Mercurial > repos > vandelj > giant_hierarchical_clustering
annotate galaxy/wrappers/ExprHeatmapClustering.xml @ 4:d75a74a93587 draft default tip
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit 89b7d0e8812f53222691cffe29bd48be6519829d"
author | vandelj |
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date | Fri, 25 Sep 2020 08:52:29 +0000 |
parents | dd0f4da5f68f |
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rev | line source |
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4
d75a74a93587
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit 89b7d0e8812f53222691cffe29bd48be6519829d"
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1 <tool name="GIANT-Heatmap and Hierarchical clustering" id="giant_hierarchical_clustering" version="0.5.4"> |
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14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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2 <description>Run hierarchical clustering and plot heatmap from expression data and/or differential expression analysis</description> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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3 <requirements> |
14045c80a222
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4 <requirement type="package" version="4.8.0">r-plotly</requirement> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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5 <requirement type="package" version="1.12.0">r-dendextend</requirement> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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6 <requirement type="package" version="0.1_20">r-ggdendro</requirement> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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7 <requirement type="package" version="3.2.1">r-ggplot2</requirement> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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8 <requirement type="package" version="0.16.0">r-heatmaply</requirement> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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9 <requirement type="package" version="0.4.8">r-circlize</requirement> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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10 <requirement type="package" version="1.18.1">bioconductor-complexheatmap</requirement> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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11 <requirement type="package" version="2.2.2">pandoc</requirement> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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12 </requirements> |
1 | 13 <code file="../../src/General_functions.py"/> |
14 <!--<code file="./src/General_functions.py"/> change for Planemo test--> | |
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14045c80a222
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15 <stdio> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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16 <regex match="Execution halted" |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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17 source="both" |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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18 level="fatal" |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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19 description="Execution halted, please contact tool developer or administrators." /> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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20 <regex match="Error in" |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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21 source="both" |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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22 level="fatal" |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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23 description="An error occured during R execution, please contact tool developer." /> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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24 <exit_code range="10" level="fatal" description="Missing file during html report, see log file for more information." /> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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25 <exit_code range="1:9" level="fatal" description="Error in R execution, see log file for more information." /> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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26 </stdio> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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27 <command> <![CDATA[ |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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28 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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29 #if ($dataToCluster.dataToCluster_selector=="expression" or $dataToCluster.dataToCluster_selector=="genericData") and $dataToCluster.expressionData: |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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30 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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31 ##start by selecting specific input data columns depending on user request |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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32 #if $dataToCluster.dataToCluster_selector=="genericData" and $dataToCluster.columnToKeep: |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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33 awk -v columns="$dataToCluster.columnToKeep" 'BEGIN{FS="\t";OFS="";ORS="";split(columns,columnsTab,",")} FNR==1{for(iColumn=1;iColumn<=length(columnsTab);iColumn++)for(iField=2;iField<=NF;iField++){if(\$iField==columnsTab[iColumn])colsToSelect[iColumn]=iField}} {line=\$1;for(iColumn=1;iColumn<=length(columnsTab);iColumn++)line=line"\t"\$colsToSelect[iColumn];print line"\n";}' $dataToCluster.expressionData > ./selectedExpressionData; |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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34 #else |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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35 cp $dataToCluster.expressionData ./selectedExpressionData; |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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36 #end if |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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37 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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38 ##reorder columns of input data based on factors file |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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39 #if $dataToCluster.reorder_sample.reordering_selector=="factorFile" and $dataToCluster.reorder_sample.factorFileData and $dataToCluster.reorder_sample.factorToUse: |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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40 awk -v factors="$dataToCluster.reorder_sample.factorToUse" 'BEGIN{FS="\t";OFS="";ORS="";split(factors,factorsTab,",")} FNR==1{for(iFactor=1;iFactor<=length(factorsTab);iFactor++)for(iField=2;iField<=NF;iField++){if(\$iField==factorsTab[iFactor])colsToSelect[iFactor]=iField}} FNR>1{line=\$1;for(iFactor=1;iFactor<=length(factorsTab);iFactor++)line=line"\t"\$colsToSelect[iFactor];print line"\n";}' $dataToCluster.reorder_sample.factorFileData > ./orderingFactor; |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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41 |
14045c80a222
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42 sort -V -k2 ./orderingFactor > ./orderingSample; |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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43 |
14045c80a222
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44 awk 'BEGIN{FS="\t";OFS="";ORS="";factorNumber=0} ARGIND==1{sampleOrdered[FNR]=\$1;factorNumber=FNR} ARGIND==2 && FNR==1{for(iElemt=1;iElemt<=factorNumber;iElemt++)for(iPosit=2;iPosit<=NF;iPosit++)if(\$iPosit==sampleOrdered[iElemt])positOrdered[iElemt]=iPosit} ARGIND==2{line=\$1;for(iElemt=1;iElemt<=factorNumber;iElemt++)if(iElemt in positOrdered)line=line"\t"\$positOrdered[iElemt];print line"\n"}' ./orderingSample ./selectedExpressionData > ./orderedExpressionData; |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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45 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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46 ##check if some input data columns were lost during the process |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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47 awk 'ARGIND==1 && FNR==1{colNumbA=NF} ARGIND==2 && FNR==1{colNumbB=NF} END{if(colNumbA!=colNumbB) print "[WARNING] "colNumbA-colNumbB" input data columns was removed during reordering due to missing information in factor file!\n"}' ./selectedExpressionData ./orderedExpressionData >> $log; |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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48 |
14045c80a222
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49 #if $advSection.conditionClusterNumber!="1": |
14045c80a222
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50 printf "[WARNING]Sample clustering option is selected, sample reordering will not be preserved!\n" >> $log; |
14045c80a222
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51 #end if |
14045c80a222
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52 #else: |
14045c80a222
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53 cp ./selectedExpressionData ./orderedExpressionData; |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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54 #end if |
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55 #end if |
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56 |
14045c80a222
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57 |
14045c80a222
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58 ##generate common file name for differential analysis results depending on input data nature |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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59 #if ($dataToCluster.dataToCluster_selector=="expression" or $dataToCluster.dataToCluster_selector=="genericData") and $dataToCluster.filtering_step.filtering_step_selector!="no" and $dataToCluster.filtering_step.select_filtering.filtering_stepBis_selector=="diffExpParam" and $dataToCluster.filtering_step.select_filtering.differentialAnalysis: |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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60 cp ${dataToCluster.filtering_step.select_filtering.differentialAnalysis} ./filteredDifferentialAnalysis; |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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61 #end if |
14045c80a222
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62 #if $dataToCluster.dataToCluster_selector=="foldChange" and $dataToCluster.differentialAnalysis: |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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63 cp $dataToCluster.differentialAnalysis ./filteredDifferentialAnalysis; |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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64 #end if |
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65 |
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66 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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67 ##generate factor information to use for barplot |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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68 #if $advSection.conditionBarColor.conditionBarColor_selector=="yes" and $advSection.conditionBarColor.factorFileDataBarPlot and $advSection.conditionBarColor.factorToUse: |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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69 awk -v factor="$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"}' $advSection.conditionBarColor.factorFileDataBarPlot > ./barPlotFactor; |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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70 #end if |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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71 |
1 | 72 Rscript '$__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' | |
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14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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76 #if $advSection.select_color.specifyColors=="true": |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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77 --personalColors '$advSection.select_color.featureMin_color,$advSection.select_color.featureMedium_color,$advSection.select_color.featureMax_color' |
14045c80a222
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78 #end if |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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79 #if $advSection.conditionBarColor.conditionBarColor_selector=="yes" and $advSection.conditionBarColor.factorFileDataBarPlot and $advSection.conditionBarColor.factorToUse: |
