Mercurial > repos > vandelj > giant_limma_analysis

annotate galaxy/wrappers/DiffExprLimma.xml @ 1:9f2ddab68c9e draft

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"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
author vandelj
date Wed, 09 Sep 2020 10:28:02 +0000
parents f274c8d45613
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
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">
0
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2 <description>Use LIMMA to detect differentially expressed genes</description>
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3 <requirements>
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4 <requirement type="package" version="1.7.1">r-r.methodss3</requirement>
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5 <requirement type="package" version="3.36.5">bioconductor-limma</requirement>
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6 <requirement type="package" version="2.36.1">bioconductor-biomart</requirement>
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7 <requirement type="package" version="3.0.0">r-ggplot2</requirement>
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8 <requirement type="package" version="4.8.0">r-plotly</requirement>
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9 <requirement type="package" version="1.3.1">r-stringr</requirement>
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10 <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>
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11 <requirement type="package" version="1.4.32">r-statmod</requirement>
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12 </requirements>
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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-->
0
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15 <stdio>
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16 <regex match="Execution halted"
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17 source="both"
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18 level="fatal"
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19 description="Execution halted, please contact tool developer or administrators." />
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20 <regex match="Error in"
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21 source="both"
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22 level="fatal"
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23 description="An error occured during R execution, please contact tool developer." />
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24 <exit_code range="15" level="fatal" description="Error during formating scripts, see log file for more information." />
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25 <exit_code range="10" level="fatal" description="Missing file during html report, see log file for more information." />
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26 <exit_code range="1:9" level="fatal" description="Error in R execution, see log file for more information." />
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27 </stdio>
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28 <command> <![CDATA[
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29 bash $scriptPrepareTable;
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30 ret_code=\$?;
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31 if [ \$ret_code != 0 ]; then
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32 exit \$ret_code;
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33 fi;
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34
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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35 cp '$__tool_directory__/../../src/LIMMA_options.py' ./LIMMA_options.py;
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36 ##change for Planemo test
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37 ##cp '$__tool_directory__/src/LIMMA_options.py' ./LIMMA_options.py;
0
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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 $blockingSection.blockingConditional.addBlocking == "true":
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40 python -c 'import LIMMA_options;LIMMA_options.replaceNamesBlockInFiles("$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:
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42 python -c 'import LIMMA_options;LIMMA_options.replaceNamesInFiles("$inputSection.inputData","./factorTable.csv","./expressionRenamed.csv","./factorTableRenamed.csv","./dictionnaryRenamed.csv")';
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43 #end if
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44
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45
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46 if [ -f ./dictionnaryRenamed.csv ]; then
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47 printf "[INFO]Renaming is done\n" >> $log;
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48 Rscript '$__tool_directory__/../../src/LIMMAscriptV4.R' -i 'expressionRenamed.csv' -l '$log' -o '$outputData' -z '$outputDfData' -f 'pdf'
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49 ##change for Planemo test
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50 ##Rscript '$__tool_directory__/src/LIMMAscriptV4.R' -i 'expressionRenamed.csv' -l '$log' -o '$outputData' -z '$outputDfData' -f 'pdf'
0
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51 -a 'factorTableRenamed.csv' -s 'sumSquareFtest' -g 'dictionnaryRenamed.csv'
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52 #if $blockingSection.blockingConditional.addBlocking == "true":
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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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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 $contrastSection.interactionSelection.interactionContrast == "true":
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63 -c '$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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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 $plotSection.geneInformation.addGeneInfo:
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74 -x '$plotSection.geneInformation.organismID'
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75 -y '$plotSection.geneInformation.infoInRowType'
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76 #end if
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77 ;
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78 ret_code=\$?;
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79 if [ \$ret_code != 0 ]; then
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80 exit \$ret_code;
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81 else
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82 bash $scriptTransfer;
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83 ret_code=\$?;
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84 if [ \$ret_code != 0 ]; then
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85 exit \$ret_code;
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86 fi
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87 fi;
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diff changeset
88 else
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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:
diff changeset
90 exit 15;
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
91 fi;
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
92 printf "[INFO]End of tool script" >> $log;
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
93 ]]>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
94 </command>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
95
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
96
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
97
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
98 <configfiles>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
99 <configfile name="scriptPrepareTable">
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
100 <![CDATA[
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
101 awk -v fact="$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:
diff changeset
102
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
103 if [ ! -e ./factorTable.csv ]; then
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
104 printf "[ERROR]factorTable.csv is missing" >> $log;
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
105 exit 15
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
106 fi
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
107
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
108
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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 changeset
111
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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:
diff changeset
114 exit 15
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
115 fi
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
116
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
117 #end if
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
118 printf "[INFO]End of scriptPrepareTable\n" >> $log
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
119 ]]>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
120 </configfile>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
121
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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 changeset
124 printf "<!DOCTYPE html>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
125 <html>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
126 <head>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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 changeset
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 changeset
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 changeset
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 changeset
