Mercurial > repos > vandelj > giant_volcano_plot

comparison galaxy/wrappers/VolcanoPlotTool.xml @ 1:75505421bcf3 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 10:38:06 +0000
parents c9a38c1eadf1
children
comparison
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0:c9a38c1eadf1 1:75505421bcf3
1 <tool name="GIANT-Plot volcanos" id="giant_volcano_plot" version="0.3.3"> 1 <tool name="GIANT-Plot volcanos" id="giant_volcano_plot" version="0.3.4">
2 <description>Plot volcano from tabular file</description> 2 <description>Plot volcano from tabular file</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.7.1">r-r.methodss3</requirement> 4 <requirement type="package" version="1.7.1">r-r.methodss3</requirement>
5 <requirement type="package" version="2.36.1">bioconductor-biomart</requirement> 5 <requirement type="package" version="2.36.1">bioconductor-biomart</requirement>
6 <requirement type="package" version="3.0.0">r-ggplot2</requirement> 6 <requirement type="package" version="3.0.0">r-ggplot2</requirement>
7 <requirement type="package" version="4.8.0">r-plotly</requirement> 7 <requirement type="package" version="4.8.0">r-plotly</requirement>
8 <requirement type="package" version="1.3.1">r-stringr</requirement> 8 <requirement type="package" version="1.3.1">r-stringr</requirement>
9 </requirements> 9 </requirements>
10 <code file="../../src/General_functions.py"/> 10 <code file="../../src/General_functions.py"/>
11 <!--<code file="./src/General_functions.py"/> change for Planemo test-->
11 <stdio> 12 <stdio>
12 <regex match="Execution halted" 13 <regex match="Execution halted"
13 source="both" 14 source="both"
14 level="fatal" 15 level="fatal"
15 description="Execution halted, please contact tool developer or administrators." /> 16 description="Execution halted, please contact tool developer or administrators." />
23 </stdio> 24 </stdio>
24 <command> <![CDATA[ 25 <command> <![CDATA[
25 #import imp 26 #import imp
26 #set $runIdentifier=str($outputData).rsplit("/")[-1].rsplit(".")[0] 27 #set $runIdentifier=str($outputData).rsplit("/")[-1].rsplit(".")[0]
27 #set $general_functions=$imp.load_source('General_functions', $__tool_directory__+'/../../src/General_functions.py') 28 #set $general_functions=$imp.load_source('General_functions', $__tool_directory__+'/../../src/General_functions.py')
29 ##change for Planemo test
30 ##set $general_functions=$imp.load_source('General_functions', $__tool_directory__+'/src/General_functions.py')
28 #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) 31 #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)
29 32
30 if [ $ret_code != 0 ]; then 33 if [ $ret_code != 0 ]; then
31 printf "[ERROR]Error during formated statistics file generation\n" >> $log; 34 printf "[ERROR]Error during formated statistics file generation\n" >> $log;
32 exit $ret_code; 35 exit $ret_code;
42 #end if 45 #end if
43 #end for 46 #end for
44 47
45 48
46 Rscript '$__tool_directory__/../../src/VolcanoPlotsScript.R' -i 'statisticsFormated.csv' -l '$log' -o '$outputData' -f 'pdf' 49 Rscript '$__tool_directory__/../../src/VolcanoPlotsScript.R' -i 'statisticsFormated.csv' -l '$log' -o '$outputData' -f 'pdf'
50 ##change for Planemo test
51 ##Rscript '$__tool_directory__/src/VolcanoPlotsScript.R' -i 'statisticsFormated.csv' -l '$log' -o '$outputData' -f 'pdf'
47 #for $i, $s in enumerate( $volcanoSection.volcanoList ) 52 #for $i, $s in enumerate( $volcanoSection.volcanoList )
48 -n '${s.volcanoName}' 53 -n '${s.volcanoName}'
49 -p '${s.pvalColumn}' 54 -p '${s.pvalColumn}'
50 -c '${s.fcColumn}' 55 -c '${s.fcColumn}'
51 -m '${s.fdrColumn}' 56 -m '${s.fdrColumn}'
322 --> 327 -->
323 <data format="txt" name="log" label="${inputSection.title}_Log" /> 328 <data format="txt" name="log" label="${inputSection.title}_Log" />
324 </outputs> 329 </outputs>
325 330
326 331
327 332
328 <tests> 333 <tests>
329 <test maxseconds="3600"> 334 <test maxseconds="3600">
330 <param name="wfile" value="wiggle.wig" /> 335 <section name="inputSection">
331 <param name="bfile" value="bedfile.bed" /> 336 <param name="inputData" value="./DiffExprLimma/output/outputStat.csv" />
332 <param name="span" value="3000" /> 337 <param name="headerNumber" value="2" />
333 <param name="pfres" value="50" /> 338 </section>
334 <param name="lowersize" value="1000" /> 339 <section name="volcanoSection" >
335 <param name="middlesize" value="2000" /> 340 <repeat name="volcanoList" >
336 <param name="uppersize" value="3000" /> 341 <param name="volcanoName" value="TreatVsControl" />
337 <param name="lowerbisize" value="2500" /> 342 <param name="pvalColumn" value="TreatVsControl_p-val" />
338 <param name="upperbisize" value="5000" /> 343 <param name="fdrColumn" value="TreatVsControl_FDR.p-val" />
339 <param name="reldist" value="3000" /> 344 <param name="fcColumn" value="TreatVsControl_log2(FC)" />
340 <param name="genome" value="hg18" /> 345 </repeat>
341 <param name="imagetype" value="PDF" /> 346 <repeat name="volcanoList" >
342 <param name="enable" value="no" /> 347 <param name="volcanoName" value="WTvsKO" />
343 <output name="outputData" file="ceas_1/ceas_1.pdf" /> 348 <param name="pvalColumn" value="WTvsKO_p-val" />
349 <param name="fdrColumn" value="WTvsKO_FDR.p-val" />
350 <param name="fcColumn" value="WTvsKO_log2(FC)" />
351 </repeat>
352 </section>
353 <section name="plotSection" >
354 <param name="fcKind" value="log2(FC)" />
355 <param name="FDRthreshold" value="0.05" />
356 <param name="FCthreshold" value="2.0" />
357 <conditional name="geneInformation">
358 <param name="addGeneInfo" value="false" />
359 </conditional>
360 <param type="select" value="png" />
361 </section>
362 <output name="outputData" file="./VolcanoPlotTool/output/outputResults.csv" />
363 <output name="html_file" file="./VolcanoPlotTool/output/outputHTML.zip" decompress="true" />
364 <output name="log" file="./VolcanoPlotTool/output/outputLog.txt" compare="sim_size" delta_frac="0.10" />
344 </test> 365 </test>
345 </tests> 366 </tests>
367
368
369
346 <help> 370 <help>
347 <![CDATA[ 371 <![CDATA[
348 **What it does ?** 372 **What it does ?**
349 373
350 This tool plot volcanos from previous differential expression analysis results containing at least Fold Change and p-val statistics for all measured genes. 374 This tool plot volcanos from previous differential expression analysis results containing at least Fold Change and p-val statistics for all measured genes.