14045c80a222
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80 --factorInfo './barPlotFactor' |
14045c80a222
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81 --sideBarColorPalette '$advSection.conditionBarColor.sideBarPalette' |
14045c80a222
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82 #end if |
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83 #if $dataToCluster.dataToCluster_selector=="genericData": |
14045c80a222
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84 --genericData |
14045c80a222
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85 #end if |
14045c80a222
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86 #if $dataToCluster.dataToCluster_selector=="expression" or $dataToCluster.dataToCluster_selector=="genericData": |
14045c80a222
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87 --expressionFile './orderedExpressionData' |
14045c80a222
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88 #if $dataToCluster.filtering_step.filtering_step_selector!="no": |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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89 --filterInputOutput '$dataToCluster.filtering_step.filtering_step_selector' |
14045c80a222
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90 #if $dataToCluster.filtering_step.select_filtering.filtering_stepBis_selector=="diffExpParam": |
14045c80a222
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91 --diffAnalyseFile './filteredDifferentialAnalysis' |
14045c80a222
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92 #if $dataToCluster.dataToCluster_selector=="expression": |
14045c80a222
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93 --comparisonName '$dataToCluster.filtering_step.select_filtering.comparisonsToInclude' |
14045c80a222
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94 --FCthreshold '$dataToCluster.filtering_step.select_filtering.FCthreshold' |
14045c80a222
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95 --pvalThreshold '$dataToCluster.filtering_step.select_filtering.pvalThreshold' |
14045c80a222
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96 #else: |
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97 #if $dataToCluster.filtering_step.select_filtering.comparisonsToIncludeLow and $dataToCluster.filtering_step.select_filtering.valThresholdLow: |
14045c80a222
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98 --comparisonNameLow '$dataToCluster.filtering_step.select_filtering.comparisonsToIncludeLow' |
14045c80a222
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99 --FCthreshold '$dataToCluster.filtering_step.select_filtering.valThresholdLow' |
14045c80a222
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100 #end if |
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101 #if $dataToCluster.filtering_step.select_filtering.comparisonsToIncludeHigh and $dataToCluster.filtering_step.select_filtering.valThresholdHigh: |
14045c80a222
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102 --comparisonNameHigh '$dataToCluster.filtering_step.select_filtering.comparisonsToIncludeHigh' |
14045c80a222
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103 --pvalThreshold '$dataToCluster.filtering_step.select_filtering.valThresholdHigh' |
14045c80a222
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104 #end if |
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105 #end if |
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106 #else: |
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107 --geneListFiltering '$dataToCluster.filtering_step.select_filtering.geneListFile' |
14045c80a222
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108 #end if |
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109 #end if |
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110 #else |
14045c80a222
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111 --diffAnalyseFile './filteredDifferentialAnalysis' |
14045c80a222
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112 --comparisonName '$dataToCluster.comparisonsToInclude' |
14045c80a222
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113 #if $dataToCluster.filtering_step.filtering_step_selector!="no": |
14045c80a222
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114 --filterInputOutput '$dataToCluster.filtering_step.filtering_step_selector' |
14045c80a222
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115 #if $dataToCluster.filtering_step.select_filtering.filtering_stepBis_selector=="diffExpParam": |
14045c80a222
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116 --FCthreshold '$dataToCluster.filtering_step.select_filtering.FCthreshold' |
14045c80a222
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117 --pvalThreshold '$dataToCluster.filtering_step.select_filtering.pvalThreshold' |
14045c80a222
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118 #else: |
14045c80a222
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119 --geneListFiltering '$dataToCluster.filtering_step.select_filtering.geneListFile' |
14045c80a222
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120 #end if |
14045c80a222
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121 #end if |
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122 #end if |
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123 ; |
14045c80a222
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124 ret_code=\$?; |
14045c80a222
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125 if [ \$ret_code != 0 ]; then |
14045c80a222
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126 exit \$ret_code; |
14045c80a222
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127 else |
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128 bash $scriptTransfer; |
14045c80a222
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129 ret_code=\$?; |
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130 if [ \$ret_code != 0 ]; then |
14045c80a222
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131 exit \$ret_code; |
14045c80a222
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132 fi |
14045c80a222
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133 fi; |
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134 printf "[INFO]End of tool script" >> $log; |
14045c80a222
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135 ]]> |
14045c80a222
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136 </command> |
14045c80a222
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137 |
14045c80a222
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138 |
14045c80a222
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139 |
14045c80a222
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140 <configfiles> |
14045c80a222
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141 <configfile name="scriptTableToHtml"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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142 <![CDATA[ |
14045c80a222
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143 printf "<!DOCTYPE html> |
14045c80a222
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144 <html> |
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145 <head> |
14045c80a222
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146 <meta http-equiv=\"Content-type\" content=\"text/html; charset=utf-8\"> |
14045c80a222
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147 <link rel=\"stylesheet\" type=\"text/css\" href=\"https://cdn.datatables.net/1.10.16/css/jquery.dataTables.min.css\"> |
14045c80a222
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148 <script type=\"text/javascript\" language=\"javascript\" src=\"https://code.jquery.com/jquery-1.12.4.js\"> |
14045c80a222
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149 </script> |
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150 <script type=\"text/javascript\" language=\"javascript\" src=\"https://cdn.datatables.net/1.10.16/js/jquery.dataTables.min.js\"> |
14045c80a222
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151 </script> |
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152 <script type=\"text/javascript\" class=\"init\"> |
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153 \\$(document).ready(function() { |
14045c80a222
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154 \\$(\'\#example\').DataTable( { |
14045c80a222
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155 \"columnDefs\": [ { |
14045c80a222
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156 \"visible\": false, |
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157 \"targets\": -1 |
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158 } ] |
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159 } ); |
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160 } ); |
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161 </script> |
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162 </head> |
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163 <body style=\"background-color:white;\"> |
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"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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|
164 <table id=\"example\" class=\"display\" cellspacing=\"0\"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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165 " > ${html_file.extra_files_path}/outputClustering.html |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
166 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
167 printf "<colgroup>\n" >> ${html_file.extra_files_path}/outputClustering.html |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
168 #if $dataToCluster.dataToCluster_selector=="foldChange" or ($dataToCluster.dataToCluster_selector=="expression" and $dataToCluster.filtering_step.filtering_step_selector!="no" and $dataToCluster.filtering_step.select_filtering.filtering_stepBis_selector=="diffExpParam"): |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
169 printf "<col span=\"2\" style=\"background-color:rgb(224,235,235)\">\n" >> ${html_file.extra_files_path}/outputClustering.html |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
170 printf "<col span=\"1\" style=\"background-color:rgb(250,235,235)\">\n" >> ${html_file.extra_files_path}/outputClustering.html |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
171 awk 'BEGIN{odd=1;FS="\t"} NR==1{for(i=4;i<=NF;i=i+5){if(odd==1){odd=0;printf "<col span=\"5\" style=\"background-color:rgb(224,238,255)\">\n"}else{odd=1;printf "<col span=\"5\" style=\"background-color:rgb(255,221,224)\">\n"}}}' $outputData >> ${html_file.extra_files_path}/outputClustering.html |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
172 #else |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
173 printf "<col span=\"1\" style=\"background-color:rgb(224,235,235)\">\n" >> ${html_file.extra_files_path}/outputClustering.html |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
174 printf "<col span=\"1\" style=\"background-color:rgb(250,235,235)\">\n" >> ${html_file.extra_files_path}/outputClustering.html |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
175 awk 'BEGIN{odd=1;FS="\t"} NR==1{for(i=3;i<=NF;i++){if(odd==1){odd=0;printf "<col span=\"1\" style=\"background-color:rgb(224,238,255)\">\n"}else{odd=1;printf "<col span=\"1\" style=\"background-color:rgb(255,221,224)\">\n"}}}' $outputData >> ${html_file.extra_files_path}/outputClustering.html |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
176 #end if |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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177 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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178 printf "</colgroup>\n" >> ${html_file.extra_files_path}/outputClustering.html |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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179 printf "<thead>\n<tr>\n" >> ${html_file.extra_files_path}/outputClustering.html |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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180 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
181 #if $dataToCluster.dataToCluster_selector=="foldChange" or ($dataToCluster.dataToCluster_selector=="expression" and $dataToCluster.filtering_step.filtering_step_selector!="no" and $dataToCluster.filtering_step.select_filtering.filtering_stepBis_selector=="diffExpParam"): |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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182 printf "<th rowspan=\"2\">Gene</th>\n" >> ${html_file.extra_files_path}/outputClustering.html |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
183 printf "<th rowspan=\"2\">Info</th>\n" >> ${html_file.extra_files_path}/outputClustering.html |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
184 printf "<th rowspan=\"2\">Cluster</th>\n" >> ${html_file.extra_files_path}/outputClustering.html |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
185 awk 'BEGIN{FS="\t"} NR==1{for(i=4;i<=NF;i=i+5)printf "<th colspan=\"5\">"\$i"</th>\n"}' $outputData >> ${html_file.extra_files_path}/outputClustering.html |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
186 printf "<th></th>\n" >> ${html_file.extra_files_path}/outputClustering.html |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
187 printf "</tr>\n<tr>\n" >> ${html_file.extra_files_path}/outputClustering.html |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
188 awk 'BEGIN{FS="\t"} NR==2{for(i=4;i<=NF;i++)printf "<th>"\$i"</th>\n"}' $outputData >> ${html_file.extra_files_path}/outputClustering.html |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
