Mercurial > repos > vandelj > giant_limma_analysis
annotate galaxy/wrappers/DiffExprLimma.xml @ 2:3dc31e252649 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 08:52:08 +0000 |
parents | 9f2ddab68c9e |
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9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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1 <tool name="GIANT-Differential Expression with LIMMA" id="giant_limma_analysis" version="0.3.9"> |
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"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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2 <description>Use LIMMA to detect differentially expressed genes</description> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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3 <requirements> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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4 <requirement type="package" version="1.7.1">r-r.methodss3</requirement> |
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"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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5 <requirement type="package" version="3.36.5">bioconductor-limma</requirement> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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6 <requirement type="package" version="2.36.1">bioconductor-biomart</requirement> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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7 <requirement type="package" version="3.0.0">r-ggplot2</requirement> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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8 <requirement type="package" version="4.8.0">r-plotly</requirement> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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9 <requirement type="package" version="1.3.1">r-stringr</requirement> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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10 <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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11 <requirement type="package" version="1.4.32">r-statmod</requirement> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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12 </requirements> |
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"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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13 <code file="../../src/LIMMA_options.py"/> |
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9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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14 <!--<code file="./src/LIMMA_options.py"/> change for Planemo test--> |
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"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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15 <stdio> |
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"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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16 <regex match="Execution halted" |
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"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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17 source="both" |
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"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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18 level="fatal" |
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"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." /> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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20 <regex match="Error in" |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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21 source="both" |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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22 level="fatal" |
f274c8d45613
"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." /> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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24 <exit_code range="15" level="fatal" description="Error during formating scripts, see log file for more information." /> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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25 <exit_code range="10" level="fatal" description="Missing file during html report, see log file for more information." /> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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26 <exit_code range="1:9" level="fatal" description="Error in R execution, see log file for more information." /> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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27 </stdio> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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28 <command> <![CDATA[ |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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29 bash $scriptPrepareTable; |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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30 ret_code=\$?; |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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31 if [ \$ret_code != 0 ]; then |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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32 exit \$ret_code; |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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33 fi; |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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34 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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35 cp '$__tool_directory__/../../src/LIMMA_options.py' ./LIMMA_options.py; |
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"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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36 ##change for Planemo test |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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37 ##cp '$__tool_directory__/src/LIMMA_options.py' ./LIMMA_options.py; |
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"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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38 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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39 #if $blockingSection.blockingConditional.addBlocking == "true": |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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40 python -c 'import LIMMA_options;LIMMA_options.replaceNamesBlockInFiles("$inputSection.inputData","./factorTable.csv","./blockingTable.csv","./expressionRenamed.csv","./factorTableRenamed.csv","./blockingTableRenamed.csv","./dictionnaryRenamed.csv")'; |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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41 #else: |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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42 python -c 'import LIMMA_options;LIMMA_options.replaceNamesInFiles("$inputSection.inputData","./factorTable.csv","./expressionRenamed.csv","./factorTableRenamed.csv","./dictionnaryRenamed.csv")'; |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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43 #end if |
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44 |
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45 |
f274c8d45613
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46 if [ -f ./dictionnaryRenamed.csv ]; then |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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47 printf "[INFO]Renaming is done\n" >> $log; |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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48 Rscript '$__tool_directory__/../../src/LIMMAscriptV4.R' -i 'expressionRenamed.csv' -l '$log' -o '$outputData' -z '$outputDfData' -f 'pdf' |
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"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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49 ##change for Planemo test |
9f2ddab68c9e
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50 ##Rscript '$__tool_directory__/src/LIMMAscriptV4.R' -i 'expressionRenamed.csv' -l '$log' -o '$outputData' -z '$outputDfData' -f 'pdf' |
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51 -a 'factorTableRenamed.csv' -s 'sumSquareFtest' -g 'dictionnaryRenamed.csv' |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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52 #if $blockingSection.blockingConditional.addBlocking == "true": |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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53 -b 'blockingTableRenamed.csv' |
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54 -u $advSection.confoundingPolicy |
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55 #end if |
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56 -r '${contrastSection.factorSelection}' |
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"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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57 #for $i, $s in enumerate( $contrastSection.contrastList ) |
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58 -p '${s.groupName}' |
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59 -m '${s.firstGroupToCompare}' |
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60 -n '${s.secondGroupToCompare}' |
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61 #end for |
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62 #if $contrastSection.interactionSelection.interactionContrast == "true": |
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"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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63 -c '$contrastSection.interactionSelection.controlSelection' |
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64 #end if |
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65 -t $plotSection.cutoffTh |
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66 -d $plotSection.FCthreshold |
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"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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67 #if $plotSection.histogramToPlot: |
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68 -h 'Histograms' |
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69 #end if |
