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comparison galaxy/wrappers/DiffExprLimma.xml @ 1:9f2ddab68c9e 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 10:28:02 +0000
parents f274c8d45613
children
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0:f274c8d45613 1:9f2ddab68c9e
1 <tool name="GIANT-Differential Expression with LIMMA" id="giant_limma_analysis" version="0.3.8"> 1 <tool name="GIANT-Differential Expression with LIMMA" id="giant_limma_analysis" version="0.3.9">
2 <description>Use LIMMA to detect differentially expressed genes</description> 2 <description>Use LIMMA to detect differentially expressed genes</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="3.36.5">bioconductor-limma</requirement> 5 <requirement type="package" version="3.36.5">bioconductor-limma</requirement>
6 <requirement type="package" version="2.36.1">bioconductor-biomart</requirement> 6 <requirement type="package" version="2.36.1">bioconductor-biomart</requirement>
9 <requirement type="package" version="1.3.1">r-stringr</requirement> 9 <requirement type="package" version="1.3.1">r-stringr</requirement>
10 <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement> 10 <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>
11 <requirement type="package" version="1.4.32">r-statmod</requirement> 11 <requirement type="package" version="1.4.32">r-statmod</requirement>
12 </requirements> 12 </requirements>
13 <code file="../../src/LIMMA_options.py"/> 13 <code file="../../src/LIMMA_options.py"/>
14 <!--<code file="./src/LIMMA_options.py"/> change for Planemo test-->
14 <stdio> 15 <stdio>
15 <regex match="Execution halted" 16 <regex match="Execution halted"
16 source="both" 17 source="both"
17 level="fatal" 18 level="fatal"
18 description="Execution halted, please contact tool developer or administrators." /> 19 description="Execution halted, please contact tool developer or administrators." />
30 if [ \$ret_code != 0 ]; then 31 if [ \$ret_code != 0 ]; then
31 exit \$ret_code; 32 exit \$ret_code;
32 fi; 33 fi;
33 34
34 cp '$__tool_directory__/../../src/LIMMA_options.py' ./LIMMA_options.py; 35 cp '$__tool_directory__/../../src/LIMMA_options.py' ./LIMMA_options.py;
36 ##change for Planemo test
37 ##cp '$__tool_directory__/src/LIMMA_options.py' ./LIMMA_options.py;
35 38
36 #if $blockingSection.blockingConditional.addBlocking == "true": 39 #if $blockingSection.blockingConditional.addBlocking == "true":
37 python -c 'import LIMMA_options;LIMMA_options.replaceNamesBlockInFiles("$inputSection.inputData","./factorTable.csv","./blockingTable.csv","./expressionRenamed.csv","./factorTableRenamed.csv","./blockingTableRenamed.csv","./dictionnaryRenamed.csv")'; 40 python -c 'import LIMMA_options;LIMMA_options.replaceNamesBlockInFiles("$inputSection.inputData","./factorTable.csv","./blockingTable.csv","./expressionRenamed.csv","./factorTableRenamed.csv","./blockingTableRenamed.csv","./dictionnaryRenamed.csv")';
38 #else: 41 #else:
39 python -c 'import LIMMA_options;LIMMA_options.replaceNamesInFiles("$inputSection.inputData","./factorTable.csv","./expressionRenamed.csv","./factorTableRenamed.csv","./dictionnaryRenamed.csv")'; 42 python -c 'import LIMMA_options;LIMMA_options.replaceNamesInFiles("$inputSection.inputData","./factorTable.csv","./expressionRenamed.csv","./factorTableRenamed.csv","./dictionnaryRenamed.csv")';
41 44
42 45
43 if [ -f ./dictionnaryRenamed.csv ]; then 46 if [ -f ./dictionnaryRenamed.csv ]; then
44 printf "[INFO]Renaming is done\n" >> $log; 47 printf "[INFO]Renaming is done\n" >> $log;
45 Rscript '$__tool_directory__/../../src/LIMMAscriptV4.R' -i 'expressionRenamed.csv' -l '$log' -o '$outputData' -z '$outputDfData' -f 'pdf' 48 Rscript '$__tool_directory__/../../src/LIMMAscriptV4.R' -i 'expressionRenamed.csv' -l '$log' -o '$outputData' -z '$outputDfData' -f 'pdf'
49 ##change for Planemo test
50 ##Rscript '$__tool_directory__/src/LIMMAscriptV4.R' -i 'expressionRenamed.csv' -l '$log' -o '$outputData' -z '$outputDfData' -f 'pdf'
46 -a 'factorTableRenamed.csv' -s 'sumSquareFtest' -g 'dictionnaryRenamed.csv' 51 -a 'factorTableRenamed.csv' -s 'sumSquareFtest' -g 'dictionnaryRenamed.csv'
47 #if $blockingSection.blockingConditional.addBlocking == "true": 52 #if $blockingSection.blockingConditional.addBlocking == "true":
48 -b 'blockingTableRenamed.csv' 53 -b 'blockingTableRenamed.csv'
49 -u $advSection.confoundingPolicy 54 -u $advSection.confoundingPolicy
50 #end if 55 #end if
358 <section name="contrastSection" title="Contrast definition" expanded="True"> 363 <section name="contrastSection" title="Contrast definition" expanded="True">
359 364