189 #else |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
190 printf "<th rowspan=\"1\">Gene</th>\n" >> ${html_file.extra_files_path}/outputClustering.html |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
191 printf "<th rowspan=\"1\">Cluster</th>\n" >> ${html_file.extra_files_path}/outputClustering.html |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
192 awk 'BEGIN{FS="\t"} NR==1{for(i=3;i<=NF;i++)printf "<th colspan=\"1\">"\$i"</th>\n"}' $outputData >> ${html_file.extra_files_path}/outputClustering.html |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
193 #end if |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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|
194 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
195 printf "<th></th>\n" >> ${html_file.extra_files_path}/outputClustering.html |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
196 printf "</tr>\n</thead>\n" >> ${html_file.extra_files_path}/outputClustering.html |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
197 printf "<tfoot>\n<tr>\n" >> ${html_file.extra_files_path}/outputClustering.html |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
198 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
199 #if $dataToCluster.dataToCluster_selector=="foldChange" or ($dataToCluster.dataToCluster_selector=="expression" and $dataToCluster.filtering_step.filtering_step_selector!="no" and $dataToCluster.filtering_step.select_filtering.filtering_stepBis_selector=="diffExpParam"): |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
200 awk 'BEGIN{FS="\t"} NR==2{for(i=1;i<=NF;i++)printf "<th>"\$i"</th>\n"}' $outputData >> ${html_file.extra_files_path}/outputClustering.html |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
201 #else |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
202 awk 'BEGIN{FS="\t"} NR==1{for(i=1;i<=NF;i++)printf "<th>"\$i"</th>\n"}' $outputData >> ${html_file.extra_files_path}/outputClustering.html |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
203 #end if |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
204 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
205 printf "<th></th>\n" >> ${html_file.extra_files_path}/outputClustering.html |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
206 printf "</tr>\n</tfoot>\n">> ${html_file.extra_files_path}/outputClustering.html |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
207 printf "<tbody>\n" >> ${html_file.extra_files_path}/outputClustering.html |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
208 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
209 #if $dataToCluster.dataToCluster_selector=="foldChange" or ($dataToCluster.dataToCluster_selector=="expression" and $dataToCluster.filtering_step.filtering_step_selector!="no" and $dataToCluster.filtering_step.select_filtering.filtering_stepBis_selector=="diffExpParam"): |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
210 awk 'BEGIN{FS="\t"} NR>2{printf "<tr>\n";for(i=1;i<=NF;i++){printf "<th>"\$i"</th>\n"};printf "<th></th>\n";printf "</tr>\n"}' $outputData >> ${html_file.extra_files_path}/outputClustering.html |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
211 #else |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
212 awk 'BEGIN{FS="\t"} NR>1{printf "<tr>\n";for(i=1;i<=NF;i++){printf "<th>"\$i"</th>\n"};printf "<th></th>\n";printf "</tr>\n"}' $outputData >> ${html_file.extra_files_path}/outputClustering.html |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
213 #end if |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
214 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
215 printf "</tbody>\n" >> ${html_file.extra_files_path}/outputClustering.html |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
216 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
217 printf "</table> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
218 </body> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
219 </html>" >> ${html_file.extra_files_path}/outputClustering.html |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
220 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
221 ]]> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
222 </configfile> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
223 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
224 <configfile name="scriptTransfer"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
225 <![CDATA[ |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
226 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
227 mkdir -p $html_file.extra_files_path |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
228 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
229 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
230 ##create HTML file for clustering output table |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
231 source $scriptTableToHtml |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
232 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
233 ##check outputClustering.html is here |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
234 if ! [ -e ${html_file.extra_files_path}/outputClustering.html ]; then |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
235 printf "[ERROR]outputClustering.html is missing.\n" >> $log; |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
236 exit 10 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
237 fi |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
238 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
239 #write header of html file |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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240 printf "<!DOCTYPE html>\n<html>\n<body>" > $html_file |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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241 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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242 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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243 ##first add reference of the clustering output table |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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244 printf "<h3>Clustering tabular</h3>\n" >> $html_file |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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changeset
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245 printf "<a href=\"outputClustering.html\">Clustering results</a>\n" >> $html_file |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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246 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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247 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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248 ##manage heatmap file |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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249 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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250 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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251 if [ -e ./plotLyDir/Heatmap.html ]; then |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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252 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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253 printf "<h3>Heatmap plot</h3>\n" >> $html_file |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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254 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
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255 ##modify HTML to point to the first script folder |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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256 sed -i "s/Heatmap_files/PlotLy_Heatmap_scripts/g" ./plotLyDir/Heatmap.html |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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257 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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258 ##copy HTML files in both folders |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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259 cp ./plotLyDir/Heatmap.html ${html_file.extra_files_path}/Heatmap.html |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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260 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
261 ##add HTML link |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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262 printf "<a href=\"Heatmap.html\">Heatmap</a>\n" >> $html_file |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
263 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
264 #if $advSection.imagePlotlyFormat=="svg": |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
265 ##before copying scripts folder modify them to replace png snapshot with svg (not proud of solution but seems to work) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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266 cd ./plotLyDir/Heatmap_files/plotly-main-*/ |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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267 awk '{gsub("\"png\"","\"svg\"",\$0);print \$0}' ./plotly-latest.min.js > ./plotly-latest.minTemp.js |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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268 awk '{gsub("Download plot as a png","Download plot as a svg",\$0);print \$0}' ./plotly-latest.minTemp.js > ./plotly-latest.min.js |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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269 rm ./plotly-latest.minTemp.js |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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270 cd ../../../ |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
271 #end if |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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272 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
273 #if $advSection.scaleSnapshot!="1.0": |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
274 ##before copying scripts folder modify scale parameter (not proud of solution but seems to work) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
275 cd ./plotLyDir/Heatmap_files/plotly-main-*/ |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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|
276 awk '{gsub("h=t\\.scale\\|\\|1","h=$advSection.scaleSnapshot",\$0);print \$0}' ./plotly-latest.min.js > ./plotly-latest.minTemp.js |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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277 mv -f ./plotly-latest.minTemp.js ./plotly-latest.min.js |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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278 cd ../../../ |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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|
279 #end if |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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|
280 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
281 ##now copy scripts folder |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
282 cp -r ./plotLyDir/Heatmap_files $html_file.extra_files_path |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
283 mv ${html_file.extra_files_path}/Heatmap_files ${html_file.extra_files_path}/PlotLy_Heatmap_scripts |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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|
284 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
285 else |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
286 printf "[ERROR]Heatmap.html is missing.\n" >> $log; |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
287 exit 10 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
288 fi |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
289 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
290 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
291 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
292 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
293 ##manage screePlot files |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
294 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
295 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
296 if [ -e ./plotLyDir/screePlot.html ]; then |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
297 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
298 printf "<h3>Scree plot</h3>\n" >> $html_file |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
299 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
300 ##modify HTML to point to the first script folder |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
301 sed -i "s/screePlot_files/PlotLy_screePlot_scripts/g" ./plotLyDir/screePlot.html |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
302 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
303 ##copy HTML files in both folders |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
304 cp ./plotLyDir/screePlot.html ${html_file.extra_files_path}/screePlot.html |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
305 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
306 ##add HTML link |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
