Merge pull request #5 from workflow4metabolomics/single_file

Single file
workflow4metabolomics · Feb 15, 2017 · dc4b136 · dc4b136
2 parents 89ce618 + 6d2518b
commit dc4b136
Show file tree

Hide file tree

Showing 13 changed files with 600 additions and 812 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -10,11 +10,9 @@ before_install:
  - virtualenv planemo-venv
  - . planemo-venv/bin/activate
  - pip install --upgrade pip setuptools
- - pip install planemo
- - planemo conda_init
-
-install:
- - planemo conda_install ${TRAVIS_BUILD_DIR}/galaxy/probmetab
+ - pip install planemo==0.37.0
 
 script:
- - planemo test --install_galaxy --no_cache_galaxy --conda_dependency_resolution ${TRAVIS_BUILD_DIR}/galaxy/probmetab
+ - planemo lint ${TRAVIS_BUILD_DIR}/galaxy/probmetab
+ - planemo test --conda_auto_init --conda_auto_install --conda_dependency_resolution --galaxy_branch release_17.01 --no_cache_galaxy ${TRAVIS_BUILD_DIR}/galaxy/probmetab
+
diff --git a/galaxy/probmetab/ProbMetab.xml b/galaxy/probmetab/ProbMetab.xml
diff --git a/galaxy/probmetab/README.txt b/galaxy/probmetab/README.txt
@@ -1,19 +1,15 @@
 Changelog/News
 --------------
 
+**Version 1.1.0 - 15/02/2017**
+
+- IMPROVEMENT: Probmetab is now compatible with merged individual data from xcms.xcmsSet
+
 **Version 1.0.1 - 16/05/2016**
 
 - TEST: refactoring to pass planemo test using conda dependencies
 
-
 **Version 1.0.0 - 10/06/2015**
 
 - NEW: ProbMetab first version
 
-
-Test Status
------------
-
-Planemo test using conda: passed
-
-Planemo shed_test : passed
diff --git a/galaxy/probmetab/lib.r b/galaxy/probmetab/lib.r
diff --git a/galaxy/probmetab/macros.xml b/galaxy/probmetab/macros.xml
@@ -16,29 +16,99 @@
     <token name="@COMMAND_CAMERA_SCRIPT@">
         LANG=C Rscript $__tool_directory__/probmetab.r
     </token>
-
-    <!-- zipfile load for planemo test -->
-    <token name="@COMMAND_ZIPFILE_LOAD@">
-        #if $zipfile_load_conditional.zipfile_load_select == "yes":
-            #if $zipfile_load_conditional.zip_file:
-                zipfile $zipfile_load_conditional.zip_file
+
+    <token name="@COMMAND_LOG_EXIT@">
+        ;
+        return=\$?;
+        mv log.txt '$log';
+        cat '$log';
+        sh -c "exit \$return"
+    </token>
+
+    <!-- raw file load for planemo test -->
+    <token name="@COMMAND_FILE_LOAD_NEUTRAL@">
+        #if $file_load_section_selected.file_load_conditional.file_load_select == "yes":
+            #if $file_load_section_selected.file_load_conditional.inputs.input == "zip_file":
+                zipfile$polarity '$file_load_section_selected.file_load_conditional.inputs.zip_file'
+            #else
+                #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section_selected.file_load_conditional.inputs.single_file ] )
+                #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section_selected.file_load_conditional.inputs.single_file ] )
+
+                singlefile_galaxyPath$polarity '$singlefile_galaxyPath'
+                singlefile_sampleName$polarity '$singlefile_sampleName'
             #end if
-        #end if    
+        #end if
+    </token>
+
+    <token name="@COMMAND_FILE_LOAD_ONE@">
+        #set file_load_section_selected = $file_load_section
+        #set polarity=""
+        @COMMAND_FILE_LOAD_NEUTRAL@
+    </token>
+
+    <token name="@COMMAND_FILE_LOAD_POSITIVE@">
+        #set file_load_section_selected = $file_load_sectionPositive
+        #set polarity="Positive"
+        @COMMAND_FILE_LOAD_NEUTRAL@
     </token>
-    <xml name="zipfile_load">
-        <conditional name="zipfile_load_conditional">
-            <param name="zipfile_load_select" type="select" label="Resubmit your zip file" help="Use only if you get a message which say that your original zip file have been deleted on the server." >
-                <option value="no" >no need</option>
-                <option value="yes" selected="peakgroups">yes</option>
-            </param>
-            <when value="no">
-            </when>
-            <when value="yes">
-                <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" />
-            </when>
-        </conditional>
+
+    <token name="@COMMAND_FILE_LOAD_NEGATIVE@">
+        #set file_load_section_selected = $file_load_sectionNegative
+        #set polarity="Negative"
+        @COMMAND_FILE_LOAD_NEUTRAL@
+    </token>
+
+    <xml name="input_file_load" token_polarity="">
+        <section name="file_load_section@POLARITY@" title="@POLARITY@ Resubmit your raw dataset or your zip file">
+            <conditional name="file_load_conditional">
+                <param name="file_load_select" type="select" label="@POLARITY@ Resubmit your dataset or your zip file" help="Use only if you get a message which say that your original dataset or zip file have been deleted on the server." >
+                    <option value="no" >no need</option>
+                    <option value="yes" >yes</option>
+                </param>
+                <when value="no">
+                </when>
+                <when value="yes">
+                    <conditional name="inputs">
+                        <param name="input" type="select" label="Choose your inputs method" >
+                            <option value="zip_file" selected="true">Zip file from your history containing your chromatograms</option>
+                            <option value="single_file">A mzXML or netCDF file from your history</option>
+                        </param>
+                        <when value="zip_file">
+                            <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" />
+                        </when>
+                        <when value="single_file">
+                            <param name="single_file" type="data" format="mzxml,netcdf" label="Single file"  multiple="true"/>
+                        </when>
+                    </conditional>
+                </when>
+            </conditional>
+        </section>
+    </xml>
+
+    <xml name="test_file_load_zip">
+        <section name="file_load_section">
+            <conditional name="file_load_conditional">
+                <param name="file_load_select" value="yes" />
+                <conditional name="inputs">
+                    <param name="input" value="zip_file" />
+                    <param name="zip_file" value="faahKO_reduce.zip"  ftype="zip" />
+                </conditional>
+            </conditional>
+        </section>
+    </xml>
+
+    <xml name="test_file_load_single" token_polarity="">>
+        <section name="file_load_section@POLARITY@">
+            <conditional name="file_load_conditional">
+                <param name="file_load_select" value="yes" />
+                <conditional name="inputs">
+                    <param name="input" value="single_file" />
+                    <param name="single_file" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF"  ftype="netcdf" />
+                </conditional>
+            </conditional>
+        </section>
     </xml>
-    
+
     <token name="@HELP_AUTHORS@">
 .. class:: infomark
 

