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comparison galaxy/wrappers/ExprHeatmapClustering.xml @ 1:0b09345fa632 draft

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author vandelj
date Mon, 14 Sep 2020 13:16:28 +0000
parents 14045c80a222
children dd0f4da5f68f
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0:14045c80a222 1:0b09345fa632
1 <tool name="GIANT-Heatmap and Hierarchical clustering" id="giant_hierarchical_clustering" version="0.5.1"> 1 <tool name="GIANT-Heatmap and Hierarchical clustering" id="giant_hierarchical_clustering" version="0.5.2">
2 <description>Run hierarchical clustering and plot heatmap from expression data and/or differential expression analysis</description> 2 <description>Run hierarchical clustering and plot heatmap from expression data and/or differential expression analysis</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="4.8.0">r-plotly</requirement> 4 <requirement type="package" version="4.8.0">r-plotly</requirement>
5 <requirement type="package" version="1.12.0">r-dendextend</requirement> 5 <requirement type="package" version="1.12.0">r-dendextend</requirement>
6 <requirement type="package" version="0.1_20">r-ggdendro</requirement> 6 <requirement type="package" version="0.1_20">r-ggdendro</requirement>
8 <requirement type="package" version="0.16.0">r-heatmaply</requirement> 8 <requirement type="package" version="0.16.0">r-heatmaply</requirement>
9 <requirement type="package" version="0.4.8">r-circlize</requirement> 9 <requirement type="package" version="0.4.8">r-circlize</requirement>
10 <requirement type="package" version="1.18.1">bioconductor-complexheatmap</requirement> 10 <requirement type="package" version="1.18.1">bioconductor-complexheatmap</requirement>
11 <requirement type="package" version="2.2.2">pandoc</requirement> 11 <requirement type="package" version="2.2.2">pandoc</requirement>
12 </requirements> 12 </requirements>
13 <code file='../../src/General_functions.py'/> 13 <code file="../../src/General_functions.py"/>
14 <!--<code file="./src/General_functions.py"/> change for Planemo test-->
14 <stdio> 15 <stdio>
15 <regex match="Execution halted" 16 <regex match="Execution halted"
16 source="both" 17 source="both"
17 level="fatal" 18 level="fatal"
18 description="Execution halted, please contact tool developer or administrators." /> 19 description="Execution halted, please contact tool developer or administrators." />
66 ##generate factor information to use for barplot 67 ##generate factor information to use for barplot
67 #if $advSection.conditionBarColor.conditionBarColor_selector=="yes" and $advSection.conditionBarColor.factorFileDataBarPlot and $advSection.conditionBarColor.factorToUse: 68 #if $advSection.conditionBarColor.conditionBarColor_selector=="yes" and $advSection.conditionBarColor.factorFileDataBarPlot and $advSection.conditionBarColor.factorToUse:
68 awk -v factor="$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"}' $advSection.conditionBarColor.factorFileDataBarPlot > ./barPlotFactor; 69 awk -v factor="$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"}' $advSection.conditionBarColor.factorFileDataBarPlot > ./barPlotFactor;
69 #end if 70 #end if
70 71
71 Rscript '$__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 '$advSection.aggloMethod' 72 Rscript '$__tool_directory__/../../src/heatMapClustering.R' --log '$log' --outputFile '$outputData' --format '$advSection.imageFormat' --clusterNumber '$advSection.clusterNumber'
73 ##change for Planemo test
74 ##Rscript '$__tool_directory__/src/heatMapClustering.R' --log '$log' --outputFile '$outputData' --format '$advSection.imageFormat' --clusterNumber '$advSection.clusterNumber'
75 --maxRows '$advSection.maxSampleToPlot' --sampleClusterNumber '$advSection.conditionClusterNumber' --dataTransformation '$advSection.dataTransformation' --distanceMeasure '$advSection.distanceMeasure' --aggloMethod '$advSection.aggloMethod'
72 #if $advSection.select_color.specifyColors=="true": 76 #if $advSection.select_color.specifyColors=="true":
