Mercurial > repos > vandelj > giant_volcano_plot
diff galaxy/wrappers/VolcanoPlotTool.xml @ 0:c9a38c1eadf1 draft
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
| author | vandelj |
|---|---|
| date | Fri, 26 Jun 2020 09:45:41 -0400 |
| parents | |
| children | 75505421bcf3 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy/wrappers/VolcanoPlotTool.xml Fri Jun 26 09:45:41 2020 -0400 @@ -0,0 +1,417 @@ +<tool name="GIANT-Plot volcanos" id="giant_volcano_plot" version="0.3.3"> + <description>Plot volcano from tabular file</description> + <requirements> + <requirement type="package" version="1.7.1">r-r.methodss3</requirement> + <requirement type="package" version="2.36.1">bioconductor-biomart</requirement> + <requirement type="package" version="3.0.0">r-ggplot2</requirement> + <requirement type="package" version="4.8.0">r-plotly</requirement> + <requirement type="package" version="1.3.1">r-stringr</requirement> + </requirements> + <code file="../../src/General_functions.py"/> + <stdio> + <regex match="Execution halted" + source="both" + level="fatal" + description="Execution halted, please contact tool developer or administrators." /> + <regex match="Error in" + source="both" + level="fatal" + description="An error occured during R execution, please contact tool developer." /> + <exit_code range="15" level="fatal" description="Error during input file formatting step, see log file for more information." /> + <exit_code range="10" level="fatal" description="Missing file during html report, see log file for more information." /> + <exit_code range="1:9" level="fatal" description="Error in R execution, see log file for more information." /> + </stdio> + <command> <![CDATA[ + #import imp + #set $runIdentifier=str($outputData).rsplit("/")[-1].rsplit(".")[0] + #set $general_functions=$imp.load_source('General_functions', $__tool_directory__+'/../../src/General_functions.py') + #set $ret_code=$general_functions.selectSubSetTable($inputSection['inputData'].file_name,$inputSection['headerNumber'].value,[0],$volcanoSection['volcanoList'],$__new_file_path__+'/'+$__user_id__+'_'+$runIdentifier+'_statisticsFormated.csv',$log.file_name) + + if [ $ret_code != 0 ]; then + printf "[ERROR]Error during formated statistics file generation\n" >> $log; + exit $ret_code; + fi; + + mv ${__new_file_path__}/${__user_id__}_${runIdentifier}_statisticsFormated.csv ./statisticsFormated.csv; + + #for $i, $s in enumerate( $volcanoSection.volcanoList ) + #if $s.volcanoName!='': + printf "\$(($i+1))\t${s.volcanoName}\n" >> ./correspondanceVolcanoNames.csv; + #else: + printf "\$(($i+1))\t\$(($i+1))_${s.pvalColumn}\n" >> ./correspondanceVolcanoNames.csv; + #end if + #end for + + + Rscript '$__tool_directory__/../../src/VolcanoPlotsScript.R' -i 'statisticsFormated.csv' -l '$log' -o '$outputData' -f 'pdf' + #for $i, $s in enumerate( $volcanoSection.volcanoList ) + -n '${s.volcanoName}' + -p '${s.pvalColumn}' + -c '${s.fcColumn}' + -m '${s.fdrColumn}' + #end for + -d '$plotSection.fcKind' + -s $plotSection.FDRthreshold + -e $plotSection.FCthreshold + #if $plotSection.geneInformation.addGeneInfo: + -x '$plotSection.geneInformation.organismID' + -y '$plotSection.geneInformation.infoInRowType' + #end if + ; + ret_code=\$?; + if [ \$ret_code != 0 ]; then + exit \$ret_code; + else + bash $scriptTransfer; + ret_code=\$?; + if [ \$ret_code != 0 ]; then + exit \$ret_code; + fi + fi; + + printf "[INFO]End of tool script" >> $log; + ]]> + </command> + + + <configfiles> + <configfile name="scriptTableToHtml"> +<![CDATA[ +printf "<!DOCTYPE html> +<html> +<head> +<meta http-equiv=\"Content-type\" content=\"text/html; charset=utf-8\"> +<link rel=\"stylesheet\" type=\"text/css\" href=\"https://cdn.datatables.net/1.10.16/css/jquery.dataTables.min.css\"> +<script type=\"text/javascript\" language=\"javascript\" src=\"https://code.jquery.com/jquery-1.12.4.js\"> +</script> +<script type=\"text/javascript\" language=\"javascript\" src=\"https://cdn.datatables.net/1.10.16/js/jquery.dataTables.min.js\"> +</script> +<script