307 printf "<a href=\"screePlot.html\">Scree plot</a>\n" >> $html_file |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
308 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
309 #if $advSection.imagePlotlyFormat=="svg": |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
310 ##before copying scripts folder modify them to replace png snapshot with svg (not proud of solution but seems to work) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
311 cd ./plotLyDir/screePlot_files/plotly-main-*/ |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
312 awk '{gsub("\"png\"","\"svg\"",\$0);print \$0}' ./plotly-latest.min.js > ./plotly-latest.minTemp.js |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
313 awk '{gsub("Download plot as a png","Download plot as a svg",\$0);print \$0}' ./plotly-latest.minTemp.js > ./plotly-latest.min.js |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
314 rm ./plotly-latest.minTemp.js |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
315 cd ../../../ |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
316 #end if |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
317 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
318 #if $advSection.scaleSnapshot!="1.0": |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
319 ##before copying scripts folder modify scale parameter (not proud of solution but seems to work) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
320 cd ./plotLyDir/screePlot_files/plotly-main-*/ |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
321 awk '{gsub("h=t\\.scale\\|\\|1","h=$advSection.scaleSnapshot",\$0);print \$0}' ./plotly-latest.min.js > ./plotly-latest.minTemp.js |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
322 mv -f ./plotly-latest.minTemp.js ./plotly-latest.min.js |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
323 cd ../../../ |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
324 #end if |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
325 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
326 ##now copy scripts folder |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
327 cp -r ./plotLyDir/screePlot_files $html_file.extra_files_path |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
328 mv ${html_file.extra_files_path}/screePlot_files ${html_file.extra_files_path}/PlotLy_screePlot_scripts |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
329 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
330 else |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
331 printf "[WARNING]screeplot.html is missing, probably due to limited number of genes.\n" >> $log; |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
332 fi |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
333 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
334 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
335 ##manage circular files |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
336 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
337 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
338 if [ -e ./plotDir/circularPlot.${advSection.imageFormat} ]; then |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
339 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
340 cp ./plotDir/circularPlot.${advSection.imageFormat} ${html_file.extra_files_path}/circularPlot.${advSection.imageFormat} |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
341 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
342 printf "<h3>Circular plot</h3>\n" >> $html_file |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
343 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
344 ##add HTML link |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
345 printf "<a href=\"circularPlot.${advSection.imageFormat}\">Circular plot</a>\n" >> $html_file |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
346 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
347 else |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
348 printf "[WARNING]circularPlot file is missing, probably due to limited number of genes.\n" >> $log; |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
349 fi |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
350 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
351 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
352 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
353 ##create footer of HTML file |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
354 printf "</body>\n</html>" >> $html_file |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
355 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
356 ]]> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
357 </configfile> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
358 </configfiles> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
359 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
360 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
361 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
362 <inputs> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
363 <param type="text" name="title" value="Heatmap_toPersonalize" label="Title for output"/> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
364 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
365 <conditional name="dataToCluster"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
366 <param name="dataToCluster_selector" type="select" label="Data to cluster"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
367 <option value="expression" selected="true">Expression data</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
368 <option value="foldChange">Differential expression analysis results</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
369 <option value="genericData">Generic data table</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
370 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
371 <when value="expression"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
372 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
373 <param type="data" name="expressionData" format="tabular" label="Normalized expression tabular file" multiple="false"/> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
374 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
375 <conditional name="reorder_sample"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
376 <param name="reordering_selector" type="select" label="Reorder samples"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
377 <option value="no" selected="true">No reordering</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
378 <option value="factorFile">Reorder sample based on a factors file</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
379 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
380 <when value="factorFile"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
381 <param type="data" name="factorFileData" format="tabular" label="Factors file" multiple="false" help="Be sure the conditions clusters number is set to 1 in advanced parameters."/> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
382 <param name="factorToUse" type="select" optional="false" multiple="true" label="Select factor(s) to use for reordering" refresh_on_change="true" dynamic_options="get_column_names(reorder_sample['factorFileData'].file_name,0)"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
383 <validator type="empty_field" message="You should specify at least one factor"></validator> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
384 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
385 </when> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
386 <when value="no"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
387 </when> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
388 </conditional> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
389 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
390 <conditional name="filtering_step"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
391 <param name="filtering_step_selector" type="select" label="Probes/genes filtering"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
392 <option value="no" selected="true">No filtering</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
393 <option value="input">Filter input probes/genes before clustering</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
394 <option value="output">Filter probes/genes after clustering (for tabular output)</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
395 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
396 <when value="input"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
397 <conditional name="select_filtering"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
398 <param name="filtering_stepBis_selector" type="select" label="Filter"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
399 <option value="diffExpParam" selected="true">Based on differential expression results (FC and p-val)</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
400 <option value="geneList">From list of genes</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
401 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
402 <when value="diffExpParam"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
403 <param type="data" name="differentialAnalysis" format="tabular" label="Differential analysis tabular file (as given by LIMMA diff.exp. tool)" optional="false" multiple="false"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
404 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
405 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
406 <param name="comparisonsToInclude" type="select" optional="false" multiple="true" label="Select comparisons to use for filtering" refresh_on_change="true" dynamic_options="get_column_names_filteredList(select_filtering['differentialAnalysis'].file_name,[0,1],5)"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
407 <validator type="empty_field" message="You should specify one factor"></validator> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
408 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
409 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
410 <param name="FCthreshold" type="float" value="2" label="Fold change threshold for input (both 'threshold' and '1/threshold' values will be used)" help="Minimum value is 1 (ie. all probes/genes are kept)" > |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
411 <validator type="in_range" min="1" exclude_min="false" message="Threshold should be greater than 1"/> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
412 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
413 <param name="pvalThreshold" type="float" value="0.05" label="FDR p-val threshold for input" help="When several comparisons are selected a conservative rule is applied (see details below)" > |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
414 <validator type="in_range" min="0" max="1" message="Threshold should be between 0 and 1"/> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
415 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
416 </when> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
417 <when value="geneList"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
418 <param type="data" format="tabular" name="geneListFile" label="List of genes to keep" multiple="false" help="Gene names should be the same as written in expression file"/> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
419 </when> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
420 </conditional> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
421 </when> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
422 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
423 <when value="output"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
424 <conditional name="select_filtering"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
425 <param name="filtering_stepBis_selector" type="select" label="Filter"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
426 <option value="diffExpParam" selected="true">Based on differential expression results (FC and p-val)</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
427 <option value="geneList">From list of genes</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
428 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
429 <when value="diffExpParam"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
430 <param type="data" name="differentialAnalysis" format="tabular" label="Differential analysis tabular file (as given by LIMMA diff.exp. tool)" optional="false" multiple="false"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
431 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
432 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
433 <param name="comparisonsToInclude" type="select" optional="false" multiple="true" label="Select comparisons to use for filtering" refresh_on_change="true" dynamic_options="get_column_names_filteredList(select_filtering['differentialAnalysis'].file_name,[0,1],5)"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
434 <validator type="empty_field" message="You should specify one factor"></validator> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
435 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
436 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
437 <param name="FCthreshold" type="float" value="2" label="Fold change threshold for output (both 'threshold' and '1/threshold' values will be used)" help="Minimum value is 1 (ie. all probes/genes are kept)" > |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
