Mercurial > repos > vandelj > giant_volcano_plot
changeset 1:75505421bcf3 draft
"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 | 866eec4605b0 |
| files | galaxy/wrappers/VolcanoPlotTool.xml src/General_functions.py |
| diffstat | 2 files changed, 55 insertions(+), 29 deletions(-) [+] |
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--- a/galaxy/wrappers/VolcanoPlotTool.xml Fri Jun 26 09:45:41 2020 -0400 +++ b/galaxy/wrappers/VolcanoPlotTool.xml Wed Sep 09 10:38:06 2020 +0000 @@ -1,4 +1,4 @@ -<tool name="GIANT-Plot volcanos" id="giant_volcano_plot" version="0.3.3"> +<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> @@ -8,6 +8,7 @@ <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" @@ -25,6 +26,8 @@ #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 [ $ret_code != 0 ]; then @@ -44,6 +47,8 @@ Rscript '$__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}' @@ -324,25 +329,44 @@ </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="outputData" file="ceas_1/ceas_1.pdf" /> + <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> + </tests> + + + <help> <![CDATA[ **What it does ?**
--- a/src/General_functions.py Fri Jun 26 09:45:41 2020 -0400 +++ b/src/General_functions.py Wed Sep 09 10:38:06 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")