132 </script>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
133 <script type=\"text/javascript\" class=\"init\">
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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 changeset
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"
vandelj
parents:
diff changeset
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"
vandelj
parents:
diff changeset
163
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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"
vandelj
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
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"
vandelj
parents:
diff changeset
168
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
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"
vandelj
parents:
diff changeset
172
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
173 printf "</table>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
174 </body>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
175 </html>" >> ${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
176
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
177 ]]>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
178 </configfile>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
179
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
180 <configfile name="scriptTransfer">
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
181 <![CDATA[
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
182
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
183
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
184 ##for LIMMA output table
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
185
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
186 mkdir -p $html_file.extra_files_path
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
187
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
188 ##create HTML file for limma output table
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
189 source $scriptTableToHtml
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
190
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
191 ##check outputLIMMA.html is here
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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
parents:
diff changeset
193 printf "[ERROR]outputLIMMA.html is missing" >> $log;
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
194 exit 10
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
195 fi
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
196
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
197 ##create header of main HTML file
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
198 printf "<!DOCTYPE html>\n<html>\n<body>" > $html_file
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
199
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
200 ##first add reference of the LIMMA output table
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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:
diff changeset
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"
vandelj
parents:
diff changeset
203
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
204
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
205
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
206 #if $plotSection.histogramToPlot:
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
207
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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:
diff changeset
209
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
210 ##create folders in media
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
211 counter=1
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
212 for histogram in \$(ls ./plotLyDir/Histograms_*html)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
213 do
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
214 histogramShort=\${histogram%\.*}
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
215 histogramShort=\${histogramShort\#\#*/}
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
216
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
217 conditionName=\${histogram%\.*}
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
218 conditionName=\${conditionName\#\#*Histograms_}
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
219
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
220 echo \$conditionName > ./temporaryConditionName
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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:
diff changeset
222
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
223 ##modify HTML to point to plotLy folder
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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:
diff changeset
225
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
226 ##copy HTML files in both folders
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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:
diff changeset
228
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
229 ##add HTML link
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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:
diff changeset
231
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
232 if [ \$counter = 1 ]; then
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
233 #if $plotSection.imagePlotlyFormat=="svg":
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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:
diff changeset
235 cd ./plotLyDir/\${histogramShort}_files/plotly-main-*/
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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:
diff changeset
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:
diff changeset
238 rm ./plotly-latest.minTemp.js
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
239 cd ../../../
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
240 #end if
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
241
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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:
diff changeset
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:
diff changeset
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:
diff changeset
245 fi
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
246
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
247 ((counter++))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
248 done
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
249
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
250 if [ \$counter = 1 ]; then
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
251 printf "[ERROR]Histograms are missing" >> $log;
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
252 exit 10
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
253 fi
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
254
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
255 #end if
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
256
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
257
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
258 if [ -e ./plotLyDir/sumSquareFtest.html ]; then
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
259
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
260 printf "<h3>Source of variation</h3>\n" >> $html_file
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
261
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
262 ##modify HTML to point to the first script folder
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
263 sed -i "s/sumSquareFtest_files/PlotLy_sumSquareFtest_scripts/g" ./plotLyDir/sumSquareFtest.html
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
264
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
265 ##copy HTML files in both folders
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
266 cp ./plotLyDir/sumSquareFtest.html ${html_file.extra_files_path}/
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
267
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
268 ##add HTML link
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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"
vandelj
parents:
diff changeset
270
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
271 #if $plotSection.imagePlotlyFormat=="svg":
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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
parents:
diff changeset
273 cd ./plotLyDir/sumSquareFtest_files/plotly-main-*/
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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"
vandelj
parents:
diff changeset
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"
vandelj
parents:
diff changeset
276 rm ./plotly-latest.minTemp.js
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
277 cd ../../../
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
278 #end if
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
279
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
280 ##now copy scripts folder
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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"
vandelj
parents:
diff changeset
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"
vandelj
parents:
diff changeset
283
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
284 else
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
285 printf "[ERROR]sumSquareFtest plot is missing" >> $log;
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
286 exit 10
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
287 fi
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
288
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
289
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
290
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
291 #if $plotSection.volcanoToPlot:
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
292
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
293 printf "<h3>Volcanos</h3>\n" >> $html_file
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
294