438 <validator type="in_range" min="1" exclude_min="false" message="Threshold should be greater than 1"/> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
439 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
440 <param name="pvalThreshold" type="float" value="0.05" label="FDR p-val threshold for output" help="When several comparisons are selected a conservative rule is applied (see details below)"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
441 <validator type="in_range" min="0" max="1" message="Threshold should be between 0 and 1"/> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
442 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
443 </when> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
444 <when value="geneList"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
445 <param type="data" format="tabular" name="geneListFile" label="List of genes to keep" multiple="false" help="Gene names should be the same as written in expression file"/> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
446 </when> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
447 </conditional> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
448 </when> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
449 <when value="no"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
450 </when> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
451 </conditional> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
452 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
453 </when> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
454 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
455 <when value="foldChange"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
456 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
457 <param type="data" name="differentialAnalysis" format="tabular" label="Differential analysis tabular file (as given by LIMMA diff.exp. tool)" optional="false" multiple="false"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
458 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
459 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
460 <param name="comparisonsToInclude" type="select" optional="false" multiple="true" label="Select comparisons to cluster" refresh_on_change="true" dynamic_options="get_column_names_filteredList(dataToCluster['differentialAnalysis'].file_name,[0,1],5)"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
461 <validator type="empty_field" message="You should specify one factor"></validator> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
462 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
463 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
464 <conditional name="filtering_step"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
465 <param name="filtering_step_selector" type="select" label="Probes/genes filtering"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
466 <option value="no" selected="true">No filtering</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
467 <option value="input">Filter input probes/genes before clustering</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
468 <option value="output">Filter probes/genes only in tabular output file</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
469 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
470 <when value="input"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
471 <conditional name="select_filtering"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
472 <param name="filtering_stepBis_selector" type="select" label="Filter"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
473 <option value="diffExpParam" selected="true">Based on differential expression results (FC and p-val)</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
474 <option value="geneList">From list of genes</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
475 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
476 <when value="diffExpParam"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
477 <param name="FCthreshold" type="float" value="2" label="Fold change threshold for input (both 'threshold' and '1/threshold' values will be used)" help="Minimum value is 1 (ie. all probes/genes are kept)" > |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
478 <validator type="in_range" min="1" exclude_min="false" message="FC threshold should be greater than 1"/> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
479 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
480 <param name="pvalThreshold" type="float" value="0.05" label="FDR p-val threshold for input" help="When several comparisons are selected a conservative rule is applied (see details below)" > |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
481 <validator type="in_range" min="0" max="1" message="Threshold should be between 0 and 1"/> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
482 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
483 </when> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
484 <when value="geneList"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
485 <param type="data" format="tabular" name="geneListFile" label="List of genes to keep" multiple="false" help="Gene names should be the same as written in diff. exp. analysis file"/> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
486 </when> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
487 </conditional> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
488 </when> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
489 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
490 <when value="output"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
491 <conditional name="select_filtering"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
492 <param name="filtering_stepBis_selector" type="select" label="Filter"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
493 <option value="diffExpParam" selected="true">Based on diff. exp. parameters (FC and p-val)</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
494 <option value="geneList">From list of genes</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
495 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
496 <when value="diffExpParam"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
497 <param name="FCthreshold" type="float" value="2" label="Fold change threshold for output (both 'threshold' and '1/threshold' values will be used)" help="Minimum value is 1 (ie. all probes/genes are kept)"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
498 <validator type="in_range" min="1" exclude_min="false" message="Threshold should be greater than 1"/> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
499 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
500 <param name="pvalThreshold" type="float" value="0.05" label="FDR p-val threshold for output" help="When several comparisons are selected a conservative rule is applied (see details below)"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
501 <validator type="in_range" min="0" max="1" message="Threshold should be between 0 and 1"/> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
502 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
503 </when> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
504 <when value="geneList"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
505 <param type="data" format="tabular" name="geneListFile" label="List of genes to keep" multiple="false" help="Gene names should be the same as written in diff. exp. analysis file"/> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
506 </when> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
507 </conditional> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
508 </when> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
509 <when value="no"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
510 </when> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
511 </conditional> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
512 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
513 </when> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
514 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
515 <when value="genericData"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
516 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
517 <param type="data" name="expressionData" format="tabular" label="Generic tabular file" multiple="false"/> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
518 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
519 <param name="columnToKeep" type="select" optional="false" multiple="true" label="Select column to cluster" refresh_on_change="true" dynamic_options="get_column_names_filteredList(dataToCluster['expressionData'].file_name,[0])"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
520 <validator type="empty_field" message="You should select at least on column"></validator> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
521 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
522 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
523 <conditional name="reorder_sample"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
524 <param name="reordering_selector" type="select" label="Reorder columns"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
525 <option value="no" selected="true">No reordering</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
526 <option value="factorFile">Reorder comlumns based on a factors file</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
527 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
528 <when value="factorFile"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
529 <param type="data" name="factorFileData" format="tabular" label="Factors file" multiple="false" help="Be sure the conditions clusters number is set to 1 in advanced parameters."/> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
530 <param name="factorToUse" type="select" optional="false" multiple="true" label="Select factor(s) to use for reordering" refresh_on_change="true" dynamic_options="get_column_names(reorder_sample['factorFileData'].file_name,0)"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
531 <validator type="empty_field" message="You should specify at least one factor"></validator> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
532 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
533 </when> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
534 <when value="no"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
535 </when> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
536 </conditional> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
537 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
538 <conditional name="filtering_step"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
539 <param name="filtering_step_selector" type="select" label="Probes/genes filtering"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
540 <option value="no" selected="true">No filtering</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
541 <option value="input">Filter input probes/genes before clustering</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
542 <option value="output">Filter probes/genes after clustering (for tabular output)</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
543 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
544 <when value="input"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
545 <conditional name="select_filtering"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
546 <param name="filtering_stepBis_selector" type="select" label="Filter"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
547 <option value="diffExpParam" selected="true">Based on tabular file content</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
548 <option value="geneList">From list of genes</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
549 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
550 <when value="diffExpParam"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
551 <param type="data" name="differentialAnalysis" format="tabular" label="Tabular file containing filtering information" optional="false" multiple="false"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
552 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
553 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
554 <param name="comparisonsToIncludeLow" type="select" optional="true" multiple="true" label="Select columns to consider for low filtering (keeping rows with higher value than a low threshold, ae. FC)" refresh_on_change="true" dynamic_options="get_column_names_filteredList(select_filtering['differentialAnalysis'].file_name,[0])"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
555 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
556 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
557 <param name="valThresholdLow" type="float" value="0.0" optional="true" label="Low filtering threshold" help="When several comparisons are selected a conservative rule is applied (see details below)"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
558 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
559 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
560 <param name="comparisonsToIncludeHigh" type="select" optional="true" multiple="true" label="Select columns to consider for high filtering (keeping rows with lower value than a high threshold, ae. p-value)" refresh_on_change="true" dynamic_options="get_column_names_filteredList(select_filtering['differentialAnalysis'].file_name,[0])"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
