diff galaxy/wrappers/ExprQCplots.xml @ 0:488e6e8bb8cb draft

"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy/wrappers/ExprQCplots.xml	Fri Jun 26 09:41:56 2020 -0400
@@ -0,0 +1,552 @@
+<tool name="GIANT-QC Plots" id="giant_plot_functions" version="0.1.3">
+  <description>Descriptive plots of .CEL collections or normalized expression data</description>
+  <requirements>
+	  <requirement type="package" version="1.40.1">bioconductor-oligo</requirement>
+	  <requirement type="package" version="2.2_13">r-ff</requirement>
+	  <requirement type="package" version="2.2.1">r-ggplot2</requirement>
+	  <requirement type="package" version="4.5.6">r-plotly</requirement>
+    <requirement type="package" version="1.8_17">r-mgcv</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 formating scripts, 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[
+    ##set $dataType=$dataFile.extension
+	   #set $dataType=$dataFile[0].ext
+	   
+	   #if $conditionInformation and $pcaSection.factorsToInclude!="None":
+       	bash $scriptPrepareTable;
+        ret_code=\$?;
+        if [ \$ret_code != 0 ]; then
+          exit \$ret_code;
+        fi; 
+     #end if
+
+	   #if ($dataType == "cel" and len($dataFile)>1) or ($dataType == "tabular" and len($dataFile)==1):
+	   Rscript '$__tool_directory__/../../src/ExprPlotsScript.R' -i '$dataFile' -l '$log' -f '$advSection.imageFormat' -j '$dataType'
+	   #if $dataType == "cel":
+	   #for $inputDataset in $dataFile
+        -c '${inputDataset.name}'
+       #end for
+	   #end if
+	   #if $conditionInformation and $pcaSection.factorsToInclude!="None":
+       	 -t 'factorTable.csv'
+       #end if
+	   #if $plotSection.histogramToPlot:
+	     -h 'Histograms'
+	   #end if
+	   #if $plotSection.maplotToPlot:
+	     -a 'MAplots'
+	   #end if
+	   #if $plotSection.boxplotToPlot:
+	     -b 'Boxplots'
+	   #end if
+	   #if $plotSection.microarrayToPlot and $dataType == "cel":
+	    -m 'Microarray'
+	   #end if
+	   #if $pcaSection.acpToPlot:
+	    -p 'PCA'
+      	-s 'screePlot'
+	   #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;
+	   #else:
+		  printf "[ERROR]Execution halted, not enough (.CEL files) or too many (tabular file) input files" >> $log;
+      exit 15;
+	   #end if
+     printf "[INFO]End of tool script" >> $log; 
+	   ]]>
+	</command>
+
+
+
+  <configfiles>
+    <configfile name="scriptPrepareTable">
+    <![CDATA[
+     awk -v fact="$pcaSection.factorsToInclude" 'BEGIN{FS="\t";OFS="";ORS="";split(fact, factors, ",");for(i in factors)factorsName[factors[i]]=1} NR==1{for(i=2;i<=NF;i++){if(\$i in factorsName)positFactor[i]=1}} {print $1;for(factorID in positFactor)print "\t"\$factorID; print "\n"}'  $conditionInformation > ./factorTable.csv;
+
+    if [ ! -e ./factorTable.csv ]; then
+      printf "[ERROR]factorTable.csv is missing" >> $log; 
+      exit 15
+    fi
+    printf "[INFO]End of scriptPrepareTable\n" >> $log 
+    ]]>
+    </configfile>
+
+    <configfile name="scriptTransfer">
+<![CDATA[
+#set $dataType=$dataFile[0].ext
+#set $cnt=1
+
+##create header of HTML file
+printf  "<!DOCTYPE html>\n<html>\n"  > $html_file
+
+##add to HTML scripts to show and hide MAplots and MicroArray pictures
+
+printf "<head>
+<script src=\"https://ajax.googleapis.com/ajax/libs/jquery/3.3.1/jquery.min.js\"></script>
+<script>
+\\$(document).ready(function(){
+    \\$(\"\#MAplotTitle\").click(function(){
+  if(\\$(\"p.MAplot\").is(\':visible\'))\\$(\"p.MAplot\").hide(1000);
+        else \\$(\"p.MAplot\").show(1000);
+    });