73 --personalColors '$advSection.select_color.featureMin_color,$advSection.select_color.featureMedium_color,$advSection.select_color.featureMax_color' 77 --personalColors '$advSection.select_color.featureMin_color,$advSection.select_color.featureMedium_color,$advSection.select_color.featureMax_color'
74 #end if 78 #end if
75 #if $advSection.conditionBarColor.conditionBarColor_selector=="yes" and $advSection.conditionBarColor.factorFileDataBarPlot and $advSection.conditionBarColor.factorToUse: 79 #if $advSection.conditionBarColor.conditionBarColor_selector=="yes" and $advSection.conditionBarColor.factorFileDataBarPlot and $advSection.conditionBarColor.factorToUse:
76 --factorInfo './barPlotFactor' 80 --factorInfo './barPlotFactor'
712 </outputs> 716 </outputs>
713 717
714 718
715 719
716 <tests> 720 <tests>
717 <test maxseconds="7200"> 721 <test maxseconds="3600">
718 <param name="dataToCluster_selector" value="expression" /> 722 <conditional name="dataToCluster">
719 <param name="expressionData" value="./NormalizedData.tabular" /> 723 <param name="dataToCluster_selector" value="expression" />
720 <param name="filtering_step_selector" value="input" /> 724 <param name="expressionData" value="./NormalizedData.tabular" />
721 <param name="filtering_stepBis_selector" value="diffExpParam" /> 725 <conditional name="reorder_sample">
722 <param name="differentialAnalysis" value="./LIMMAstatistics.tabular" /> 726 <param name="reordering_selector" value="no" />
723 <param name="comparisonsToInclude" value="WT*WY14643-KO*WY14643" /> 727 </conditional>
724 <param name="FCthreshold" value="1.2" /> 728 <conditional name="filtering_step">
725 <param name="pvalThreshold" value="0.05" /> 729 <param name="filtering_step_selector" value="input" />
726 <output name="log" file="./HierarchicalClustering/ExpressionClustering.log" lines_diff="6" /> 730 <conditional name="select_filtering">
727 </test> 731 <param name="filtering_stepBis_selector" value="diffExpParam" />
728 <test maxseconds="7200"> 732 <param name="differentialAnalysis" value="./DiffExprLimma/output/outputStat.csv" />
729 <param name="dataToCluster_selector" value="foldChange" /> 733 <param name="comparisonsToInclude" value="TreatVsControl" />
730 <param name="differentialAnalysis" value="./LIMMAstatistics.tabular" /> 734 <param name="FCthreshold" value="2.0" />
731 <param name="comparisonsToInclude" value="WT*WY14643+KO*WY14643-WT*Control-KO*Control,WT*WY14643+WT*Control-KO*WY14643-KO*Control" /> 735 <param name="pvalThreshold" value="0.05" />
732 <param name="filtering_step_selector" value="output" /> 736 </conditional>
733 <param name="filtering_stepBis_selector" value="diffExpParam" /> 737 </conditional>
734 <param name="FCthreshold" value="1.2" /> 738 </conditional>
735 <param name="pvalThreshold" value="0.05" /> 739 <section name="advSection" >
736 <output name="outputData" file="./HierarchicalClustering/foldChangeClustering.tabular" /> 740 <param name="clusterNumber" value="5" />
737 <output name="log" file="./HierarchicalClustering/foldChangeClustering.log" lines_diff="6" /> 741 <param name="conditionClusterNumber" value="3" />
742 <param name="dataTransformation" value="no" />
743 <param name="distanceMeasure" value="euclidean" />
744 <param name="aggloMethod" value="ward.D2" />
745 <conditional name="conditionBarColor">
746 <param name="conditionBarColor_selector" value="yes" />
747 <param name="factorFileDataBarPlot" value="./FactorFileGenerator/output/conditionsFile.csv" />
748 <param name="factorToUse" value="Treatment" />
749 <param name="sideBarPalette" value="Spectral" />
750 </conditional>
751 <param name="maxSampleToPlot" value="1000" />
752 <conditional name="select_color">
753 <param name="specifyColors" value="false" />
754 </conditional>
755 <param name="imageFormat" value="png" />
756 <param name="imagePlotlyFormat" value="png" />
757 <param name="scaleSnapshot" value="1.0" />
758 </section>
759 <output name="outputData" file="./ExprHeatmapClustering/output/outputResults.csv" />
760 <output name="html_file" file="./ExprHeatmapClustering/output/outputHTML.zip" decompress="true" />
761 <output name="log" file="./ExprHeatmapClustering/output/outputLog.txt" compare="sim_size" delta_frac="0.10" />
738 </test> 762 </test>
739 </tests> 763 </tests>
740 764
741 765
742 766