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70 #if $plotSection.volcanoToPlot: |
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71 -v 'Volcanos' |
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72 #end if |
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73 #if $plotSection.geneInformation.addGeneInfo: |
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"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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74 -x '$plotSection.geneInformation.organismID' |
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"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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75 -y '$plotSection.geneInformation.infoInRowType' |
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76 #end if |
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77 ; |
f274c8d45613
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78 ret_code=\$?; |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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79 if [ \$ret_code != 0 ]; then |
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80 exit \$ret_code; |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
81 else |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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82 bash $scriptTransfer; |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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83 ret_code=\$?; |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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84 if [ \$ret_code != 0 ]; then |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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85 exit \$ret_code; |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
86 fi |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
87 fi; |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
88 else |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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89 printf "[ERROR]Error during renaming, factor information file should not contain special characters '*',':',',','|' in factor names and possible values\n" >> $log; |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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90 exit 15; |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
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91 fi; |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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92 printf "[INFO]End of tool script" >> $log; |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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93 ]]> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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94 </command> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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95 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
96 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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97 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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98 <configfiles> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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99 <configfile name="scriptPrepareTable"> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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100 <![CDATA[ |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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101 awk -v fact="$contrastSection.factorSelection" 'BEGIN{OFS="";ORS="";FS="\t";split(fact,tab,",");for(i in tab)dico[tab[i]]=1} FNR==1{for(i=2;i<=NF;i++){if(\$i in dico)colToSelect[i]=1}} {print \$1;for(i in colToSelect)print "\t"\$i ; print "\n"}' $inputSection.conditionInformation > ./factorTable.csv; |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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102 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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103 if [ ! -e ./factorTable.csv ]; then |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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104 printf "[ERROR]factorTable.csv is missing" >> $log; |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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105 exit 15 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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106 fi |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
107 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
108 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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109 #if $blockingSection.blockingConditional.addBlocking == "true": |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
110 awk -v fact="$blockingSection.blockingConditional.blockingToInclude" ' BEGIN{OFS="";ORS="";FS="\t";split(fact, facto, ",");for(i in facto)factors[facto[i]]=1} FNR==1{for(i=2;i<=NF;i++)if(\$i in factors)dico[i]=1} {print $1;for(factorID in dico)print "\t"\$factorID; print "\n"}' $inputSection.conditionInformation > ./blockingTable.csv; |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
111 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
112 if [ ! -e ./blockingTable.csv ]; then |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
113 printf "[ERROR]blockingTable.csv is missing" >> $log; |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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114 exit 15 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
115 fi |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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|
116 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
117 #end if |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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|
118 printf "[INFO]End of scriptPrepareTable\n" >> $log |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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|
119 ]]> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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|
120 </configfile> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
121 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
122 <configfile name="scriptTableToHtml"> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
123 <![CDATA[ |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
124 printf "<!DOCTYPE html> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
125 <html> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
126 <head> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
127 <meta http-equiv=\"Content-type\" content=\"text/html; charset=utf-8\"> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
128 <link rel=\"stylesheet\" type=\"text/css\" href=\"https://cdn.datatables.net/1.10.16/css/jquery.dataTables.min.css\"> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
129 <script type=\"text/javascript\" language=\"javascript\" src=\"https://code.jquery.com/jquery-1.12.4.js\"> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
130 </script> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
131 <script type=\"text/javascript\" language=\"javascript\" src=\"https://cdn.datatables.net/1.10.16/js/jquery.dataTables.min.js\"> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
132 </script> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
133 <script type=\"text/javascript\" class=\"init\"> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
134 \\$(document).ready(function() { |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
135 \\$(\'\#example\').DataTable( { |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
136 \"columnDefs\": [ { |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
137 \"visible\": false, |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
138 \"targets\": -1 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
139 } ] |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
140 } ); |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
141 } ); |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
142 </script> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
143 </head> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
144 <body style=\"background-color:white;\"> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
145 <table id=\"example\" class=\"display\" cellspacing=\"0\"> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
146 " > ${html_file.extra_files_path}/outputLIMMA.html |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
147 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
148 printf "<colgroup>\n" >> ${html_file.extra_files_path}/outputLIMMA.html |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
149 printf "<col span=\"2\" style=\"background-color:rgb(224,235,235)\">\n" >> ${html_file.extra_files_path}/outputLIMMA.html |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
150 awk 'BEGIN{odd=1;FS="\t"} NR==1{for(i=3;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}/outputLIMMA.html |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
151 printf "</colgroup>\n" >> ${html_file.extra_files_path}/outputLIMMA.html |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
152 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
153 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
154 printf "<thead>\n<tr>\n" >> ${html_file.extra_files_path}/outputLIMMA.html |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
155 printf "<th rowspan=\"2\">Gene</th>\n" >> ${html_file.extra_files_path}/outputLIMMA.html |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
156 printf "<th rowspan=\"2\">Info</th>\n" >> ${html_file.extra_files_path}/outputLIMMA.html |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
157 awk 'BEGIN{FS="\t"} NR==1{for(i=3;i<=NF;i=i+5)printf "<th colspan=\"5\">"\$i"</th>\n"}' $outputData >> ${html_file.extra_files_path}/outputLIMMA.html |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
158 printf "<th></th>\n" >> ${html_file.extra_files_path}/outputLIMMA.html |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
159 printf "</tr>\n<tr>\n" >> ${html_file.extra_files_path}/outputLIMMA.html |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
160 awk 'BEGIN{FS="\t"} NR==2{for(i=3;i<=NF;i++)printf "<th>"\$i"</th>\n"}' $outputData >> ${html_file.extra_files_path}/outputLIMMA.html |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