+    \\$(\"\#MicroarrayTitle\").click(function(){
+  if(\\$(\"p.Microarray\").is(\':visible\'))\\$(\"p.Microarray\").hide(1000);
+        else \\$(\"p.Microarray\").show(1000);
+    });
+});
+</script>
+</head>\n<body>\n" >> $html_file
+
+mkdir -p $html_file.extra_files_path
+
+
+
+#if $plotSection.histogramToPlot:
+
+printf "<h3>Histograms</h3>\n" >> $html_file
+##create folders in media
+counter=1
+for histogram in \$(ls ./plotLyDir/Histograms*html)
+do
+histogramShort=\${histogram%\.*}
+histogramShort=\${histogramShort\#\#*/}
+
+##modify HTML to point to plotLy folder
+sed -i "s/\${histogramShort}_files/PlotLy_scripts/g" \$histogram
+
+##copy HTML files in both folders
+cp \$histogram ${html_file.extra_files_path}/Histograms\${counter}.html
+
+##add HTML link
+printf "<a href=\"Histograms\${counter}.html\">Histograms\${counter}</a>\n"  >> $html_file
+
+if [ \$counter = 1 ]; then
+
+#if $advSection.imagePlotlyFormat=="svg":
+##before copying modify plotLy script to replace png snapshot with svg (not proud of solution but seems to work)
+cd ./plotLyDir/\${histogramShort}_files/plotlyjs-*/
+awk '{gsub("e=\"png\"","e=\"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
+
+##copy only scripts folder for the first histogram
+cp -r ./plotLyDir/\${histogramShort}_files $html_file.extra_files_path
+mv ${html_file.extra_files_path}/\${histogramShort}_files ${html_file.extra_files_path}/PlotLy_scripts
+fi
+
+((counter++))
+done
+
+if [ \$counter = 1 ]; then
+  printf "[ERROR]Histograms are missing" >> $log; 
+  exit 10
+fi
+
+#end if
+
+
+
+#if $plotSection.boxplotToPlot:
+
+printf "<h3>Boxplots</h3>\n" >> $html_file
+
+##create folders in media
+counter=1
+for boxplot in \$(ls ./plotLyDir/Boxplots*html)
+do
+boxplotShort=\${boxplot%\.*}
+boxplotShort=\${boxplotShort\#\#*/}
+
+##modify HTML to point to plotLy folder
+sed -i "s/\${boxplotShort}_files/PlotLy_scripts/g" \$boxplot
+
+##copy HTML files in both folders
+cp \$boxplot ${html_file.extra_files_path}/Boxplots\${counter}.html
+
+##add HTML link
+printf "<a href=\"Boxplots\${counter}.html\">Boxplots\${counter}</a>\n"  >> $html_file
+
+if [ \$counter = 1 ]; then
+#if $advSection.imagePlotlyFormat=="svg":
+##before copying modify plotLy script to replace png snapshot with svg (not proud of solution but seems to work)
+cd ./plotLyDir/\${boxplotShort}_files/plotlyjs-*/
+awk '{gsub("e=\"png\"","e=\"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
+
+##copy only scripts folder for the first boxplot
+cp -r ./plotLyDir/\${boxplotShort}_files $html_file.extra_files_path
+mv ${html_file.extra_files_path}/\${boxplotShort}_files ${html_file.extra_files_path}/PlotLy_scripts
+fi
+
+((counter++))
+done
+
+if [ \$counter = 1 ]; then
+  printf "[ERROR]Boxplots are missing" >> $log; 
+  exit 10
+fi
+
+#end if
+
+
+
+#if $plotSection.maplotToPlot:
+
+printf "<h3 id=\"MAplotTitle\">MA plots (show/hide)</h3>\n" >> $html_file
+
+##create folders in media
+counter=1
+for MAplot in \$(ls ./plotLyDir/MAplots_*html)
+do
+MAplotShort=\${MAplot%\.*}
+MAplotShort=\${MAplotShort\#\#*/}
+
+conditionName=\${MAplot%\.*}
+conditionName=\${conditionName\#\#*MAplots_}
+
+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/\${MAplotShort}_files/PlotLy_scripts/g" \$MAplot
+
+##copy HTML files in both folders
+cp \$MAplot ${html_file.extra_files_path}/MAplot_\$conditionName.html
+
+##add HTML link
+printf "<p class=\"MAplot\">\n<a href=\"MAplot_\$conditionName.html\">MAplot \$conditionFormatedName</a>\n</p>\n"  >> $html_file
+
+if [ \$counter = 1 ]; then
