+> $log;
+ exit 10
+fi
+
+##create header of main HTML file
+printf "\n\n" > $html_file
+
+##first add reference of the LIMMA output table
+printf "LIMMA statistics (p.val, FC)
\n" >> $html_file
+printf "LIMMA results\n" >> $html_file
+
+
+
+#if $plotSection.histogramToPlot:
+
+printf "P-val histograms
\n" >> $html_file
+
+##create folders in media
+counter=1
+for histogram in \$(ls ./plotLyDir/Histograms_*html)
+do
+histogramShort=\${histogram%\.*}
+histogramShort=\${histogramShort\#\#*/}
+
+conditionName=\${histogram%\.*}
+conditionName=\${conditionName\#\#*Histograms_}
+
+echo \$conditionName > ./temporaryConditionName
+conditionFormatedName=\$(awk 'BEGIN{FS="\t"} ARGIND==1{dico[\$1]=\$2} ARGIND==2{print dico[\$1]}' ./correspondanceFileNames.csv ./temporaryConditionName)
+
+##modify HTML to point to plotLy folder
+sed -i "s/\${histogramShort}_files/PlotLy_Histogram_scripts/g" \$histogram
+
+##copy HTML files in both folders
+cp \$histogram ${html_file.extra_files_path}/Histogram_\$conditionName.html
+
+##add HTML link
+printf "\nHistogram \$conditionFormatedName\n
\n" >> $html_file
+
+if [ \$counter = 1 ]; then
+#if $plotSection.imagePlotlyFormat=="svg":
+##before copying scripts folder modify them to replace png snapshot with svg (not proud of solution but seems to work)
+cd ./plotLyDir/\${histogramShort}_files/plotly-main-*/
+awk '{gsub("\"png\"","\"svg\"",\$0);print \$0}' ./plotly-latest.min.js > ./plotly-latest.minTemp.js
+awk '{gsub("Download plot as a png","Download plot as a svg",\$0);print \$0}' ./plotly-latest.minTemp.js > ./plotly-latest.min.js
+rm ./plotly-latest.minTemp.js
+cd ../../../
+#end if
+
+##now copy only scripts folder for the first histogram and rename
+cp -r ./plotLyDir/\${histogramShort}_files $html_file.extra_files_path
+mv ${html_file.extra_files_path}/\${histogramShort}_files ${html_file.extra_files_path}/PlotLy_Histogram_scripts
+fi
+
+((counter++))
+done
+
+if [ \$counter = 1 ]; then
+ printf "[ERROR]Histograms are missing" >> $log;
+ exit 10
+fi
+
+#end if
+
+
+if [ -e ./plotLyDir/sumSquareFtest.html ]; then
+
+printf "Source of variation
\n" >> $html_file
+
+##modify HTML to point to the first script folder
+sed -i "s/sumSquareFtest_files/PlotLy_sumSquareFtest_scripts/g" ./plotLyDir/sumSquareFtest.html
+
+##copy HTML files in both folders
+cp ./plotLyDir/sumSquareFtest.html ${html_file.extra_files_path}/
+
+##add HTML link
+printf "F-ratio barplot\n" >> $html_file
+
+#if $plotSection.imagePlotlyFormat=="svg":
+##before copying scripts folder modify them to replace png snapshot with svg (not proud of solution but seems to work)
+cd ./plotLyDir/sumSquareFtest_files/plotly-main-*/
+awk '{gsub("\"png\"","\"svg\"",\$0);print \$0}' ./plotly-latest.min.js > ./plotly-latest.minTemp.js
+awk '{gsub("Download plot as a png","Download plot as a svg",\$0);print \$0}' ./plotly-latest.minTemp.js > ./plotly-latest.min.js
+rm ./plotly-latest.minTemp.js
+cd ../../../
+#end if
+
+##now copy scripts folder
+cp -r ./plotLyDir/sumSquareFtest_files $html_file.extra_files_path
+mv ${html_file.extra_files_path}/sumSquareFtest_files ${html_file.extra_files_path}/PlotLy_sumSquareFtest_scripts
+
+else
+ printf "[ERROR]sumSquareFtest plot is missing" >> $log;
+ exit 10
+fi
+
+
+
+#if $plotSection.volcanoToPlot:
+
+printf "Volcanos
\n" >> $html_file
+
+##create folders in media
+counter=1
+for volcano in \$(ls ./plotLyDir/Volcanos_*html)
+do
+volcanoShort=\${volcano%\.*}
+volcanoShort=\${volcanoShort\#\#*/}
+
+conditionName=\${volcano%\.*}
+conditionName=\${conditionName\#\#*Volcanos_}
+
+echo \$conditionName > ./temporaryConditionName
+conditionFormatedName=\$(awk 'BEGIN{FS="\t"} ARGIND==1{dico[\$1]=\$2} ARGIND==2{print dico[\$1]}' ./correspondanceFileNames.csv ./temporaryConditionName)
+
+
+##modify HTML to point to plotLy folder
+sed -i "s/\${volcanoShort}_files/PlotLy_Volcano_scripts/g" \$volcano
+
+##copy HTML files in both folders
+cp \$volcano ${html_file.extra_files_path}/Volcano_\$conditionName.html
+
+##add HTML link
+printf "\nVolcano \$conditionFormatedName\n
\n" >> $html_file
+
+if [ \$counter = 1 ]; then
+
+#if $plotSection.imagePlotlyFormat=="svg":
+##before copying scripts folder modify them to replace png snapshot with svg (not proud of solution but seems to work)
+cd ./plotLyDir/\${volcanoShort}_files/plotly-main-*/
+awk '{gsub("\"png\"","\"svg\"",\$0);print \$0}' ./plotly-latest.min.js > ./plotly-latest.minTemp.js
+awk '{gsub("Download plot as a png","Download plot as a svg",\$0);print \$0}' ./plotly-latest.minTemp.js > ./plotly-latest.min.js
+rm ./plotly-latest.minTemp.js
+cd ../../../
+#end if
+
+##now copy only scripts folder for the first volcano and rename
+cp -r ./plotLyDir/\${volcanoShort}_files $html_file.extra_files_path
+mv ${html_file.extra_files_path}/\${volcanoShort}_files ${html_file.extra_files_path}/PlotLy_Volcano_scripts
+fi
+
+((counter++))
+done
+
+if [ \$counter = 1 ]; then
+ printf "[ERROR]Volcano plots are missing" >> $log;
+ exit 10
+fi
+
+#end if
+
+
+##create footer of HTML file
+printf "\n" >> $html_file
+]]>
+
+