161 printf "<th></th>\n" >> ${html_file.extra_files_path}/outputLIMMA.html |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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162 printf "</tr>\n</thead>\n" >> ${html_file.extra_files_path}/outputLIMMA.html |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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163 |
f274c8d45613
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164 printf "<tfoot>\n<tr>\n" >> ${html_file.extra_files_path}/outputLIMMA.html |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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165 awk 'BEGIN{FS="\t"} NR==2{for(i=1;i<=NF;i++)printf "<th>"\$i"</th>\n"}' $outputData >> ${html_file.extra_files_path}/outputLIMMA.html |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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166 printf "<th></th>\n" >> ${html_file.extra_files_path}/outputLIMMA.html |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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167 printf "</tr>\n</tfoot>\n">> ${html_file.extra_files_path}/outputLIMMA.html |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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168 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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169 printf "<tbody>\n" >> ${html_file.extra_files_path}/outputLIMMA.html |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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170 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}/outputLIMMA.html |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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171 printf "</tbody>\n" >> ${html_file.extra_files_path}/outputLIMMA.html |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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172 |
f274c8d45613
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vandelj
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173 printf "</table> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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174 </body> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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175 </html>" >> ${html_file.extra_files_path}/outputLIMMA.html |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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176 |
f274c8d45613
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177 ]]> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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178 </configfile> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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179 |
f274c8d45613
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180 <configfile name="scriptTransfer"> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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181 <![CDATA[ |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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182 |
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183 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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184 ##for LIMMA output table |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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185 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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186 mkdir -p $html_file.extra_files_path |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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187 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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188 ##create HTML file for limma output table |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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189 source $scriptTableToHtml |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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190 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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191 ##check outputLIMMA.html is here |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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192 if ! [ -e ${html_file.extra_files_path}/outputLIMMA.html ]; then |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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193 printf "[ERROR]outputLIMMA.html is missing" >> $log; |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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194 exit 10 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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195 fi |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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196 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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197 ##create header of main HTML file |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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198 printf "<!DOCTYPE html>\n<html>\n<body>" > $html_file |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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199 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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200 ##first add reference of the LIMMA output table |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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201 printf "<h3>LIMMA statistics (p.val, FC)</h3>\n" >> $html_file |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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202 printf "<a href=\"outputLIMMA.html\">LIMMA results</a>\n" >> $html_file |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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203 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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204 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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205 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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206 #if $plotSection.histogramToPlot: |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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207 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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208 printf "<h3>P-val histograms</h3>\n" >> $html_file |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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209 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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210 ##create folders in media |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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211 counter=1 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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212 for histogram in \$(ls ./plotLyDir/Histograms_*html) |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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213 do |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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214 histogramShort=\${histogram%\.*} |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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215 histogramShort=\${histogramShort\#\#*/} |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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216 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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217 conditionName=\${histogram%\.*} |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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218 conditionName=\${conditionName\#\#*Histograms_} |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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219 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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220 echo \$conditionName > ./temporaryConditionName |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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221 conditionFormatedName=\$(awk 'BEGIN{FS="\t"} ARGIND==1{dico[\$1]=\$2} ARGIND==2{print dico[\$1]}' ./correspondanceFileNames.csv ./temporaryConditionName) |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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222 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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223 ##modify HTML to point to plotLy folder |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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224 sed -i "s/\${histogramShort}_files/PlotLy_Histogram_scripts/g" \$histogram |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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225 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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226 ##copy HTML files in both folders |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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227 cp \$histogram ${html_file.extra_files_path}/Histogram_\$conditionName.html |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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228 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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229 ##add HTML link |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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230 printf "<p>\n<a href=\"Histogram_\$conditionName.html\">Histogram \$conditionFormatedName</a>\n</p>\n" >> $html_file |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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231 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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232 if [ \$counter = 1 ]; then |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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233 #if $plotSection.imagePlotlyFormat=="svg": |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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234 ##before copying scripts folder modify them to replace png snapshot with svg (not proud of solution but seems to work) |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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235 cd ./plotLyDir/\${histogramShort}_files/plotly-main-*/ |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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236 awk '{gsub("\"png\"","\"svg\"",\$0);print \$0}' ./plotly-latest.min.js > ./plotly-latest.minTemp.js |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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237 awk '{gsub("Download plot as a png","Download plot as a svg",\$0);print \$0}' ./plotly-latest.minTemp.js > ./plotly-latest.min.js |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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238 rm ./plotly-latest.minTemp.js |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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239 cd ../../../ |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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240 #end if |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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241 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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242 ##now copy only scripts folder for the first histogram and rename |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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243 cp -r ./plotLyDir/\${histogramShort}_files $html_file.extra_files_path |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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244 mv ${html_file.extra_files_path}/\${histogramShort}_files ${html_file.extra_files_path}/PlotLy_Histogram_scripts |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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|