561 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
562 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
563 <param name="valThresholdHigh" type="float" value="0.0" optional="true" label="High filtering threshold" help="When several columns are selected a conservative rule is applied (see details below)" > |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
564 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
565 </when> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
566 <when value="geneList"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
567 <param type="data" format="tabular" name="geneListFile" label="List of genes to keep" multiple="false" help="Gene names should be the same as written in input file"/> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
568 </when> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
569 </conditional> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
570 </when> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
571 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
572 <when value="output"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
573 <conditional name="select_filtering"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
574 <param name="filtering_stepBis_selector" type="select" label="Filter"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
575 <option value="diffExpParam" selected="true">Based on tabular file content</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
576 <option value="geneList">From list of genes</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
577 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
578 <when value="diffExpParam"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
579 <param type="data" name="differentialAnalysis" format="tabular" label="Tabular file containing filtering information" optional="false" multiple="false"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
580 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
581 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
582 <param name="comparisonsToIncludeLow" type="select" optional="true" multiple="true" label="Select columns to consider for low filtering (keeping rows with higher value than a low threshold, ae. FC)" refresh_on_change="true" dynamic_options="get_column_names_filteredList(select_filtering['differentialAnalysis'].file_name,[0])"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
583 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
584 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
585 <param name="valThresholdLow" type="float" value="0.0" optional="true" label="Low filtering threshold" help="When several comparisons are selected a conservative rule is applied (see details below)"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
586 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
587 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
588 <param name="comparisonsToIncludeHigh" type="select" optional="true" multiple="true" label="Select columns to consider for high filtering (keeping rows with lower value than a high threshold, ae. p-value)" refresh_on_change="true" dynamic_options="get_column_names_filteredList(select_filtering['differentialAnalysis'].file_name,[0])"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
589 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
590 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
591 <param name="valThresholdHigh" type="float" value="0.0" optional="true" label="High filtering threshold" help="When several columns are selected a conservative rule is applied (see details below)" > |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
592 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
593 </when> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
594 <when value="geneList"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
595 <param type="data" format="tabular" name="geneListFile" label="List of genes to keep" multiple="false" help="Gene names should be the same as written in input file"/> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
596 </when> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
597 </conditional> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
598 </when> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
599 <when value="no"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
600 </when> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
601 </conditional> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
602 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
603 </when> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
604 </conditional> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
605 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
606 <section name="advSection" title="Advanced parameters" expanded="false"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
607 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
608 <param name="clusterNumber" type="integer" value="5" label="Requested number of genes clusters" help="Use scree plot to adjust the number of genes clusters"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
609 <validator type="in_range" min="2" message="Cluster number should be greater than 1"/> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
610 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
611 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
612 <param name="conditionClusterNumber" type="integer" value="1" label="Requested number of conditions clusters (1 = no clustering)"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
613 <validator type="in_range" min="1" message="Cluster number should be greater than 0"/> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
614 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
615 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
616 <param name="dataTransformation" type="select" label="Apply mathematical transformation to data before clustering"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
617 <option value="no" selected="true">No</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
618 <option value="log">Natural Logarithm</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
619 <option value="log2">Base 2 Logarithm</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
620 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
621 |
3 | 622 <param name="distanceMeasure" type="select" label="Distance measure used for clustering"> |
0
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
623 <option value="euclidean" selected="true">euclidean</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
624 <option value="manhattan">manhattan</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
625 <option value="binary">binary</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
626 <option value="pearson">pearson</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
627 <option value="spearman">spearman</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
628 <option value="kendall">kendall</option> |
3 | 629 <option value="absPearson">absolute pearson</option> |
630 <option value="absSpearman">absolute spearman</option> | |
631 <option value="absKendall">absolute kendall</option> | |
0
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
632 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
633 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
634 <param name="aggloMethod" type="select" label="Agglomeration method used for clustering" help="See documentation of 'hclust' R method for more information"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
635 <option value="complete">complete</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
636 <option value="median">median</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
637 <option value="centroid">centroid</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
638 <option value="average">average</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
639 <option value="single">single</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
640 <option value="mcquitty">mcquitty</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
641 <option value="ward.D">ward1</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
642 <option value="ward.D2" selected="true">ward2</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
643 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
644 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
645 <conditional name="conditionBarColor"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
646 <param name="conditionBarColor_selector" type="select" label="Add side bar color for samples/comparisons"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
647 <option value="no" selected="true">No</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
648 <option value="yes">Yes please</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
649 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
650 <when value="yes"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
651 <param type="data" name="factorFileDataBarPlot" format="tabular" label="Factors file" multiple="false" help="Available only for expression data clustering"/> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
652 <param name="factorToUse" type="select" optional="false" multiple="false" label="Select factor to use for coloring side bar" refresh_on_change="true" dynamic_options="get_column_names(conditionBarColor['factorFileDataBarPlot'].file_name,0)"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
653 <validator type="empty_field" message="You should specify one factor"></validator> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
654 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
655 <param name="sideBarPalette" type="select" label="Side bar color palette"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
656 <option value="Spectral" selected="true">Spectral</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
657 <option value="Set1">Set1</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
658 <option value="Set2">Set2</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
659 <option value="Set3">Set3</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
660 <option value="RdYlBu">RdYlBu</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
661 <option value="RdYlGn">RdYlGn</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
662 <option value="PiYG">PiYG</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
663 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
664 </when> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
665 <when value="no"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
666 </when> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
667 </conditional> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
668 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
669 <param name="maxSampleToPlot" type="integer" value="1000" label="Maximum gene number to plot"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
670 <validator type="in_range" min="2" message="The number should be greater than 1"/> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
671 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
672 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
673 <conditional name="select_color"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
674 <param type="boolean" name="specifyColors" checked="false" label="Personalized heatmap colors"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
675 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
676 <when value="true"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
677 <param name="featureMin_color" type="color" label="Min value color" value="#ff00ff"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
678 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
679 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
680 <param name="featureMedium_color" type="color" label="Medium value color" value="#4455ff"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
681 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
682 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
683 <param name="featureMax_color" type="color" label="Max value color" value="#00ffff"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
684 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
685 </when> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
686 <when value="false"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
687 </when> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
688 </conditional> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
689 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
690 <param type="select" name="imageFormat" display="radio" label="Output format"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
691 <option value="png">PNG format</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
692 <option value="pdf">PDF format</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
693 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
694 <param type="select" name="imagePlotlyFormat" display="radio" label="Html snapshot format"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
695 <option value="png">PNG format</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
696 <option value="svg">SVG format</option> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
697 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
698 <param name="scaleSnapshot" type="float" value="1.0" label="Scale html snapshots to increase resolution" help="Minimum value is 1.0 (default resolution)" > |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