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
295 ##create folders in media
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
296 counter=1
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
297 for volcano in \$(ls ./plotLyDir/Volcanos_*html)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
298 do
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
299 volcanoShort=\${volcano%\.*}
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
300 volcanoShort=\${volcanoShort\#\#*/}
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
301
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
302 conditionName=\${volcano%\.*}
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
303 conditionName=\${conditionName\#\#*Volcanos_}
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
304
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
305 echo \$conditionName > ./temporaryConditionName
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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"
vandelj
parents:
diff changeset
307
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
308
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
309 ##modify HTML to point to plotLy folder
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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"
vandelj
parents:
diff changeset
311
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
312 ##copy HTML files in both folders
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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:
diff changeset
314
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
315 ##add HTML link
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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"
vandelj
parents:
diff changeset
317
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
318 if [ \$counter = 1 ]; then
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
319
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
320 #if $plotSection.imagePlotlyFormat=="svg":
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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:
diff changeset
322 cd ./plotLyDir/\${volcanoShort}_files/plotly-main-*/
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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 changeset
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:
diff changeset
325 rm ./plotly-latest.minTemp.js
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
326 cd ../../../
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
327 #end if
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
328
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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:
diff changeset
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"
vandelj
parents:
diff changeset
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"
vandelj
parents:
diff changeset
332 fi
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
333
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
334 ((counter++))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
335 done
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
336
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
337 if [ \$counter = 1 ]; then
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
338 printf "[ERROR]Volcano plots are missing" >> $log;
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
339 exit 10
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
340 fi
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
341
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
342 #end if
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
343
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
344
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
345 ##create footer of HTML file
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
346 printf "</body>\n</html>" >> $html_file
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
347 ]]>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
348 </configfile>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
349 </configfiles>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
350
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
351
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
352
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
353 <inputs>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
354 <section name="inputSection" title="Input files" expanded="True">
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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"
vandelj
parents:
diff changeset
356
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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"
vandelj
parents:
diff changeset
358
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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
parents:
diff changeset
360 </param>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
361 </section>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
362
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
363 <section name="contrastSection" title="Contrast definition" expanded="True">
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
364
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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
parents:
diff changeset
366
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
367 <repeat name="contrastList" title="Contrast">
1
9f2ddab68c9e "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents: 0
diff changeset
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:
diff changeset
369
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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:
diff changeset
371 </param>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
372
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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 changeset
374 </param>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
375 </repeat>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
376
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
377 <conditional name="interactionSelection">
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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 changeset
379 <when value="true">
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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 changeset
381 </param>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
382 </when>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
383 <when value="false">
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
384 </when>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
385 </conditional>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
386
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
387 </section>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
388
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
389
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
390
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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 changeset
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 changeset
394 <when value="true">
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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:
diff changeset
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 changeset
397 </param>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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 changeset
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 changeset
407 </param>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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 changeset
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 changeset
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 changeset
414 </param>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
415
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
416 <conditional name="geneInformation">
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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
parents:
diff changeset
418 <when value="true">
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
419 <param name="organismID" label="Organism" type="select">
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
420 <options from_data_table="LimmaTool" >
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
421 <column name="name" index="1"/>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
422 <column name="value" index="0"/>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
423 <filter type="unique_value" column="0"/>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
424 </options>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
425 </param>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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 changeset
428 <column name="name" index="3"/>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
429 <column name="value" index="2"/>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
430 <filter type="param_value" ref="organismID" column="0"/>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
431 </options>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
432 </param>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
433 </when>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
434 <when value="false">
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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 changeset
437
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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 changeset
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 changeset
442 </section>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
443
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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 changeset
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 changeset
451 </inputs>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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 changeset