type=\"text/javascript\" class=\"init\"> +\\$(document).ready(function() { + \\$(\'\#example\').DataTable( { + \"columnDefs\": [ { + \"visible\": false, + \"targets\": -1 + } ] + } ); +} ); +</script> +</head> +<body style=\"background-color:white;\"> +<table id=\"example\" class=\"display\" cellspacing=\"0\"> +" > ${html_file.extra_files_path}/output.html + +printf "<colgroup>\n" >> ${html_file.extra_files_path}/output.html +printf "<col span=\"2\" style=\"background-color:rgb(224,235,235)\">\n" >> ${html_file.extra_files_path}/output.html +awk 'BEGIN{odd=1;FS="\t"} NR==1{for(i=3;i<=NF;i=i+4){if(odd==1){odd=0;printf "<col span=\"4\" style=\"background-color:rgb(224,238,255)\">\n"}else{odd=1;printf "<col span=\"4\" style=\"background-color:rgb(255,221,224)\">\n"}}}' $outputData >> ${html_file.extra_files_path}/output.html +printf "</colgroup>\n" >> ${html_file.extra_files_path}/output.html + + +printf "<thead>\n<tr>\n" >> ${html_file.extra_files_path}/output.html +printf "<th rowspan=\"2\">Gene</th>\n" >> ${html_file.extra_files_path}/output.html +printf "<th rowspan=\"2\">Info</th>\n" >> ${html_file.extra_files_path}/output.html +awk 'BEGIN{FS="\t"} NR==1{for(i=3;i<=NF;i=i+4)printf "<th colspan=\"4\">"\$i"</th>\n"}' $outputData >> ${html_file.extra_files_path}/output.html +printf "<th></th>\n" >> ${html_file.extra_files_path}/output.html +printf "</tr>\n<tr>\n" >> ${html_file.extra_files_path}/output.html +awk 'BEGIN{FS="\t"} NR==2{for(i=3;i<=NF;i++)printf "<th>"\$i"</th>\n"}' $outputData >> ${html_file.extra_files_path}/output.html +printf "<th></th>\n" >> ${html_file.extra_files_path}/output.html +printf "</tr>\n</thead>\n" >> ${html_file.extra_files_path}/output.html + +printf "<tfoot>\n<tr>\n" >> ${html_file.extra_files_path}/output.html +awk 'BEGIN{FS="\t"} NR==2{for(i=1;i<=NF;i++)printf "<th>"\$i"</th>\n"}' $outputData >> ${html_file.extra_files_path}/output.html +printf "<th></th>\n" >> ${html_file.extra_files_path}/output.html +printf "</tr>\n</tfoot>\n">> ${html_file.extra_files_path}/output.html + +printf "<tbody>\n" >> ${html_file.extra_files_path}/output.html +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}/output.html +printf "</tbody>\n" >> ${html_file.extra_files_path}/output.html + +printf "</table> +</body> +</html>" >> ${html_file.extra_files_path}/output.html + +]]> + </configfile> + + <configfile name="scriptTransfer"> +<![CDATA[ + + +##for output table + +mkdir -p $html_file.extra_files_path + +##create HTML file for limma output table +source $scriptTableToHtml + +##check output.html is here +if ! [ -e ${html_file.extra_files_path}/output.html ]; then + printf "[ERROR]output.html is missing" >> $log; + exit 10 +fi + +##create header of main HTML file +printf "<!DOCTYPE html>\n<html>\n<body>" > $html_file + +##first add reference of the output table +printf "<h3>Statistics (p.val, adjusted p.val, FC, log2FC)</h3>\n" >> $html_file +printf "<a href=\"output.html\">Access to statistics</a>\n" >> $html_file + + + +printf "<h3>Volcanos</h3>\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_} + +##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 + +##get user name of Volcano +echo \$conditionName > ./temporaryConditionName +conditionFormatedName=\$(awk 'BEGIN{FS="\t"} ARGIND==1{dico[\$1]=\$2} ARGIND==2{print dico[\$1]}' ./correspondanceVolcanoNames.csv ./temporaryConditionName) + +##add HTML link +printf "<p>\n<a href=\"Volcano_\$conditionName.html\">Volcano \$conditionFormatedName</a>\n</p>\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 + + + +##create footer of HTML file +printf "</body>\n</html>" >> $html_file +]]> + </configfile> + </configfiles> + + + + <inputs> + <section name="inputSection" title="Input files" expanded="True"> + <param type="text" name="title" value="Volcano_toPersonalize" label="Title for output"/> + + <param type="data" name="inputData" format="tabular" label="Differential results file" optional="false" multiple="false" refresh_on_change="true"/> + + <param name="headerNumber" type="select" label="Select