+##copy only scripts folder for the first MAplot
+
+#if $advSection.imagePlotlyFormat=="svg":
+##before copying modify plotLy script to replace png snapshot with svg (not proud of solution but seems to work)
+cd ./plotLyDir/\${MAplotShort}_files/plotlyjs-*/
+awk '{gsub("e=\"png\"","e=\"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
+
+cp -r ./plotLyDir/\${MAplotShort}_files $html_file.extra_files_path
+mv ${html_file.extra_files_path}/\${MAplotShort}_files ${html_file.extra_files_path}/PlotLy_scripts
+fi
+
+((counter++))
+done
+
+if [ \$counter = 1 ]; then
+  printf "[ERROR]MAplots are missing" >> $log; 
+  exit 10
+fi
+
+#end if  
+
+
+
+
+#if $plotSection.microarrayToPlot and $dataType == "cel":
+
+printf "<h3 id=\"MicroarrayTitle\">Microarray</h3>\n" >> $html_file
+for microarray in \$(ls ./plotDir/Microarray_*)
+do
+conditionName=\${microarray%\.*}
+conditionName=\${conditionName\#\#*Microarray_}
+
+echo \$conditionName > ./temporaryConditionName
+conditionFormatedName=\$(awk 'BEGIN{FS="\t"} ARGIND==1{dico[\$1]=\$2} ARGIND==2{print dico[\$1]}' ./correspondanceFileNames.csv ./temporaryConditionName)
+
+cp \$microarray ${html_file.extra_files_path}/Microarray_\$conditionName.${advSection.imageFormat}
+printf "<p class=\"Microarray\"><a href=\"Microarray_\$conditionName.${advSection.imageFormat}\">Microarray \$conditionFormatedName</a>\n</p>"  >> $html_file
+done
+
+#end if
+
+
+
+
+#if $pcaSection.acpToPlot:
+
+printf "<h3>PCA</h3>\n" >> $html_file
+
+##create folders in media
+counter=1
+for pca in \$(ls ./plotLyDir/PCA*html)
+do
+pcaShort=\${pca%\.*}
+pcaShort=\${pcaShort\#\#*/}
+
+conditionName=\${pca%\.*}
+conditionName=\${conditionName\#\#*PCA_}
+
+echo \$conditionName > ./temporaryConditionName
+conditionFormatedName=\$(awk 'BEGIN{FS="\t"} ARGIND==1{dico[\$1]=\$2} ARGIND==2{split(\$0,tab,"_AND_");if(length(tab)==1){if(\$0 in dico){print dico[\$0]}else{print $0}}else{print dico[tab[1]]" * "dico[tab[2]]}}' ./correspondanceFileNames.csv ./temporaryConditionName)
+
+##modify HTML to point to plotLy folder
+sed -i "s/\${pcaShort}_files/PlotLy_scripts/g" \$pca
+
+##copy HTML files in both folders
+cp \$pca ${html_file.extra_files_path}/PCA_\$conditionName.html
+
+##add HTML link
+printf "<p><a href=\"PCA_\$conditionName.html\">PCA \$conditionFormatedName</a>\n</p>"  >> $html_file
+
+
+if [ \$counter = 1 ]; then
+
+#if $advSection.imagePlotlyFormat=="svg":
+##before copying modify plotLy script to replace png snapshot with svg (not proud of solution but seems to work)
+cd ./plotLyDir/\${pcaShort}_files/plotlyjs-*/
+awk '{gsub("e=\"png\"","e=\"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
+
+##copy only scripts folder for the first pca
+cp -r ./plotLyDir/\${pcaShort}_files $html_file.extra_files_path
+mv ${html_file.extra_files_path}/\${pcaShort}_files ${html_file.extra_files_path}/PlotLy_scripts
+fi
+
+((counter++))
+done
+
+if [ \$counter = 1 ]; then
+  printf "[ERROR]PCA plots are missing" >> $log; 
+  exit 10
+fi
+
+##now for screePlot
+if [ -e ./plotLyDir/screePlot.html ]; then
+  ##copy HTML files in both folders
+  cp ./plotLyDir/screePlot.html ${html_file.extra_files_path}/screePlot.html
+  ##add HTML link
+  printf "<p><a href=\"screePlot.html\">Scree plot</a>\n</p>"  >> $html_file
+else
+  printf "[ERROR]screePlot.html is missing" >> $log; 
+  exit 10
+fi
+
+##copy scripts folder
+
+#if $advSection.imagePlotlyFormat=="svg":
+##but before copying modify plotLy script to replace png snapshot with svg (not proud of solution but seems to work)
