Mercurial > repos > vandelj > giant_limma_analysis
changeset 1:9f2ddab68c9e draft
"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 | 3dc31e252649 |
| files | galaxy/wrappers/DiffExprLimma.xml src/General_functions.py |
| diffstat | 2 files changed, 68 insertions(+), 30 deletions(-) [+] |
line wrap: on
line diff
--- a/galaxy/wrappers/DiffExprLimma.xml Fri Jun 26 09:43:41 2020 -0400 +++ b/galaxy/wrappers/DiffExprLimma.xml Wed Sep 09 10:28:02 2020 +0000 @@ -1,4 +1,4 @@ -<tool name="GIANT-Differential Expression with LIMMA" id="giant_limma_analysis" version="0.3.8"> +<tool name="GIANT-Differential Expression with LIMMA" id="giant_limma_analysis" version="0.3.9"> <description>Use LIMMA to detect differentially expressed genes</description> <requirements> <requirement type="package" version="1.7.1">r-r.methodss3</requirement> @@ -11,6 +11,7 @@ <requirement type="package" version="1.4.32">r-statmod</requirement> </requirements> <code file="../../src/LIMMA_options.py"/> + <!--<code file="./src/LIMMA_options.py"/> change for Planemo test--> <stdio> <regex match="Execution halted" source="both" @@ -32,6 +33,8 @@ fi; cp '$__tool_directory__/../../src/LIMMA_options.py' ./LIMMA_options.py; + ##change for Planemo test + ##cp '$__tool_directory__/src/LIMMA_options.py' ./LIMMA_options.py; #if $blockingSection.blockingConditional.addBlocking == "true": python -c 'import LIMMA_options;LIMMA_options.replaceNamesBlockInFiles("$inputSection.inputData","./factorTable.csv","./blockingTable.csv","./expressionRenamed.csv","./factorTableRenamed.csv","./blockingTableRenamed.csv","./dictionnaryRenamed.csv")'; @@ -43,6 +46,8 @@ if [ -f ./dictionnaryRenamed.csv ]; then printf "[INFO]Renaming is done\n" >> $log; Rscript '$__tool_directory__/../../src/LIMMAscriptV4.R' -i 'expressionRenamed.csv' -l '$log' -o '$outputData' -z '$outputDfData' -f 'pdf' + ##change for Planemo test + ##Rscript '$__tool_directory__/src/LIMMAscriptV4.R' -i 'expressionRenamed.csv' -l '$log' -o '$outputData' -z '$outputDfData' -f 'pdf' -a 'factorTableRenamed.csv' -s 'sumSquareFtest' -g 'dictionnaryRenamed.csv' #if $blockingSection.blockingConditional.addBlocking == "true": -b 'blockingTableRenamed.csv' @@ -360,7 +365,7 @@ <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." /> <repeat name="contrastList" title="Contrast"> - <param type="text" name="groupName" value="" label="Contrast name"/> + <param name="groupName" type="text" value="" label="Contrast name"/> <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)"> </param> @@ -477,23 +482,54 @@ <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" /> - <output name="outputDfData" file="ceas_1/ceas_1.pdf" /> + <section name="inputSection"> + <param name="inputData" value="./NormalizedData.tabular" /> + <param name="conditionInformation" value="./FactorFileGenerator/output/conditionsFile.csv" /> + </section> + <section name="contrastSection"> + <param name="factorSelection" value="Strain,Treatment" /> + <repeat name="contrastList" > + <param name="groupName" value="TreatVsControl" /> + <param name="firstGroupToCompare" value="WT*Treat,KO*Treat" /> + <param name="secondGroupToCompare" value="WT*Control,KO*Control" /> + </repeat> + <repeat name="contrastList" > + <param name="groupName" value="WTvsKO" /> + <param name="firstGroupToCompare" value="WT*Control,WT*Treat" /> + <param name="secondGroupToCompare" value="KO*Control,KO*Treat" /> + </repeat> + <conditional name="interactionSelection"> + <param name="interactionContrast" value="true" /> + <param name="controlSelection" value="Strain:WT,Treatment:Control" /> + </conditional> + </section> + <section name="blockingSection"> + <conditional name="blockingConditional"> + <param name="addBlocking" value="false"/> + </conditional> + </section> + <section name="plotSection"> + <param name="cutoffTh" value="0.05"/> + <param name="FCthreshold" value="1.2"/> + <param