diff --git a/galaxy/probmetab/probmetab.r b/galaxy/probmetab/probmetab.r
@@ -4,16 +4,16 @@
 
 
 # ----- LOG -----
-log_file=file("probmetab.log", open = "wt")
+log_file=file("log.txt", open = "wt")
 sink(log_file)
 sink(log_file, type = "out")
 
 # ----- PACKAGE -----
 cat("\tPACKAGE INFO\n")
 pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "igraph", "xcms","snow","CAMERA","batch","ProbMetab")
 for(p in pkgs) {
-	suppressWarnings( suppressPackageStartupMessages( stopifnot( library(p, quietly=TRUE, logical.return=TRUE, character.only=TRUE))))
-	cat(p,"\t",as.character(packageVersion(p)),"\n",sep="")
+    suppressWarnings( suppressPackageStartupMessages( stopifnot( library(p, quietly=TRUE, logical.return=TRUE, character.only=TRUE))))
+    cat(p,"\t",as.character(packageVersion(p)),"\n",sep="")
 }
 
 source_local <- function(fname){
@@ -22,8 +22,10 @@ source_local <- function(fname){
     source(paste(base_dir, fname, sep="/"))
 }
 cat("\n\n")
+
+
 # ----- ARGUMENTS -----
-cat("\tARGUMENTS INFO\n") 
+cat("\tARGUMENTS INFO\n")
 listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
 write.table(as.matrix(listArguments), col.names=F, quote=F, sep='\t')
 