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 changeset
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="${inputSection.title}_HistogramsList" type="list">
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
463 <discover_datasets pattern="(?P&lt;designation&gt;Histograms[0-9]+)\.(?P&lt;ext&gt;[^\._]+)?" directory="plotDir" visible="false"/>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
464 <filter>plotSection['histogramToPlot']</filter>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
465 </collection>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
466
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
467 <collection name="outputVolcanosList" label="${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&lt;designation&gt;Volcanos\_.*)\.(?P&lt;ext&gt;[^\._]+)?" 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 changeset
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
diff changeset
500 </repeat>
9f2ddab68c9e "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents: 0
diff changeset
501 <conditional name="interactionSelection">
9f2ddab68c9e "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents: 0
diff changeset
502 <param name="interactionContrast" value="true" />
9f2ddab68c9e "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents: 0
diff changeset
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
diff changeset
504 </conditional>
9f2ddab68c9e "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents: 0
diff changeset
505 </section>
9f2ddab68c9e "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents: 0
diff changeset
506 <section name="blockingSection">
9f2ddab68c9e "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents: 0
diff changeset
507 <conditional name="blockingConditional">
9f2ddab68c9e "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents: 0
diff changeset
508 <param name="addBlocking" value="false"/>
9f2ddab68c9e "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents: 0
diff changeset
509 </conditional>
9f2ddab68c9e "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents: 0
diff changeset
510 </section>
9f2ddab68c9e "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents: 0
diff changeset
511 <section name="plotSection">
9f2ddab68c9e "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents: 0
diff changeset
512 <param name="cutoffTh" value="0.05"/>
9f2ddab68c9e "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents: 0
diff changeset
513 <param name="FCthreshold" value="1.2"/>
9f2ddab68c9e "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents: 0
diff changeset
514 <param name="histogramToPlot" value="true"/>
9f2ddab68c9e "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents: 0
diff changeset
515 <param name="volcanoToPlot" value="false"/>
9f2ddab68c9e "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents: 0
diff changeset
516 <conditional name="geneInformation">
9f2ddab68c9e "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents: 0
diff changeset
517 <param name="addGeneInfo" value="false"/>
9f2ddab68c9e "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents: 0
diff changeset
518 </conditional>
9f2ddab68c9e "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents: 0
diff changeset
519 <param name="imagePlotlyFormat" value="png"/>
9f2ddab68c9e "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents: 0
diff changeset
520 </section>
9f2ddab68c9e "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents: 0
diff changeset
521 <section name="advSection">
9f2ddab68c9e "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents: 0
diff changeset
522 <param name="confoundingPolicy" value="additive"/>
9f2ddab68c9e "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents: 0
diff changeset
523 </section>
9f2ddab68c9e "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents: 0
diff changeset
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 changeset
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 changeset
528 </test>
1
9f2ddab68c9e "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents: 0
diff changeset
529 </tests>
9f2ddab68c9e "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
vandelj
parents: 0
diff changeset
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 changeset
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 changeset
535 **What it does ?**
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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 changeset
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 changeset
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 changeset
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"
vandelj
parents:
diff changeset
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
parents:
diff changeset
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:
diff changeset
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"
vandelj
parents:
diff changeset
585
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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:
diff changeset
587
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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:
diff changeset
589
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
590 \- **Paired analysis / confounding factors**
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
591
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
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:
diff changeset
593
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
594 \- **Output section**
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
595
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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"
vandelj
parents:
diff changeset
597
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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"
vandelj
parents:
diff changeset
599
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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:
diff changeset
601
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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"
vandelj
parents:
diff changeset
603
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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"
vandelj
parents:
diff changeset
605
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
606 \- **Organism** coresponding to experimental data used.
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
607
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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"
vandelj
parents:
diff changeset
609
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
610 - **Html snapshot format** : for interactive plotly plots.
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
611
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
612 \- **Advanced Parameters**
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
613
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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"
vandelj
parents:
diff changeset
615
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
616 -----
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
617
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
618 **Outputs**
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
619
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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"
vandelj
parents:
diff changeset
621
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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"
vandelj
parents:
diff changeset
623
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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"
vandelj
parents:
diff changeset
625
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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"
vandelj
parents:
diff changeset
627
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
628 ]]> </help>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
629
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
630
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
631 <citations>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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"
vandelj
parents:
diff changeset
633 }</citation>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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634
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
635 <citation type="bibtex">@article{doi:10.1093/nar/gkv007,
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
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"
vandelj
parents:
diff changeset
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"
vandelj
parents:
diff changeset
638 journal = {Nucleic Acids Research},
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
639 volume = {43},
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
640 number = {7},
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
641 pages = {e47},
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
642 year = {2015},
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
643 doi = {10.1093/nar/gkv007},
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
644 URL = {http://dx.doi.org/10.1093/nar/gkv007},
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
645 eprint = {/oup/backfile/content_public/journal/nar/43/7/10.1093_nar_gkv007/2/gkv007.pdf}
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
646 }</citation>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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647
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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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"
vandelj
parents:
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649 }</citation>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
650 </citations>
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
651
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
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652 </tool>