number of header lines in file" refresh_on_change="true"> + <option value="0">0</option> + <option value="1">1</option> + <option value="2" selected="true">2</option> + <option value="3">3</option> + <option value="4">4</option> + <option value="5">5</option> + </param> + </section> + + <section name="volcanoSection" title="Volcano definition" expanded="True"> + + + <repeat name="volcanoList" title="Volcano"> + + <param type="text" name="volcanoName" value="" label="Volcano name"/> + + <param name="pvalColumn" type="select" label="Select column containing p-val statistics" refresh_on_change="true" optional="false" multiple="false" dynamic_options="get_column_names_mergeNumber(inputSection['inputData'].file_name,inputSection['headerNumber'],[0])" help="Do not select ajusted p-val here"/> + + <param name="fdrColumn" type="select" label="Select column containing adjusted p-val statistics (if available)" refresh_on_change="true" optional="true" multiple="false" dynamic_options="get_column_names_mergeNumber(inputSection['inputData'].file_name,inputSection['headerNumber'],[0])" help="If adjusted p-val are available, otherwise it will be computed from p-values."/> + + <param name="fcColumn" type="select" label="Select column containing log2(FoldChange) values" refresh_on_change="true" optional="false" multiple="false" dynamic_options="get_column_names_mergeNumber(inputSection['inputData'].file_name,inputSection['headerNumber'],[0])" help="If only FC are available as input, please select FC column and check options below." /> + + </repeat> + + </section> + + + <section name="plotSection" title="Output section" expanded="True"> + + <param name="fcKind" type="select" display="radio" label="Select FC values kind selected as input column" help="Info:log2(FC) will be displayed in volcano plots"> + <option value="log2FC" selected="true">log2(FC)</option> + <option value="FC">FC</option> + </param> + + <param name="FDRthreshold" type="float" value="0.05" label="Output adjusted p-val threshold" > + <validator type="in_range" min="0" max="1" message="Threshold should be between 0 and 1"/> + </param> + + <param name="FCthreshold" type="float" value="2" label="Output Fold Change threshold (both 'log2(threshold)' and 'log2(1/threshold)' values will be used)" > + <validator type="in_range" min="1" exclude_min="false" message="Threshold should be greater or equal to 1"/> + </param> + + <conditional name="geneInformation"> + <param name="addGeneInfo" type="boolean" label="Add gene/probe information" checked="false"/> + <when value="true"> + <param name="organismID" label="Organism" type="select"> + <options from_data_table="LimmaTool" > + <column name="name" index="1"/> + <column name="value" index="0"/> + <filter type="unique_value" column="0"/> + </options> + </param> + <param name="infoInRowType" label="Nature of row names" type="select"> + <options from_data_table="LimmaTool" > + <column name="name" index="3"/> + <column name="value" index="2"/> + <filter type="param_value" ref="organismID" column="0"/> + </options> + </param> + </when> + <when value="false"> + </when> + </conditional> + + <param type="select" name="imagePlotlyFormat" display="radio" label="Html snapshot format"> + <option value="png">PNG format</option> + <option value="svg">SVG format</option> + </param> + </section> + + </inputs> + + + + <outputs> + <data format="tabular" name="outputData" label="${inputSection.title}_statistics"/> + + <data format="html" name="html_file" label="${inputSection.title}_HTML.html"/> + <!-- + <collection name="outputHistogramsList" label="${inputSection.title}_HistogramsList" type="list"> + <discover_datasets pattern="(?P<designation>Histograms[0-9]+)\.(?P<ext>[^\._]+)?" directory="plotDir" visible="false"/> + <filter>plotSection['histogramToPlot']</filter> + </collection> + + <collection name="outputVolcanosList" label="${inputSection.title}_VolcanosList" type="list"> + <discover_datasets pattern="(?P<designation>Volcanos\_.*)\.