+cd ./plotLyDir/screePlot_files/plotlyjs-*/
+awk '{gsub("e=\"png\"","e=\"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
+
+cp -r ./plotLyDir/screePlot_files $html_file.extra_files_path
+
+#end if
+
+
+##create footer of HTML file
+printf  "</body>\n</html>" >> $html_file
+]]>
+    </configfile>
+  </configfiles>
+
+
+
+  <inputs>
+    <param type="text" name="title" value="PlotFigure_toPersonalize" label="Title for output">
+	</param>		 
+    <param type="data" name="dataFile" format="cel,tabular" label="Select one .CEL collection or one tabular file" optional="false" multiple="true" >
+	</param>
+
+	<section name="plotSection" title="Plots selection" expanded="True">
+    <param type="boolean" name="histogramToPlot" checked="true" label="Plot histograms" help="Plot intensity distribution for each condition (pm probes for .cel)">
+    </param>
+    <param type="boolean" name="maplotToPlot" checked="true" label="Plot MA plots" help="Plot MA plot for each condition, median value is used as reference">
+    </param>
+    <param type="boolean" name="boxplotToPlot" checked="true" label="Plot boxplots" help="Plot intensity through boxplot for each condition (pm probes for .cel)">
+    </param>
+	<param type="boolean" name="microarrayToPlot" checked="true" label="Display microarray images (only for .CEL files)">
+    </param>
+
+    </section>
+	<section name="pcaSection" title="PCA analysis" expanded="True">
+	<param type="boolean" name="acpToPlot" checked="true" label="Plot 3D PCA" help="3D plot of conditions in the space defined by the 3 principal components">
+    </param>
+    <param type="data" name="conditionInformation" format="tabular" label="Factor information tabular file (optional)" optional="true" multiple="false">
+    </param>
+    <param name="factorsToInclude" type="select" optional="true" multiple="true" label="Select factor informations to display (optional)"
+    	refresh_on_change="true"  dynamic_options="get_column_names(pcaSection['conditionInformation'].file_name,0)">
+                 <validator type="empty_field" message="You should specify one factor"></validator>
+	</param>
+
+    </section>
+
+	<section name="advSection" title="Advanced parameters" expanded="False">
+    <param type="select" name="imageFormat" display="radio" label="Output microarray image format">
+      <option value="png">PNG format</option>
+      <option value="pdf">PDF format</option>
+    </param>
+    <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="html" name="html_file" label="${title}_HTML.html"/>
+		<!--
+		<collection name="outputHistogramsList" label="${title}_HistogramsList" type="list">
+		  <discover_datasets pattern="(?P&lt;designation&gt;Histograms[0-9]+)\.(?P&lt;ext&gt;[^\._]+)?" directory="plotDir" visible="false"/>
+		  <filter>plotSection['histogramToPlot']</filter>
+		</collection>
+		
+		<collection name="outputMAplotsList" label="${title}_MAplotsList" type="list">
+		  <discover_datasets pattern="(?P&lt;designation&gt;MAplots[0-9]+)\.(?P&lt;ext&gt;[^\._]+)?" directory="plotDir" visible="false"/>
+		  <filter>plotSection['maplotToPlot']</filter>
+		</collection>
+		
+		<collection name="outputBoxplotsList" label="${title}_BoxplotsList" type="list">
+		  <discover_datasets pattern="(?P&lt;designation&gt;Boxplots[0-9]+)\.(?P&lt;ext&gt;[^\._]+)?" directory="plotDir" visible="false"/>
+		  <filter>plotSection['boxplotToPlot']</filter>
+		</collection>
+		
+		<collection name="outputMicroarrayList" label="${title}_MicroarrayList" type="list">