245 fi |
f274c8d45613
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246 |
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247 ((counter++)) |
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248 done |
f274c8d45613
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249 |
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250 if [ \$counter = 1 ]; then |
f274c8d45613
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251 printf "[ERROR]Histograms are missing" >> $log; |
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252 exit 10 |
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253 fi |
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254 |
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255 #end if |
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256 |
f274c8d45613
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257 |
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258 if [ -e ./plotLyDir/sumSquareFtest.html ]; then |
f274c8d45613
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259 |
f274c8d45613
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260 printf "<h3>Source of variation</h3>\n" >> $html_file |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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261 |
f274c8d45613
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262 ##modify HTML to point to the first script folder |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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263 sed -i "s/sumSquareFtest_files/PlotLy_sumSquareFtest_scripts/g" ./plotLyDir/sumSquareFtest.html |
f274c8d45613
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264 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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265 ##copy HTML files in both folders |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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266 cp ./plotLyDir/sumSquareFtest.html ${html_file.extra_files_path}/ |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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267 |
f274c8d45613
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268 ##add HTML link |
f274c8d45613
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269 printf "<a href=\"sumSquareFtest.html\">F-ratio barplot</a>\n" >> $html_file |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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270 |
f274c8d45613
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271 #if $plotSection.imagePlotlyFormat=="svg": |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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272 ##before copying scripts folder modify them to replace png snapshot with svg (not proud of solution but seems to work) |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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273 cd ./plotLyDir/sumSquareFtest_files/plotly-main-*/ |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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274 awk '{gsub("\"png\"","\"svg\"",\$0);print \$0}' ./plotly-latest.min.js > ./plotly-latest.minTemp.js |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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275 awk '{gsub("Download plot as a png","Download plot as a svg",\$0);print \$0}' ./plotly-latest.minTemp.js > ./plotly-latest.min.js |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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276 rm ./plotly-latest.minTemp.js |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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277 cd ../../../ |
f274c8d45613
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278 #end if |
f274c8d45613
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279 |
f274c8d45613
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280 ##now copy scripts folder |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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281 cp -r ./plotLyDir/sumSquareFtest_files $html_file.extra_files_path |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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282 mv ${html_file.extra_files_path}/sumSquareFtest_files ${html_file.extra_files_path}/PlotLy_sumSquareFtest_scripts |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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283 |
f274c8d45613
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284 else |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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285 printf "[ERROR]sumSquareFtest plot is missing" >> $log; |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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286 exit 10 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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287 fi |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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288 |
f274c8d45613
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289 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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290 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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291 #if $plotSection.volcanoToPlot: |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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292 |
f274c8d45613
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293 printf "<h3>Volcanos</h3>\n" >> $html_file |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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294 |
f274c8d45613
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vandelj
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295 ##create folders in media |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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296 counter=1 |
f274c8d45613
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297 for volcano in \$(ls ./plotLyDir/Volcanos_*html) |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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298 do |
f274c8d45613
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299 volcanoShort=\${volcano%\.*} |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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300 volcanoShort=\${volcanoShort\#\#*/} |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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301 |
f274c8d45613
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302 conditionName=\${volcano%\.*} |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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303 conditionName=\${conditionName\#\#*Volcanos_} |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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parents:
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304 |
f274c8d45613
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vandelj
parents:
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305 echo \$conditionName > ./temporaryConditionName |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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306 conditionFormatedName=\$(awk 'BEGIN{FS="\t"} ARGIND==1{dico[\$1]=\$2} ARGIND==2{print dico[\$1]}' ./correspondanceFileNames.csv ./temporaryConditionName) |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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307 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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308 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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309 ##modify HTML to point to plotLy folder |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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310 sed -i "s/\${volcanoShort}_files/PlotLy_Volcano_scripts/g" \$volcano |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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parents:
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311 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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312 ##copy HTML files in both folders |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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313 cp \$volcano ${html_file.extra_files_path}/Volcano_\$conditionName.html |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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314 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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315 ##add HTML link |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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316 printf "<p>\n<a href=\"Volcano_\$conditionName.html\">Volcano \$conditionFormatedName</a>\n</p>\n" >> $html_file |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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317 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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|
318 if [ \$counter = 1 ]; then |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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319 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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|
