0">r-plotly</requirement> @@ -10,7 +10,8 @@ <requirement type="package" version="1.18.1">bioconductor-complexheatmap</requirement> <requirement type="package" version="2.2.2">pandoc</requirement> </requirements> - <code file='../../src/General_functions.py'/> + <code file="../../src/General_functions.py"/> + <!--<code file="./src/General_functions.py"/> change for Planemo test--> <stdio> <regex match="Execution halted" source="both" @@ -68,7 +69,10 @@ awk -v factor="$advSection.conditionBarColor.factorToUse" 'BEGIN{FS="\t";OFS="";ORS=""} NR==1{for(i=2;i<=NF;i++)if(\$i==factor)colToKeep=i} {print \$1"\t"\$colToKeep"\n"}' $advSection.conditionBarColor.factorFileDataBarPlot > ./barPlotFactor; #end if - Rscript '$__tool_directory__/../../src/heatMapClustering.R' --log '$log' --outputFile '$outputData' --format '$advSection.imageFormat' --clusterNumber '$advSection.clusterNumber' --maxRows '$advSection.maxSampleToPlot' --sampleClusterNumber '$advSection.conditionClusterNumber' --dataTransformation '$advSection.dataTransformation' --distanceMeasure '$advSection.distanceMeasure' --aggloMethod '$advSection.aggloMethod' + Rscript '$__tool_directory__/../../src/heatMapClustering.R' --log '$log' --outputFile '$outputData' --format '$advSection.imageFormat' --clusterNumber '$advSection.clusterNumber' + ##change for Planemo test + ##Rscript '$__tool_directory__/src/heatMapClustering.R' --log '$log' --outputFile '$outputData' --format '$advSection.imageFormat' --clusterNumber '$advSection.clusterNumber' + --maxRows '$advSection.maxSampleToPlot' --sampleClusterNumber '$advSection.conditionClusterNumber' --dataTransformation '$advSection.dataTransformation' --distanceMeasure '$advSection.distanceMeasure' --aggloMethod '$advSection.aggloMethod' #if $advSection.select_color.specifyColors=="true": --personalColors '$advSection.select_color.featureMin_color,$advSection.select_color.featureMedium_color,$advSection.select_color.featureMax_color' #end if @@ -714,27 +718,47 @@ <tests> - <test maxseconds="7200"> - <param name="dataToCluster_selector" value="expression" /> - <param name="expressionData" value="./NormalizedData.tabular" /> - <param name="filtering_step_selector" value="input" /> - <param name="filtering_stepBis_selector" value="diffExpParam" /> - <param name="differentialAnalysis" value="./LIMMAstatistics.tabular" /> - <param name="comparisonsToInclude" value="WT*WY14643-KO*WY14643" /> - <param name="FCthreshold" value="1.2" /> - <param name="pvalThreshold" value="0.05" /> - <output name="log" file="./HierarchicalClustering/ExpressionClustering.log" lines_diff="6" /> - </test> - <test maxseconds="7200"> - <param name="dataToCluster_selector" value="foldChange" /> - <param name="differentialAnalysis" value="./LIMMAstatistics.tabular" /> - <param name="comparisonsToInclude" value="WT*WY14643+KO*WY14643-WT*Control-KO*Control,WT*WY14643+WT*Control-KO*WY14643-KO*Control" /> - <param name="filtering_step_selector" value="output" /> - <param name="filtering_stepBis_selector" value="diffExpParam" /> - <param name="FCthreshold" value="1.2" /> - <param name="pvalThreshold" value="0.05" /> - <output name="outputData" file="./HierarchicalClustering/foldChangeClustering.tabular" /> - <output name="log" file="./HierarchicalClustering/foldChangeClustering.log" lines_diff="6" /> + <test maxseconds="3600"> + <conditional name="dataToCluster"> + <param name="dataToCluster_selector" value="expression" /> + <param name="expressionData" value="./NormalizedData.tabular" /> + <conditional name="reorder_sample"> + <param name="reordering_selector" value="no" /> + </conditional> + <conditional name="filtering_step"> + <param name="filtering_step_selector" value="input" /> + <conditional name="select_filtering"> + <param name="filtering_stepBis_selector" value="diffExpParam" /> + <param name="differentialAnalysis" value="./DiffExprLimma/output/outputStat.csv" /> + <param name="comparisonsToInclude" value="TreatVsControl" /> + <param name="FCthreshold" value="2.0" /> + <param name="pvalThreshold" value="0.05" /> + </conditional> + </conditional> + </conditional> + <section name="advSection" > + <param name="clusterNumber" value="5" /> + <param name="conditionClusterNumber" value="3" /> + <param name="dataTransformation" value="no" /> + <param name="distanceMeasure" value="euclidean" /> + <param name="aggloMethod" value="ward.D2" /> + <conditional name="conditionBarColor"> + <param name="conditionBarColor_selector" value="yes" /> + <param name="factorFileDataBarPlot" value="./FactorFileGenerator/output/conditionsFile.csv" /> + <param name="factorToUse" value="Treatment" /> + <param name="sideBarPalette" value="Spectral" /> + </conditional> + <param name="maxSampleToPlot" value="1000" /> + <conditional name="select_color"> + <param name="specifyColors" value="false" /> + </conditional> + <param name="imageFormat" value="png" /> + <param name="imagePlotlyFormat" value="png" /> + <param name="scaleSnapshot" value="1.0" /> + </section> + <output name="outputData" file="./ExprHeatmapClustering/output/outputResults.csv" /> + <output name="html_file" file="./ExprHeatmapClustering/output/outputHTML.zip" decompress="true" /> + <output name="log" file="./ExprHeatmapClustering/output/outputLog.txt" compare="sim_size" delta_frac="0.10" /> </test> </tests> |