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"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit 89b7d0e8812f53222691cffe29bd48be6519829d"
author vandelj
date Fri, 25 Sep 2020 08:53:21 +0000
parents 75505421bcf3
children
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<tool name="GIANT-Plot volcanos" id="giant_volcano_plot" version="0.3.4">
  <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"/>
  <!--<code file="./src/General_functions.py"/> change for Planemo test-->
  <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')
    ##change for Planemo test
    ##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 '$outputData' -f 'pdf'
    ##change for Planemo test
    ##Rscript '$__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&lt;designation&gt;Histograms[0-9]+)\.(?P&lt;ext&gt;[^\._]+)?" directory="plotDir" visible="false"/>
	  <filter>plotSection['histogramToPlot']</filter>
	</collection>
	
	<collection name="outputVolcanosList" label="${inputSection.title}_VolcanosList" type="list">
	  <discover_datasets pattern="(?P&lt;designation&gt;Volcanos\_.*)\.(?P&lt;ext&gt;[^\._]+)?" 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">
    <section name="inputSection">
      <param name="inputData" value="./DiffExprLimma/output/outputStat.csv" />
      <param name="headerNumber" value="2" />
    </section>
    <section name="volcanoSection" >
      <repeat name="volcanoList" >
        <param name="volcanoName" value="TreatVsControl" />
        <param name="pvalColumn" value="TreatVsControl_p-val" />
        <param name="fdrColumn" value="TreatVsControl_FDR.p-val" />
        <param name="fcColumn" value="TreatVsControl_log2(FC)" />
      </repeat>
      <repeat name="volcanoList" >
        <param name="volcanoName" value="WTvsKO" />
        <param name="pvalColumn" value="WTvsKO_p-val" />
        <param name="fdrColumn" value="WTvsKO_FDR.p-val" />
        <param name="fcColumn" value="WTvsKO_log2(FC)" />
      </repeat>
    </section>
    <section name="plotSection" >
      <param name="fcKind" value="log2(FC)" />
      <param name="FDRthreshold" value="0.05" />
      <param name="FCthreshold" value="2.0" />
      <conditional name="geneInformation">
        <param name="addGeneInfo" value="false" />
      </conditional>
      <param type="select" value="png" />
    </section>
    <output name="outputData" file="./VolcanoPlotTool/output/outputResults.csv" />
    <output name="html_file" file="./VolcanoPlotTool/output/outputHTML.zip" decompress="true" />
    <output name="log" file="./VolcanoPlotTool/output/outputLog.txt" compare="sim_size" delta_frac="0.10" />
  </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>