# HG changeset patch
# User vandelj
# Date 1599647334 0
# Node ID 0435f94d27a76e3a9fba3fdf0c45165f0fe84ed9
# Parent  488e6e8bb8cbe105fd0c0e4baf138ca37f5ccbdf
"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"

diff -r 488e6e8bb8cb -r 0435f94d27a7 galaxy/wrappers/ExprQCplots.xml
--- a/galaxy/wrappers/ExprQCplots.xml	Fri Jun 26 09:41:56 2020 -0400
+++ b/galaxy/wrappers/ExprQCplots.xml	Wed Sep 09 10:28:54 2020 +0000
@@ -1,4 +1,4 @@
-<tool name="GIANT-QC Plots" id="giant_plot_functions" version="0.1.3">
+<tool name="GIANT-QC Plots" id="giant_plot_functions" version="0.1.4">
   <description>Descriptive plots of .CEL collections or normalized expression data</description>
   <requirements>
 	  <requirement type="package" version="1.40.1">bioconductor-oligo</requirement>
@@ -8,6 +8,7 @@
     <requirement type="package" version="1.8_17">r-mgcv</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"
@@ -22,8 +23,8 @@
     <exit_code range="1:9" level="fatal" description="Error in R execution, see log file for more information." />
   </stdio>
   <command>	<![CDATA[
-    ##set $dataType=$dataFile.extension
-	   #set $dataType=$dataFile[0].ext
+    ##set $dataType=$inputData.extension
+	   #set $dataType=$inputData[0].ext
 	   
 	   #if $conditionInformation and $pcaSection.factorsToInclude!="None":
        	bash $scriptPrepareTable;
@@ -33,10 +34,12 @@
         fi; 
      #end if
 
-	   #if ($dataType == "cel" and len($dataFile)>1) or ($dataType == "tabular" and len($dataFile)==1):
-	   Rscript '$__tool_directory__/../../src/ExprPlotsScript.R' -i '$dataFile' -l '$log' -f '$advSection.imageFormat' -j '$dataType'
+	   #if ($dataType == "cel" and len($inputData)>1) or ($dataType == "tabular" and len($inputData)==1):
+	   Rscript '$__tool_directory__/../../src/ExprPlotsScript.R' -i '$inputData' -l '$log' -f '$advSection.imageFormat' -j '$dataType'
+     ##change for Planemo test
+     ##Rscript '$__tool_directory__/src/ExprPlotsScript.R' -i '$inputData' -l '$log' -f '$advSection.imageFormat' -j '$dataType'
 	   #if $dataType == "cel":
-	   #for $inputDataset in $dataFile
+	   #for $inputDataset in $inputData
         -c '${inputDataset.name}'
        #end for
 	   #end if
@@ -95,7 +98,7 @@
 
     <configfile name="scriptTransfer">
 <![CDATA[
-#set $dataType=$dataFile[0].ext
+#set $dataType=$inputData[0].ext
 #set $cnt=1
 
 ##create header of HTML file
@@ -381,7 +384,7 @@
   <inputs>
     <param type="text" name="title" value="PlotFigure_toPersonalize" label="Title for output">
 	</param>		 
-    <param type="data" name="dataFile" format="cel,tabular" label="Select one .CEL collection or one tabular file" optional="false" multiple="true" >
+    <param type="data" name="inputData" format="cel,tabular" label="Select one .CEL collection or one tabular file" optional="false" multiple="true" >
 	</param>
 
 	<section name="plotSection" title="Plots selection" expanded="True">
@@ -396,7 +399,7 @@
 
     </section>
 	<section name="pcaSection" title="PCA analysis" expanded="True">
-	<param type="boolean" name="acpToPlot" checked="true" label="Plot 3D PCA" help="3D plot of conditions in the space defined by the 3 principal components">
+	  <param type="boolean" name="acpToPlot" checked="true" label="Plot 3D PCA" help="3D plot of conditions in the space defined by the 3 principal components">
     </param>
     <param type="data" name="conditionInformation" format="tabular" label="Factor information tabular file (optional)" optional="true" multiple="false">
     </param>
@@ -442,7 +445,7 @@
 		
 		<collection name="outputMicroarrayList" label="${title}_MicroarrayList" type="list">
 		  <discover_datasets pattern="(?P&lt;designation&gt;Microarray\_.*)\.(?P&lt;ext&gt;[^\._]+)?" directory="plotDir" visible="false"/>
-		  <filter>plotSection['microarrayToPlot'] and dataFile[0].ext == "cel"</filter>
+		  <filter>plotSection['microarrayToPlot'] and inputData[0].ext == "cel"</filter>
 		</collection>
 
 		<collection name="outputPCAList" label="${title}_PCA" type="list">
@@ -458,20 +461,25 @@
 
  <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="log" file="ceas_1/ceas_1.pdf" />
+    <param name="inputData" value="./NormalizedData.tabular" />
+    <section name="plotSection" >
+      <param name="histogramToPlot" value="true" />
+      <param name="maplotToPlot" value="true" />
+      <param name="boxplotToPlot" value="true" />
+      <param name="microarrayToPlot" value="false" />
+    </section>
+    <section name="pcaSection" >
+      <param name="acpToPlot" value="true" />
+      <param name="conditionInformation" value="./FactorFileGenerator/output/conditionsFile.csv" />
+      <param name="factorsToInclude" value="Strain,Treatment" />
+    </section>
+    <section name="advSection" >
+      <param name="imageFormat" value="png" />
+      <param name="imagePlotlyFormat" value="png" />
+    </section>
+    <output name="html_file" file="./ExprQCplots/output/outputHTML.zip" decompress="true" >
+    </output>  
+    <output name="log" file="./ExprQCplots/output/outputLog.txt" compare="sim_size" delta_frac="0.10" />    
   </test>
 </tests> 
 
diff -r 488e6e8bb8cb -r 0435f94d27a7 src/General_functions.py
--- a/src/General_functions.py	Fri Jun 26 09:41:56 2020 -0400
+++ b/src/General_functions.py	Wed Sep 09 10:28:54 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")