699 <validator type="in_range" min="1.0" exclude_min="false" message="Scale should be greater than 1"/> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
700 </param> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
701 </section> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
702 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
703 </inputs> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
704 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
705 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
706 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
707 <outputs> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
708 <data format="tabular" name="outputData" label="${title}_ClusteringResults"/> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
709 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
710 <data format="html" name="html_file" label="${title}_HTML.html"/> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
711 <!-- |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
712 <collection name="outputHeatmap" label="${title}_Heatmap" type="list"> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
713 <discover_datasets pattern="(?P<designation>Heatmap.*)\.(?P<ext>[^\._]+)?" directory="plotDir" visible="false"/> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
714 <discover_datasets pattern="(?P<designation>screePlot.*)\.(?P<ext>[^\._]+)?" directory="plotDir" visible="false"/> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
715 <discover_datasets pattern="(?P<designation>circularPlot.*)\.(?P<ext>[^\._]+)?" directory="plotDir" visible="false"/> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
716 </collection> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
717 --> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
718 <data format="txt" name="log" label="${title}_Log" /> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
719 </outputs> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
720 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
721 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
722 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
723 <tests> |
1 | 724 <test maxseconds="3600"> |
725 <conditional name="dataToCluster"> | |
726 <param name="dataToCluster_selector" value="expression" /> | |
727 <param name="expressionData" value="./NormalizedData.tabular" /> | |
728 <conditional name="reorder_sample"> | |
729 <param name="reordering_selector" value="no" /> | |
730 </conditional> | |
731 <conditional name="filtering_step"> | |
732 <param name="filtering_step_selector" value="input" /> | |
733 <conditional name="select_filtering"> | |
734 <param name="filtering_stepBis_selector" value="diffExpParam" /> | |
735 <param name="differentialAnalysis" value="./DiffExprLimma/output/outputStat.csv" /> | |
736 <param name="comparisonsToInclude" value="TreatVsControl" /> | |
737 <param name="FCthreshold" value="2.0" /> | |
738 <param name="pvalThreshold" value="0.05" /> | |
739 </conditional> | |
740 </conditional> | |
741 </conditional> | |
742 <section name="advSection" > | |
743 <param name="clusterNumber" value="5" /> | |
744 <param name="conditionClusterNumber" value="3" /> | |
745 <param name="dataTransformation" value="no" /> | |
746 <param name="distanceMeasure" value="euclidean" /> | |
747 <param name="aggloMethod" value="ward.D2" /> | |
748 <conditional name="conditionBarColor"> | |
749 <param name="conditionBarColor_selector" value="yes" /> | |
750 <param name="factorFileDataBarPlot" value="./FactorFileGenerator/output/conditionsFile.csv" /> | |
751 <param name="factorToUse" value="Treatment" /> | |
752 <param name="sideBarPalette" value="Spectral" /> | |
753 </conditional> | |
754 <param name="maxSampleToPlot" value="1000" /> | |
755 <conditional name="select_color"> | |
756 <param name="specifyColors" value="false" /> | |
757 </conditional> | |
758 <param name="imageFormat" value="png" /> | |
759 <param name="imagePlotlyFormat" value="png" /> | |
760 <param name="scaleSnapshot" value="1.0" /> | |
761 </section> | |
762 <output name="outputData" file="./ExprHeatmapClustering/output/outputResults.csv" /> | |
763 <output name="html_file" file="./ExprHeatmapClustering/output/outputHTML.zip" decompress="true" /> | |
764 <output name="log" file="./ExprHeatmapClustering/output/outputLog.txt" compare="sim_size" delta_frac="0.10" /> | |
0
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
765 </test> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
766 </tests> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
767 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
768 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
769 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
770 <help> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
771 <![CDATA[ |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
772 **What it does** |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
773 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
774 Run hierarchical clustering on gene expression data or differential expression analysis (from arrays and RNA-seq studies) and diplay correponding heatmap. |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
775 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
776 ----- |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
777 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
778 **Parameters** |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
779 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
780 \- **Title** to personalize output file names (please avoid special characters). |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
781 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
782 \- **Data to cluster**, genes can be clustered based on : expression data, results from differential analysis tool or any tabular file content. |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
783 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
784 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
785 - **Expression data** with samples as columns and genes as rows (header row contains sample names and first column gene identifiers). |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
786 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
787 :: |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
788 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
789 Conditions 157_(HuGene-2_0-st).CEL 156_(HuGene-2_0-st).CEL 155_(HuGene-2_0-st).CEL 154_(HuGene-2_0-st).CEL |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
790 DDX11L2 4.500872 4.429759 4.780281 4.996189 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
791 MIR1302-2 3.415065 3.520472 3.471503 3.567988 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
792 OR4F5 3.737956 3.011586 3.424494 3.497545 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
793 VWA1 5.189621 5.129595 4.806793 5.227014 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
794 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
795 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
796 - **Differential expression analysis results** with contrasts statistics (p-val, FDR p-val, FC, log2(FC) and t-statistic) as columns and genes as rows (first and second rows contain comparison definition and first and second columns contain gene identifiers and functional informations). Please respect the GIANT-Differential Expression Analysis tool output format. |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
797 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
798 :: |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
799 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
800 LIMMA comparison WT*Treat WT*Treat WT*Treat WT*Treat WT*Treat |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
801 Gene Info p-val FDR.p-val FC log2(FC) t-stat |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
802 ARSD na 0.0057 0.41 0.8389 -0.2534 -5.175 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
803 TTTY10 na 1.6e-07 0.0074 0.6403 -0.6432 -6.122 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
804 MIR548AL na 0.072 0.2914 1.711 0.775 10.43 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
805 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
806 \- **Comparisons to cluster** when clustering is performed on differential results, log2(FC) values of selected comparisons will be used. |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
807 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
808 - **Generic tabular data** with samples as columns and genes as rows (header row contains sample names and first column gene identifiers). |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
809 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
810 :: |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
811 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
812 Conditions SampleA SampleB SampleC SampleD |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
813 DDX11L2 4.500872 4.429759 4.780281 4.996189 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
814 MIR1302-2 3.415065 3.520472 3.471503 3.567988 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
815 OR4F5 3.737956 3.011586 3.424494 3.497545 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
816 VWA1 5.189621 5.129595 4.806793 5.227014 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
817 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
818 \- **Samples to cluster** when clustering is performed on generic data, user have to select the columns to consider in clustering (first column, containing gene identifiers, will be automatically selected). |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
819 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
820 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
821 \- **Reorder samples** (only available for expression and generic data clustering). |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
822 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
823 - **Based on a factors file**, samples will be sorted in an alphabetical/numerical order for the selected factors. Names in the 1st column of the factors file have to match with the columns names of the data to cluster. |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
824 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
825 :: |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
826 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
827 Conditions Sex Treatment Reaction |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
828 154_(HuGene-2_0-st).CEL 1 TreatA Pos |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
829 156_(HuGene-2_0-st).CEL 0 NoTreat Pos |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
830 157_(HuGene-2_0-st).CEL 0 TreatB Neg |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
831 155_(HuGene-2_0-st).CEL 0 NoTreat Neg |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
832 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
833 \- **Genes filtering** can be applied before or after clustering step. |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
834 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
835 - **Filtering before clustering** allows to restrict clustering to differentially expressed genes using differential analysis results (available for expression data and differential results clustering) or any generic file (available for generic data clustering). As an alternative, a specific gene list file can be directly used for filtering. |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
836 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
837 - **Filtering after clustering** will have no effect on clustering or generated heatmaps. This filter is only applied to generated tabular files to keep differentially expressed genes (using differential analysis file or any generic file) or specific user defined genes (using gene list file). |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
838 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
839 \- **Filter approaches** : three filtering strategies can be applied before/after clustering depending on the nature of clustered data. These strategies use : differential analysis results (available for expression data and differential results clustering), generic file content (available for generic data clustering) or a gene list file (available for any input data). |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
840 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
841 - **From differential analysis results** to filter genes based on fold change and FDR p-val for selected comparisons. |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
842 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
843 \- **Differential expression results file** is requested only for expression data clustering. For differential results clustering, the same differential results file selected as "data to cluster" is used. (see "Data to cluster section" for requested format) |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
844 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
845 \- **Comparisons to use** are requested only for expression data clustering. For differential results clustering, the same comparisons selected in "data to cluster" section will be used. If several comparisons are selected, genes that satisfy both fold change and FDR p-val thresholds in at least one of these comparisons are kept. |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