320 #if $plotSection.imagePlotlyFormat=="svg": |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
321 ##before copying scripts folder modify them to replace png snapshot with svg (not proud of solution but seems to work) |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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322 cd ./plotLyDir/\${volcanoShort}_files/plotly-main-*/ |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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|
323 awk '{gsub("\"png\"","\"svg\"",\$0);print \$0}' ./plotly-latest.min.js > ./plotly-latest.minTemp.js |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
324 awk '{gsub("Download plot as a png","Download plot as a svg",\$0);print \$0}' ./plotly-latest.minTemp.js > ./plotly-latest.min.js |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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|
325 rm ./plotly-latest.minTemp.js |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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326 cd ../../../ |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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327 #end if |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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328 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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|
329 ##now copy only scripts folder for the first volcano and rename |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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330 cp -r ./plotLyDir/\${volcanoShort}_files $html_file.extra_files_path |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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331 mv ${html_file.extra_files_path}/\${volcanoShort}_files ${html_file.extra_files_path}/PlotLy_Volcano_scripts |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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332 fi |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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|
333 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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334 ((counter++)) |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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335 done |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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336 |
f274c8d45613
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337 if [ \$counter = 1 ]; then |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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338 printf "[ERROR]Volcano plots are missing" >> $log; |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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339 exit 10 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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340 fi |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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341 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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342 #end if |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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343 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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344 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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345 ##create footer of HTML file |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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346 printf "</body>\n</html>" >> $html_file |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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347 ]]> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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348 </configfile> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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349 </configfiles> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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350 |
f274c8d45613
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351 |
f274c8d45613
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352 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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353 <inputs> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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354 <section name="inputSection" title="Input files" expanded="True"> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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355 <param type="text" name="title" value="LIMMA_toPersonalize" label="Title for output"/> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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356 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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357 <param type="data" name="inputData" format="tabular" label="Normalized expression tabular file" optional="false" multiple="false" help="Expression data have to be log2 transformed."/> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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358 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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359 <param type="data" name="conditionInformation" format="tabular" label="Factor information tabular file" optional="false" multiple="false"> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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360 </param> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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361 </section> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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362 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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|
363 <section name="contrastSection" title="Contrast definition" expanded="True"> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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364 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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365 <param name="factorSelection" type="select" label="Select all factors to include in the global model (excepting confounding factors)" refresh_on_change="true" display="checkboxes" optional="false" multiple="true" dynamic_options="get_column_names(inputSection['conditionInformation'].file_name)" help="Confounding factors are selected in the coresponding section below." /> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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366 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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367 <repeat name="contrastList" title="Contrast"> |
1
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
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0
diff
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368 <param name="groupName" type="text" value="" label="Contrast name"/> |
0
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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369 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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370 <param name="firstGroupToCompare" type="select" label="Select factor levels of 1st group" display="checkboxes" multiple="true" refresh_on_change="true" dynamic_options="get_row_names_allInteractions(inputSection['conditionInformation'].file_name,factorSelection)"> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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|
371 </param> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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|
372 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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|
373 <param name="secondGroupToCompare" type="select" label="Select factor levels of 2nd group" display="checkboxes" multiple="true" refresh_on_change="true" dynamic_options="get_row_names_allInteractions(inputSection['conditionInformation'].file_name,factorSelection)"> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
374 </param> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
375 </repeat> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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|
376 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
377 <conditional name="interactionSelection"> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
378 <param name="interactionContrast" type="boolean" label="Add interaction contrasts" checked="false" help="If you have selected two factors at least."/> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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379 <when value="true"> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
380 <param name="controlSelection" type="select" label="Select one control level for each factor (and only one)" display="checkboxes" multiple="true" refresh_on_change="true" dynamic_options="get_allrow_names(inputSection['conditionInformation'].file_name,factorSelection)"> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
381 </param> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
382 </when> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
383 <when value="false"> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
384 </when> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
385 </conditional> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
386 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
387 </section> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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|
388 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
389 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
390 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
391 <section name="blockingSection" title="Paired analysis/confounding factor" expanded="True"> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
392 <conditional name="blockingConditional"> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
393 <param name="addBlocking" type="boolean" label="Add confounding factors" checked="false" help="To control factors producing spurious association as batch effects or to analyze paired data"/> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
394 <when value="true"> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
395 <param name="blockingToInclude" type="select" label="Select confounding factors" multiple="true" dynamic_options="get_column_names(inputSection['conditionInformation'].file_name)"> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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|