+		  <discover_datasets pattern="(?P&lt;designation&gt;Microarray\_.*)\.(?P&lt;ext&gt;[^\._]+)?" directory="plotDir" visible="false"/>
+		  <filter>plotSection['microarrayToPlot'] and dataFile[0].ext == "cel"</filter>
+		</collection>
+
+		<collection name="outputPCAList" label="${title}_PCA" type="list">
+		  <discover_datasets pattern="(?P&lt;designation&gt;PCA[0-9]+)\.(?P&lt;ext&gt;[^\._]+)?" directory="plotDir" visible="false"/>
+		  <discover_datasets pattern="(?P&lt;designation&gt;screePlot)\.(?P&lt;ext&gt;[^\._]+)?" directory="plotDir" visible="false"/>
+		  <filter>pcaSection['acpToPlot']</filter>
+		</collection>
+		-->
+    <data name="log" label="${title}_Log" format="txt"/>
+  </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="log" file="ceas_1/ceas_1.pdf" />
+  </test>
+</tests> 
+
+
+
+  <help>
+<![CDATA[
+**What it does ?**
+
+This tool generate descriptive plots for Affymetrix raw data (.CEL file) or any tabular file containing expression data (from arrays or RNA-seq).
+
+-----
+
+**Parameters**
+
+\- **Title** to personalize output file names (please avoid special characters and spaces).
+
+\- **Input Data** 
+
+- **.CEL files** of your study (you can select multiple .CEL files or unique collection). For vizualization purposes, expression data extracted from .CEL files will be automatically log2 transformed by the tool.
+
+OR
+
+- **Expression tabular file** with samples as columns and genes as rows (header row contains sample names and first column gene identifiers). For better vizualization, expression data sould be preferentially already log2 transformed, no such transformation will be performed by the tool.
+
+    ::
+
+        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                        
+        DDX11L2     4.500872                4.429759                 4.780281                   4.996189             
+        MIR1302-2   3.415065                3.520472                 3.471503                   3.567988           
+        OR4F5       3.737956                3.011586                 3.424494                   3.497545
+        VWA1        5.189621                5.129595                 4.806793                   5.227014
+
+\- **Plots selection**
+: to select required plots
+
+- **Plot histograms**
+- **Plot MA plots**
+- **Plot boxplots**
+- **Display microarray images** (only if "Input Data" are .CEL files)
+
+\- **PCA analysis**
+
+- **Plot 3D PCA** plot the 3 first principal components
+- **Factor information tabular file** with factors as columns and samples as rows (header row contains factor names and first column sample names). Can help to discriminate samples in PCA plot.
+
+    ::
+
+        Conditions                Sex   Treatment Reaction
+        138_(HuGene-2_0-st).CEL   1     TreatA    Pos
+        148_(HuGene-2_0-st).CEL   0     NoTreat   Pos
+        139_(HuGene-2_0-st).CEL   0     TreatB    Neg
+        149_(HuGene-2_0-st).CEL   0     NoTreat   Neg
+
+- **Select factor informations** you want to display in PCA plot (1 for samples colors and 1 for samples shapes)
+
+\- **Advanced parameters**
+
+- **Output microarray image format** available only for .CEL input files
+- **Html snapshot format** : format of plot images taken from interactive view
+
+-----
+
+\- **Outputs**
+
+- **HTML file** to access interactive version of plots through PlotLy html pages
+- **LOG file** for job logs. In case of job failure, please attached this file to 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>