360 <param name="factorSelection" type="select" label="Select all factors to include in the global model (excepting confounding factors)" refresh_on_change="true" display="checkboxes" optional="false" multiple="true" dynamic_options="get_column_names(inputSection['conditionInformation'].file_name)" help="Confounding factors are selected in the coresponding section below." /> 365 <param name="factorSelection" type="select" label="Select all factors to include in the global model (excepting confounding factors)" refresh_on_change="true" display="checkboxes" optional="false" multiple="true" dynamic_options="get_column_names(inputSection['conditionInformation'].file_name)" help="Confounding factors are selected in the coresponding section below." />
361 366
362 <repeat name="contrastList" title="Contrast"> 367 <repeat name="contrastList" title="Contrast">
363 <param type="text" name="groupName" value="" label="Contrast name"/> 368 <param name="groupName" type="text" value="" label="Contrast name"/>
364 369
365 <param name="firstGroupToCompare" type="select" label="Select factor levels of 1st group" display="checkboxes" multiple="true" refresh_on_change="true" dynamic_options="get_row_names_allInteractions(inputSection['conditionInformation'].file_name,factorSelection)"> 370 <param name="firstGroupToCompare" type="select" label="Select factor levels of 1st group" display="checkboxes" multiple="true" refresh_on_change="true" dynamic_options="get_row_names_allInteractions(inputSection['conditionInformation'].file_name,factorSelection)">
366 </param> 371 </param>
367 372
368 <param name="secondGroupToCompare" type="select" label="Select factor levels of 2nd group" display="checkboxes" multiple="true" refresh_on_change="true" dynamic_options="get_row_names_allInteractions(inputSection['conditionInformation'].file_name,factorSelection)"> 373 <param name="secondGroupToCompare" type="select" label="Select factor levels of 2nd group" display="checkboxes" multiple="true" refresh_on_change="true" dynamic_options="get_row_names_allInteractions(inputSection['conditionInformation'].file_name,factorSelection)">
475 480
476 481
477 482
478 <tests> 483 <tests>
479 <test maxseconds="3600"> 484 <test maxseconds="3600">
480 <param name="wfile" value="wiggle.wig" /> 485 <section name="inputSection">
481 <param name="bfile" value="bedfile.bed" /> 486 <param name="inputData" value="./NormalizedData.tabular" />
482 <param name="span" value="3000" /> 487 <param name="conditionInformation" value="./FactorFileGenerator/output/conditionsFile.csv" />
483 <param name="pfres" value="50" /> 488 </section>
484 <param name="lowersize" value="1000" /> 489 <section name="contrastSection">
485 <param name="middlesize" value="2000" /> 490 <param name="factorSelection" value="Strain,Treatment" />
486 <param name="uppersize" value="3000" /> 491 <repeat name="contrastList" >
487 <param name="lowerbisize" value="2500" /> 492 <param name="groupName" value="TreatVsControl" />
488 <param name="upperbisize" value="5000" /> 493 <param name="firstGroupToCompare" value="WT*Treat,KO*Treat" />
489 <param name="reldist" value="3000" /> 494 <param name="secondGroupToCompare" value="WT*Control,KO*Control" />
490 <param name="genome" value="hg18" /> 495 </repeat>
491 <param name="imagetype" value="PDF" /> 496 <repeat name="contrastList" >
492 <param name="enable" value="no" /> 497 <param name="groupName" value="WTvsKO" />
493 <output name="outputData" file="ceas_1/ceas_1.pdf" /> 498 <param name="firstGroupToCompare" value="WT*Control,WT*Treat" />
494 <output name="outputDfData" file="ceas_1/ceas_1.pdf" /> 499 <param name="secondGroupToCompare" value="KO*Control,KO*Treat" />
500 </repeat>
501 <conditional name="interactionSelection">
502 <param name="interactionContrast" value="true" />
503 <param name="controlSelection" value="Strain:WT,Treatment:Control" />
504 </conditional>
505 </section>
506 <section name="blockingSection">
507 <conditional name="blockingConditional">
508 <param name="addBlocking" value="false"/>
509 </conditional>
510 </section>
511 <section name="plotSection">
512 <param name="cutoffTh" value="0.05"/>
513 <param name="FCthreshold" value="1.2"/>
514 <param name="histogramToPlot" value="true"/>
515 <param name="volcanoToPlot" value="false"/>
516 <conditional name="geneInformation">
517 <param name="addGeneInfo" value="false"/>
518 </conditional>
519 <param name="imagePlotlyFormat" value="png"/>
520 </section>
521 <section name="advSection">
522 <param name="confoundingPolicy" value="additive"/>
523 </section>
524 <output name="outputData" file="./DiffExprLimma/output/outputStat.csv" />
525 <output name="outputDfData" file="./DiffExprLimma/output/outputStatDetailed.csv" />
526 <output name="html_file" file="./DiffExprLimma/output/outputHTML.zip" decompress="true" />
527 <output name="log" file="./DiffExprLimma/output/outputLog.txt" compare="sim_size" delta_frac="0.10" />
495 </test> 528 </test>
496 </tests> 529 </tests>
530
531
532
497 <help> 533 <help>
498 <![CDATA[ 534 <![CDATA[
499 **What it does ?** 535 **What it does ?**
500 536
501 This tool compute differential expressions for a set of genes. 537 This tool compute differential expressions for a set of genes.