396 <validator type="empty_field" message="You should select at least one factor"></validator> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
397 </param> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
398 </when> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
399 <when value="false"> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
400 </when> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
401 </conditional> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
402 </section> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
403 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
404 <section name="plotSection" title="Output section" expanded="True"> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
405 <param name="cutoffTh" type="float" value="0.05" label="Output FDR p-val threshold" > |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
406 <validator type="in_range" min="0" max="1" message="Threshold should be between 0 and 1"/> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
407 </param> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
408 <param name="FCthreshold" type="float" value="2" label="Output Fold Change threshold (both 'log2(threshold)' and 'log2(1/threshold)' values will be used)" > |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
409 <validator type="in_range" min="1" exclude_min="false" message="Threshold should be greater or equal to 1"/> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
410 </param> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
411 <param type="boolean" name="histogramToPlot" checked="true" label="Plot histograms" help="Plot nominal p-val distribution for each comparison."> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
412 </param> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
413 <param type="boolean" name="volcanoToPlot" checked="true" label="Plot volcanos" help="Plot volcano for each comparison."> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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414 </param> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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415 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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416 <conditional name="geneInformation"> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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417 <param name="addGeneInfo" type="boolean" label="Add gene/probe information" checked="false"/> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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418 <when value="true"> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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419 <param name="organismID" label="Organism" type="select"> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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420 <options from_data_table="LimmaTool" > |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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421 <column name="name" index="1"/> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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422 <column name="value" index="0"/> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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423 <filter type="unique_value" column="0"/> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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424 </options> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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425 </param> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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426 <param name="infoInRowType" label="Nature of row names" type="select"> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
427 <options from_data_table="LimmaTool" > |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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428 <column name="name" index="3"/> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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429 <column name="value" index="2"/> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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430 <filter type="param_value" ref="organismID" column="0"/> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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431 </options> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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|
432 </param> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
433 </when> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
434 <when value="false"> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
435 </when> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
436 </conditional> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
437 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
438 <param type="select" name="imagePlotlyFormat" display="radio" label="Html snapshot format"> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
439 <option value="png">PNG format</option> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
440 <option value="svg">SVG format</option> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
441 </param> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
442 </section> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
443 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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|
444 <section name="advSection" title="Advanced parameters" expanded="False"> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
445 <param type="select" name="confoundingPolicy" display="radio" label="Confounding effect policy" help="DO NOT modify this parameter unless you know what you are doing!"> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
446 <option value="additive">As an additive factor (default)</option> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
447 <option value="correlated">As a correlation constraint</option> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
448 </param> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
449 </section> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
450 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
451 </inputs> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
452 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
453 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
454 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
455 <outputs> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
456 <data format="tabular" name="outputData" label="${inputSection.title}_LIMMAstatistics"/> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
457 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
458 <data format="tabular" name="outputDfData" label="${inputSection.title}_LIMMAdetailed"/> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
459 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
460 <data format="html" name="html_file" label="${inputSection.title}_HTML.html"/> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
461 <!-- |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
462 <collection name="outputHistogramsList" label="${inputSection.title}_HistogramsList" type="list"> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
463 <discover_datasets pattern="(?P<designation>Histograms[0-9]+)\.(?P<ext>[^\._]+)?" directory="plotDir" visible="false"/> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
464 <filter>plotSection['histogramToPlot']</filter> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
465 </collection> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
466 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
467 <collection name="outputVolcanosList" label="${inputSection.title}_VolcanosList" type="list"> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
468 <discover_datasets pattern="(?P<designation>Volcanos\_.*)\.(?P<ext>[^\._]+)?" directory="plotDir" visible="false"/> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
469 <filter>plotSection['volcanoToPlot']</filter> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
470 </collection> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
471 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
472 <data name="fRatioOutput" format="png" label="${inputSection.title}_F-ratio"> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
473 <change_format> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
474 <when input="plotSection['imageFormat']" value="pdf" format="pdf" /> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
475 </change_format> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
476 </data> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
477 --> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
478 <data format="txt" name="log" label="${inputSection.title}_Log" /> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
479 </outputs> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
480 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
481 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
482 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
483 <tests> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
484 <test maxseconds="3600"> |
1
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
diff
changeset
|
485 <section name="inputSection"> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
diff
changeset
|
486 <param name="inputData" value="./NormalizedData.tabular" /> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
diff
changeset
|
487 <param name="conditionInformation" value="./FactorFileGenerator/output/conditionsFile.csv" /> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
diff
changeset
|
488 </section> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
diff
changeset
|
489 <section name="contrastSection"> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
diff
changeset
|
490 <param name="factorSelection" value="Strain,Treatment" /> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
diff
changeset
|
491 <repeat name="contrastList" > |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
diff
changeset
|
492 <param name="groupName" value="TreatVsControl" /> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
diff
changeset
|
493 <param name="firstGroupToCompare" value="WT*Treat,KO*Treat" /> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
diff
changeset
|
494 <param name="secondGroupToCompare" value="WT*Control,KO*Control" /> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