846 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
847 \- **Fold change threshold** to use for filtering, genes with fold change >= threshold or fold change <= 1/threshold will be kept (set this threshold to 1 if you do not want to filter on fold change). |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
848 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
849 \- **FDR p-val threshold** to use for filtering, genes with FDR p-val <= threshold will be kept (set this threshold to 1 if you do not want to filter on FDR p-val). |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
850 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
851 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
852 - **From generic tabular file** to filter genes based on selected columns values. |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
853 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
854 \- **Generic tabular file** contains gene in the first column and various informations used for filtering in the following (same format as clustered generic tabular file). |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
855 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
856 \- **Low filtering columns** used to discard rows with values below a given threshold (typically for Fold Change filtering). If several columns are selected, rows satisfying threshold condition in at least one of these columns are kept. |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
857 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
858 \- **Low filtering threshold** below which the rows are discarded, the same threshold is applied for all selected columns. |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
859 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
860 \- **High filtering columns** used to discard rows with values above a given threshold (typically for p-value filtering). If several columns are selected, rows satisfying threshold condition in at least one of these columns are kept. |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
861 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
862 \- **High filtering threshold** above which the rows are discarded, the same threshold is applied for all selected columns. |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
863 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
864 - **From list of genes** to focus on pre-identified genes. |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
865 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
866 \- **Gene list file** with genes identifiers as one column file without header. |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
867 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
868 :: |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
869 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
870 DDX11L2 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
871 VWA1 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
872 TTTY10 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
873 ARSD |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
874 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
875 ----- |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
876 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
877 **Advanced parameters** |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
878 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
879 \- **Genes cluster number** used by hierarchical clustering (minimum is 2). See generated screeplot to adjust this number before re-running a clustering. |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
880 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
881 \- **Samples/comparisons clusters number** used by hierarchical clustering applied on columns/conditions. Set to 1 (ie. no clustering) if you need to conserve input columns order for visualization purposes. Columns clusters information is not included (yet) in output tabular file. |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
882 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
883 \- **Mathematical transformation** can be applied to clustered data before clustering and visualization. Data used for the filtering step are not modified by this transformation. |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
884 |
3 | 885 \- **Distance measure** used to cluster rows and columns. For "euclidean", "manhattan" and "binary" distances the 'dist' R function is directly called, for "pearson", "spearman" and "kendall" distances the '(1-correlation)/2' term is used as a classical distance, for "absPearson", "absSpearman" and "absKendall" the 'abs(1-correlation)'' term is used. |
0
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
886 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
887 \- **Agglomeration method** used to cluster rows and columns. |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
888 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
889 \- **Add side bar** to vizualize factor values for displayed columns/conditions, represented as a colored side bar in the heatmap. |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
890 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
891 - **Factor file** that contains factor information for coloring (same format as the factor file used for input data columns reordering). |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
892 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
893 - **Factor to use** to color side bar depending on its values for displayed columns/conditions. |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
894 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
895 - **Color palette used** for coloring factor values (see RColorBrewer R package documentation for more information on proposed palettes). |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
896 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
897 \- **Maximum gene number** : for readability and running time considerations only, number of displayed rows (genes) in heatmaps/circular plot can be limited. Clustering information in generated tabular file and scree plot are computed from a global clustering considering all genes (excepting those filtered out before clustering). Heatmap and circular plot are displayed for a random gene selection, to avoid such random selection we advise you to use input filtering option before clustering to have a gene number below this limit. |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
898 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
899 \- **Personalized heatmap colors** to build color gradient choosing start, middle and end colors. |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
900 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
901 \- **Output format** for circular plots only. |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
902 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
903 \- **Html snapshot format** for interactive plotly plots. |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
904 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
905 \- **Scale html snapshots** to increase resolution of snapshots taken from interactive plotly plots. |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
906 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
907 ----- |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
908 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
909 **Outputs** |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
910 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
911 \- **Tabular clustering file** containing cluster information for each gene satifying filtering steps. If expression or generic data was clustered, a two columns file is generated with gene identifiers and cluster numbers with possibly additional columns containing informations used for filtering. If differential results was clustered, a similar file is returned with an additional column containing cluster numbers and differential statistics coresponding to comparisons used for filtering. |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
912 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
913 \- **HTML file** to access interactive version of heatmap and screeplot through PlotLy html pages, circular plot image and tabulated clustering results. As a reminder, when the number of genes to display in heatmap/circular plot exceeds the maximum gene number parameter, a random sampling is performed for plotting efficiency. Thus, clustering displayed on heatmap/circular plot may slighlty differ from clustering information contained in tabular file as heatmap/circular plot clustering is done over a subset of genes whereas tabular file contains clustering results performed on all genes. |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
914 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
915 \- **LOG file** containing information about execution. Useful especially if tool execution fails. Please attach this log file in any bug report. |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
916 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
917 ]]> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
918 </help> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
919 <citations> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
920 <citation type="bibtex">@misc{vandel_jimmy_2018_1477870, author = {Vandel, J. and Gheeraert, C. and Eeckhoute, J. and Staels, B. and Lefebvre, P. and Dubois-Chevalier, J.}, title = {GIANT: Galaxy-based Interactive tools for ANalaysis of Transcriptomic data}, month = nov, year = 2018, doi = {10.5281/zenodo.1477870}, url = {https://doi.org/10.5281/zenodo.1477870} |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
921 }</citation> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
922 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
923 <citation type="bibtex">@article{, |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
924 author = {Galili, Tal and O'Callaghan, Alan and |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
925 Sidi, Jonathan and Sievert, Carson}, |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
926 title = {heatmaply: an R package for creating interactive cluster |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
927 heatmaps for online publishing}, |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
928 journal = {Bioinformatics}, |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
929 year = {2017}, |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
930 doi = {10.1093/bioinformatics/btx657}, |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
931 url = {http://dx.doi.org/10.1093/bioinformatics/btx657}, |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
932 eprint = |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
933 {https://academic.oup.com/bioinformatics/article-pdf/doi/10.1093/bioinformatics/btx657/21358327/btx657.pdf} |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
934 }</citation> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
935 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
936 <citation type="bibtex">@article{doi:10.1093/bioinformatics/btu393, |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
937 author = {Gu, Zuguang and Gu, Lei and Eils, Roland and Schlesner, Matthias and Brors, Benedikt}, |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
938 title = {circlize implements and enhances circular visualization in R }, |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
939 journal = {Bioinformatics}, |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
940 volume = {30}, |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
941 number = {19}, |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
942 pages = {2811-2812}, |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
943 year = {2014}, |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
944 doi = {10.1093/bioinformatics/btu393}, |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
945 URL = {http://dx.doi.org/10.1093/bioinformatics/btu393}, |
14045c80a222
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946 eprint = {/oup/backfile/content_public/journal/bioinformatics/30/19/10.1093_bioinformatics_btu393/2/btu393.pdf} |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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947 }</citation> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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948 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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949 <citation type="bibtex">@online{plotly, author = {Plotly Technologies Inc.}, title = {Collaborative data science}, publisher = {Plotly Technologies Inc.}, address = {Montreal, QC}, year = {2015}, url = {https://plot.ly} |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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950 }</citation> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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951 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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952 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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953 </citations> |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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954 |
14045c80a222
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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955 </tool> |