name="histogramToPlot" value="true"/> + <param name="volcanoToPlot" value="false"/> + <conditional name="geneInformation"> + <param name="addGeneInfo" value="false"/> + </conditional> + <param name="imagePlotlyFormat" value="png"/> + </section> + <section name="advSection"> + <param name="confoundingPolicy" value="additive"/> + </section> + <output name="outputData" file="./DiffExprLimma/output/outputStat.csv" /> + <output name="outputDfData" file="./DiffExprLimma/output/outputStatDetailed.csv" /> + <output name="html_file" file="./DiffExprLimma/output/outputHTML.zip" decompress="true" /> + <output name="log" file="./DiffExprLimma/output/outputLog.txt" compare="sim_size" delta_frac="0.10" /> </test> -</tests> + </tests> + + + <help> <![CDATA[ **What it does ?**
--- a/src/General_functions.py Fri Jun 26 09:43:41 2020 -0400 +++ b/src/General_functions.py Wed Sep 09 10:28:02 2020 +0000 @@ -1,5 +1,6 @@ import re import numpy as np +import galaxy.model def get_column_names( file_path, toNotConsider=-1, each=1): options=[] @@ -76,7 +77,7 @@ def get_condition_file_names( file_list, toNotConsider=-1, each=1): options=[] - if not isinstance(file_list,list):#if input file is a tabular file, act as get_column_names + if not (isinstance(file_list,list) or isinstance(file_list,galaxy.model.HistoryDatasetCollectionAssociation) or isinstance(file_list,galaxy.model.DatasetCollection)) :#if input file is a tabular file, act as get_column_names inputfile = open(file_list.file_name) firstLine = next(inputfile).strip().split("\t") cpt=0 @@ -88,13 +89,17 @@ if cpt==each: cpt=0 inputfile.close() - else:#if input file is a .cel file list or a collection - if not hasattr(file_list[0],'collection'):#if it is not a collection, get name easily - for i, field_component in enumerate( file_list ): - options.append( ( field_component.name, field_component.name, False ) ) - else:#if the file is a collection, have to get deeper in the corresponding HistoryDatasetCollectionAssociation object - for i, field_component in enumerate( file_list[0].collection.elements ): - options.append( ( field_component.element_identifier, field_component.element_identifier, False ) ) + else:#if input file is a .cel file list, a DatasetCollection or a HistoryDatasetCollectionAssociation + if isinstance(file_list,list):#if it is a list, retrieve names easily + for i, field_component in enumerate( file_list ): + options.append( ( field_component.name, field_component.name, False ) ) + else:#if the file is a DatasetCollection, have to get deeper in the corresponding DatasetCollection object + if isinstance(file_list,galaxy.model.DatasetCollection):#if it is a list, retrieve names easily + for i, field_component in enumerate( file_list.elements ): + options.append( ( field_component.element_identifier, field_component.element_identifier, False ) ) + else:#if the file is a HistoryDatasetCollectionAssociation, have to get a little bit deeper in the corresponding HistoryDatasetCollectionAssociation object + for i, field_component in enumerate( file_list.collection.elements ): + options.append( ( field_component.element_identifier, field_component.element_identifier, False ) ) return options def generateFactorFile( file_list, factor_list, outputFileName, logFile): @@ -102,10 +107,7 @@ outputfile = open(outputFileName, 'w') outputLog = open(logFile, 'w') sampleList=[] - if not isinstance(file_list,list): - conditionNames=get_condition_file_names(file_list,0) #unique expression file, remove the first column (index=0) - else : - conditionNames=get_condition_file_names(file_list) #.CEL files + conditionNames=get_condition_file_names(file_list,0) #if it's a unique expression file, remove the first column (index=0) for iSample, sample_component in enumerate (conditionNames): sampleList.append(str(sample_component[1])) outputLog.write("[INFO] "+str(len(sampleList))+" sample are detected as input\n")