@@ -35,68 +37,53 @@ cat("\tINFILE PROCESSING INFO\n")
 # ----- INFILE PROCESSING -----
 
 if(listArguments[["mode_acquisition"]]=="one") {
-	load(listArguments[["xa"]])
-
-    if (!is.null(listArguments[["zipfile"]])){
-        zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL
-    }
-
-    #Unzip the chromatograms file for plotting EIC pour the HTML file
-	if(exists("zipfile"))
-	{
-		if (zipfile!=""){
-			directory=unzip(zipfile)
-		}
-	}	
-	if (!exists("xa")) {
-		xa=xsAnnotate_object
-	}
-	source_local("lib.r")
-	if (!exists("variableMetadata")) variableMetadata= getVariableMetadata(xa);
-
+    load(listArguments[["image"]])
+    cat("\t\tXA OBJECT INFO\n")
+    print(xa)
+
+    source_local("lib.r")
+    rawFilePath = getRawfilePathFromArguments(listArguments)
+    zipfile = rawFilePath$zipfile
+    singlefile = rawFilePath$singlefile
+    retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
+
+    if (!exists("variableMetadata")) variableMetadata= getVariableMetadata(xa);
+
 } else if(listArguments[["inputs_mode"]]=="two"){
-	load(listArguments[["image_pos"]])
-
-    if (!is.null(listArguments[["zipfile"]])){
-        zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL
-    }
-
-	#Unzip the chromatograms file for plotting EIC pour the HTML file
-	if(exists("zipfile")) {
-		if (zipfile!=""){
-			directory=unzip(zipfile)
-		}
-	}
-	if (!exists("xa")) {
-		xa=xsAnnotate_object
-	}
-	xaP=xa
-	source_local("lib.r")	
-	if (!exists("variableMetadata")) variableMetadataP= getVariableMetadata(xa)
-	else variableMetadataP=variableMetadata
-
-
-	load(listArguments[["image_neg"]])
-
-    if (!is.null(listArguments[["zipfile"]])){
-        zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL
-    }
-
-	#Unzip the chromatograms file for plotting EIC pour the HTML file
-	if(exists("zipfile")) {
-
-	 	if (zipfile!=""){
-			directory=unzip(zipfile)
-		}
-	}
-	if (!exists("xa")) {
-		xa=xsAnnotate_object
-	}
-	xaN=xa
-	source_local("lib.r")
-
-	if (!exists("variableMetadata")) variableMetadataN= getVariableMetadata(xa)
-	else variableMetadataN=variableMetadata
+
+    # POSITIVE
+    load(listArguments[["image_pos"]])
+
+    if (!exists("xa")) xaP=xsAnnotate_object
+    else xaP=xa
+    cat("\t\tXA-POSITIVE OBJECT INFO\n")
+    print(xaP)
+
+    if (!exists("variableMetadata")) variableMetadataP = getVariableMetadata(xa)
+    else variableMetadataP = variableMetadata
+
+    source_local("lib.r")
+    rawFilePath = getRawfilePathFromArguments(listArguments)
+    zipfilePos = rawFilePath$zipfile
+    singlefilePos = rawFilePath$singlefile
+    retrieveRawfileInTheWorkingDirectory(singlefilePos, zipfilePos)
+
+    # NEGATIVE
+    load(listArguments[["image_neg"]])
+
+    if (!exists("xa"))  xaN=xsAnnotate_object
+    else xaN=xa
+    cat("\t\tXA-NEGATIVE OBJECT INFO\n")
+    print(xaP)
+
+    if (!exists("variableMetadata")) variableMetadataN = getVariableMetadata(xa)
+    else variableMetadataN = variableMetadata
+
+    source_local("lib.r")
+    rawFilePath = getRawfilePathFromArguments(listArguments)
+    zipfileNeg = rawFilePath$zipfile
+    singlefileNeg = rawFilePath$singlefile
+    retrieveRawfileInTheWorkingDirectory(singlefileNeg, zipfileNeg)
 }
 
 #Import the different functions
@@ -107,13 +94,12 @@ source_local("export.class.table-color-graph.R")
 cat("\tMAIN PROCESSING INFO\n")
 
 if(listArguments[["mode_acquisition"]]=="one") {
-	results=probmetab(xa=xa, variableMetadata=variableMetadata,listArguments=listArguments)
+    results=probmetab(xa=xa, variableMetadata=variableMetadata,listArguments=listArguments)
 } else if(listArguments[["inputs_mode"]]=="two"){
-	results=probmetab(xaP=xaP, xaN=xaN,variableMetadataP=variableMetadataP, variableMetadataN=variableMetadataN, listArguments=listArguments)
+    results=probmetab(xaP=xaP, xaN=xaN,variableMetadataP=variableMetadataP, variableMetadataN=variableMetadataN, listArguments=listArguments)
 }
 #delete the parameters to avoid the passage to the next tool in .RData image
 #rm(listArguments)
 cat("\tDONE\n")
 #saving R data in .Rdata file to save the variables used in the present tool
 #save.image(paste("probmetab","RData",sep="."))
-
diff --git a/.../test-data/faahOK-single.xset.merged.group.retcor.group.fillPeaks.annotate.negative.Rdata b/.../test-data/faahOK-single.xset.merged.group.retcor.group.fillPeaks.annotate.negative.Rdata
diff --git a/galaxy/probmetab/test-data/ko15.CDF b/galaxy/probmetab/test-data/ko15.CDF
diff --git a/galaxy/probmetab/test-data/ko16.CDF b/galaxy/probmetab/test-data/ko16.CDF
diff --git a/galaxy/probmetab/test-data/wt15.CDF b/galaxy/probmetab/test-data/wt15.CDF
diff --git a/galaxy/probmetab/test-data/wt16.CDF b/galaxy/probmetab/test-data/wt16.CDF
diff --git a/galaxy/probmetab/tool_test_output.html b/galaxy/probmetab/tool_test_output.html
diff --git a/galaxy/probmetab/tool_test_output.json b/galaxy/probmetab/tool_test_output.json