(?P<ext>[^\._]+)?" directory="plotDir" visible="false"/> + <filter>plotSection['volcanoToPlot']</filter> + </collection> + + <data name="fRatioOutput" format="png" label="${inputSection.title}_F-ratio"> + <change_format> + <when input="plotSection['imageFormat']" value="pdf" format="pdf" /> + </change_format> + </data> + --> + <data format="txt" name="log" label="${inputSection.title}_Log" /> + </outputs> + + + + <tests> + <test maxseconds="3600"> + <param name="wfile" value="wiggle.wig" /> + <param name="bfile" value="bedfile.bed" /> + <param name="span" value="3000" /> + <param name="pfres" value="50" /> + <param name="lowersize" value="1000" /> + <param name="middlesize" value="2000" /> + <param name="uppersize" value="3000" /> + <param name="lowerbisize" value="2500" /> + <param name="upperbisize" value="5000" /> + <param name="reldist" value="3000" /> + <param name="genome" value="hg18" /> + <param name="imagetype" value="PDF" /> + <param name="enable" value="no" /> + <output name="outputData" file="ceas_1/ceas_1.pdf" /> + </test> +</tests> + <help> +<![CDATA[ +**What it does ?** + +This tool plot volcanos from previous differential expression analysis results containing at least Fold Change and p-val statistics for all measured genes. + +----- + +**Parameters** + +\- **Input files** + +- **Title** to personalize output file names (avoiding special characters). + +- **Differential expression analysis results** with at least contrast statistics (p-val and FC or log2(FC)) as columns and genes as rows. GIANT-Differential Expression Analysis with LIMMA tool output can be used as a model. + + :: + + LIMMA comparison WT*Treat WT*Treat WT*Treat WT*Treat WT*Treat + Gene Info p-val FDR.p-val FC log2(FC) t-stat + ARSD na 0.0057 0.41 0.8389 -0.2534 -5.175 + TTTY10 na 1.6e-07 0.0074 0.6403 -0.6432 -6.122 + MIR548AL na 0.072 0.2914 1.711 0.775 10.43 + +- **Header lines number** to skip in the differential results file, i.e lines containing column content descripion. + + +\- **Volcano definition** (add as many volcanos as needed) + + - **Volcano name** for better ouput identification (avoiding special characters). + + - **Select p-val statistics column** containing p-value statistics for all genes in the coresponding contrast, FDR correction will be automatically applied on these p-values if adjusted p-values column is not selected in the following option. + + - **Select adjusted p-val column** (optional) if adjusted p-values have been allready computed and are available in the input file. If not, FDR correction will be applied on available p-value statistics. + + - **Select log2(FoldChange) or FoldChange column** corresponding to the same contrast as previously selected (adjusted)p-value columns. + + +\- **Output section** + +- **FC information available as input** : select if FoldChange columns selected during volcanos definition are allready log2 transformed. + +- **Output adjusted/FDR p-val threshold** : only genes with adjusted p-val <= this threshold (in at least one of requested volcanos) will be in result tab. + +- **Output Fold Change threshold** : only genes with absolute FC >= this threshold (in at least one of requested volcanos) will be in result tab (both 'log2(threshold)' and 'log2(1/threshold)' values will be used). + +- **Add gene/probe information** : if yes, add description of genes to the result tab. + +- **Html snapshot format** : format of plot images taken from interactive view + +----- + +**Outputs** + +- **tabular file** containing statistics used for volcano plots, represented as a tab delimited matrix where each colum contains statistics for each gene (in rows). + +- **HTML file** to access interactive version of volcanos through PlotLy html pages and tabulated volcano statistics. + +- **LOG file** for job log. If you see errors, please attached this in the bug report + +]]> </help> + + + <citations> + <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} + }</citation> + + <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} + }</citation> + </citations> + +</tool>