diff
changeset
|
495 </repeat> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
diff
changeset
|
496 <repeat name="contrastList" > |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
diff
changeset
|
497 <param name="groupName" value="WTvsKO" /> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
diff
changeset
|
498 <param name="firstGroupToCompare" value="WT*Control,WT*Treat" /> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
diff
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|
499 <param name="secondGroupToCompare" value="KO*Control,KO*Treat" /> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
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|
500 </repeat> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
diff
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|
501 <conditional name="interactionSelection"> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
diff
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502 <param name="interactionContrast" value="true" /> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
diff
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|
503 <param name="controlSelection" value="Strain:WT,Treatment:Control" /> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
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504 </conditional> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
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|
505 </section> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
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|
506 <section name="blockingSection"> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
diff
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|
507 <conditional name="blockingConditional"> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
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508 <param name="addBlocking" value="false"/> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
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509 </conditional> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
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|
510 </section> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
diff
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|
511 <section name="plotSection"> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
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512 <param name="cutoffTh" value="0.05"/> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
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513 <param name="FCthreshold" value="1.2"/> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
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|
514 <param name="histogramToPlot" value="true"/> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
diff
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|
515 <param name="volcanoToPlot" value="false"/> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
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516 <conditional name="geneInformation"> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
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|
517 <param name="addGeneInfo" value="false"/> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
diff
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|
518 </conditional> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
diff
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|
519 <param name="imagePlotlyFormat" value="png"/> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
diff
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|
520 </section> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
diff
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|
521 <section name="advSection"> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
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522 <param name="confoundingPolicy" value="additive"/> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
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|
523 </section> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
diff
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|
524 <output name="outputData" file="./DiffExprLimma/output/outputStat.csv" /> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
diff
changeset
|
525 <output name="outputDfData" file="./DiffExprLimma/output/outputStatDetailed.csv" /> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
diff
changeset
|
526 <output name="html_file" file="./DiffExprLimma/output/outputHTML.zip" decompress="true" /> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
diff
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|
527 <output name="log" file="./DiffExprLimma/output/outputLog.txt" compare="sim_size" delta_frac="0.10" /> |
0
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
528 </test> |
1
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
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|
529 </tests> |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
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|
530 |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
diff
changeset
|
531 |
9f2ddab68c9e
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents:
0
diff
changeset
|
532 |
0
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
533 <help> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
534 <![CDATA[ |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
535 **What it does ?** |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
536 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
537 This tool compute differential expressions for a set of genes. |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
538 This tool use the LIMMA function from R package limma. (only adapted for arrays data) |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
539 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
540 ----- |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
541 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
542 **Parameters** |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
543 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
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|
544 \- **Input Files** |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
545 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
546 - **Title** to personalize output file names (please avoid special characters). |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
547 - **Normalized expression tabular file** with samples as columns and genes as rows (header contains sample names and first column gene identifiers). WARNING Expression data have to be already log2 transformed. |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
548 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
549 :: |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
550 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
551 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 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
552 DDX11L2 4.500872 4.429759 4.780281 4.996189 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
553 MIR1302-2 3.415065 3.520472 3.471503 3.567988 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
554 OR4F5 3.737956 3.011586 3.424494 3.497545 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
555 VWA1 5.189621 5.129595 4.806793 5.227014 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
556 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
557 - **Factor information tabular file** with factors as columns and samples as rows (header contains factor names and first column sample names). |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
558 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
559 :: |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
560 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
561 Conditions Sex Treatment Reaction |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
562 138_(HuGene-2_0-st).CEL 1 TreatA Pos |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
563 148_(HuGene-2_0-st).CEL 0 NoTreat Pos |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
564 139_(HuGene-2_0-st).CEL 0 TreatB Neg |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
565 149_(HuGene-2_0-st).CEL 0 NoTreat Neg |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
566 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
567 \- **Contrast definition** |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
568 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
569 - **Select all factors to include in the global model** : automatically extracted from factor information file. Confounding factors or paired-analysis information (replicates number,dates...) should not be selected here, but in specific section below. |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
570 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
571 - **Contrast** |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
572 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
573 \- **Contrast Name** displayed in output file |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
574 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
575 \- **Select factor levels of 1st group** : the contrast will be computed with the formula "1st group versus 2nd group" so "1st group - 2nd group". |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
576 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
577 \- **Select factor levels of 2nd group** : see below for some examples |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
578 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
579 :: |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
580 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
|
581 Nb Factors List of Factors Factor levels Expected Contrast Select as 1st gr Select as 2nd gr |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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582 1 Strain WT, KO KO vs WT KO WT |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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583 2 Strain, Treatment WT, KO, NoTreat,TreatA TreatA vs NoTreat in WT mice TreatA*WT NoTreat*WT |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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584 2 Strain, Treatment WT, KO, NoTreat,TreatA Treatment effect on Strain dependent genes See results of interaction contrast |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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585 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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586 - **Add interaction contrasts** : to compute automatically each level of interaction |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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587 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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588 \- **Control groups** for each factor, select its level used as control. Thus interaction contrasts will be computed for each factor level regarding to this control level. |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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589 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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590 \- **Paired analysis / confounding factors** |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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parents:
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591 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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parents:
diff
changeset
|
592 - **Add confounding factors** which can define "blocks" in the data different from those selected previously in the global model. Typically confounding factors are linked to batch effect (dates...) or paired-analysis situation (replicates number...). |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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593 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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594 \- **Output section** |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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595 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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|
596 - **Output FDR p-val threshold**, only genes with FDR <= this threshold (in at least one of defined contrasts) are kept in tabular result file and displayed dynamically in volcano plot. |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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597 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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598 - **Plot histograms** of unadjusted p-values for each defined contrast. |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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|
599 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff
changeset
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600 - **Plot volcanos** for each defined contrast with specified FDR p-val and FC thresholds. |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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changeset
|
601 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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602 - **Output Fold Change threshold** only genes with absolute FC >= this threshold (in at least one of defined contrast) are kept in tabular result file and displayed dynamically in volcano plot (both 'log2(threshold)' and 'log2(1/threshold)' values will be used). |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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603 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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604 - **Add gene/probe information** : if yes, add description of genes to the result tab. |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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605 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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606 \- **Organism** coresponding to experimental data used. |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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607 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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608 \- **Nature of row names** coresponding to experimental data used in input. |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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609 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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610 - **Html snapshot format** : for interactive plotly plots. |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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611 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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612 \- **Advanced Parameters** |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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613 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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614 - **Confounding effect policy** : DO NOT modify this parameter unless you know what you are doing! See Limma documentation for more information. |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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615 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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616 ----- |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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617 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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618 **Outputs** |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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619 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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parents:
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620 - **LIMMA statistic tabular** is the main result file for LIMMA, represented as tab delimited matrix. First and second columns contain respectively gene names and information grabbed from BiomaRt R package. Then, the following colums contain differential expression statistics (p.val, FDR, FC, log2FC and t-statistic) for defined contrasts, for each gene (in rows). |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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621 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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parents:
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622 - **LIMMA detailed tabular** contains specific statistics required for additional analysis tools (eg SMAGEXP tool), represented as tab delimited matrix where each colum contains specific statistics (residual, eBayes prior and total degree of freedom) between groups for each gene (in rows). |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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623 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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624 - **HTML file** to access interactive version of histograms, F-Ratio barplots and volcanos through PlotLy html pages and tabulated differential results. |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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625 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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626 - **LOG file** for job log. If you see errors, please attached this in the bug report |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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627 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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628 ]]> </help> |
f274c8d45613
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629 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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630 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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631 <citations> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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632 <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} |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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633 }</citation> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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634 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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635 <citation type="bibtex">@article{doi:10.1093/nar/gkv007, |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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636 author = {Ritchie, Matthew E. and Phipson, Belinda and Wu, Di and Hu, Yifang and Law, Charity W. and Shi, Wei and Smyth, Gordon K.}, |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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637 title = {limma powers differential expression analyses for RNA-sequencing and microarray studies}, |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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638 journal = {Nucleic Acids Research}, |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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639 volume = {43}, |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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640 number = {7}, |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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641 pages = {e47}, |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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642 year = {2015}, |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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643 doi = {10.1093/nar/gkv007}, |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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644 URL = {http://dx.doi.org/10.1093/nar/gkv007}, |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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645 eprint = {/oup/backfile/content_public/journal/nar/43/7/10.1093_nar_gkv007/2/gkv007.pdf} |
f274c8d45613
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646 }</citation> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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647 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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648 <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} |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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649 }</citation> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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650 </citations> |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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651 |
f274c8d45613
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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652 </tool> |