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changeset 49:f772a5caa86a

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Added more options and better documentation. Added MsClust support for parsing XCMS alignment results. Improved output reports for XCMS wrappers. New tools.
author pieter.lukasse@wur.nl
date Wed, 10 Dec 2014 22:03:27 +0100
parents 26b93438f30e
children 93102202ab79
files MsClust.jar README.rst metaMS_cmd_annotate.r metaMS_cmd_interface.r metaMS_cmd_pick_and_group.r metams_lcms_annotate.xml metams_lcms_pick_and_group.xml msclust.xml next.r static/images/CAMERA_results.png static/images/massEIC.png xcms_differential_analysis.r xcms_differential_analysis.xml xcms_get_alignment_eic.r xcms_get_alignment_eic.xml xcms_get_mass_eic.r xcms_get_mass_eic.xml
diffstat 17 files changed, 1036 insertions(+), 188 deletions(-) [+]
line wrap: on
line diff
Binary file MsClust.jar has changed
--- a/README.rst	Wed Nov 19 15:11:45 2014 +0100
+++ b/README.rst	Wed Dec 10 22:03:27 2014 +0100
@@ -19,6 +19,8 @@
 ============== ======================================================================
 Date            Changes
 -------------- ----------------------------------------------------------------------
+December 2014  * Added MsClust support for parsing XCMS alignment results.
+               * Improved output reports for XCMS wrappers.
 November 2014  * Added XCMS related tool wrappers (for metaMS and diffreport)
 September 2014 * Added new membership cutoff option for final clusters in MsClust
                * Improved MsClust memory usage for large datasets 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metaMS_cmd_annotate.r	Wed Dec 10 22:03:27 2014 +0100
@@ -0,0 +1,83 @@
+## read args:
+args <- commandArgs(TRUE)
+## the constructed DB, e.g. "E:/Rworkspace/metaMS/data/LCDBtest.RData"
+args.constructedDB <- args[1]
+## data file in xset format:
+args.xsetData <- args[2]
+## settings file, e.g. "E:/Rworkspace/metaMS/data/settings.r", should contain assignment to an object named "customMetaMSsettings" 
+args.settings <- args[3]
+
+## output file names, e.g. "E:/Rworkspace/metaMS/data/out.txt"
+args.outAnnotationTable <- args[4]
+
+## report files
+args.htmlReportFile <- args[5]
+args.htmlReportFile.files_path <- args[6]
+
+if (length(args) == 7)
+{
+	args.outLogFile <- args[7]
+	# suppress messages:
+	# Send all STDERR to STDOUT using sink() see http://mazamascience.com/WorkingWithData/?p=888
+	msg <- file(args.outLogFile, open="wt")
+	sink(msg, type="message") 
+	sink(msg, type="output")
+}
+
+cat("\nSettings used===============:\n")
+cat(readChar(args.settings, 1e5))
+
+
+tryCatch(
+        {
+	        library(metaMS)
+	
+			## load the constructed DB :
+			tempEnv <- new.env()
+			testDB <- load(args.constructedDB, envir=tempEnv)
+			xsetData <- readRDS(args.xsetData)
+			
+			## load settings "script" into "customMetaMSsettings" 
+			source(args.settings, local=tempEnv)
+			message(paste(" loaded : ", args.settings))
+			
+			# Just to highlight: if you want to use more than one 
+			# trigger runLC: 
+			LC <- runLC(xset=xsetData, settings = tempEnv[["customMetaMSsettings"]], DB = tempEnv[[testDB[1]]]$DB, nSlaves=20, returnXset = TRUE)
+			
+			# write out runLC annotation results:
+			write.table(LC$PeakTable, args.outAnnotationTable, sep="\t", row.names=FALSE)
+			
+			# the used constructed DB (write to log):
+			cat("\nConstructed DB info===============:\n")
+			str(tempEnv[[testDB[1]]]$Info)
+			cat("\nConstructed DB table===============:\n") 
+			if (length(args) == 7)
+			{
+				write.table(tempEnv[[testDB[1]]]$DB, args.outLogFile, append=TRUE, row.names=FALSE)
+				write.table(tempEnv[[testDB[1]]]$Reftable, args.outLogFile, sep="\t", append=TRUE, row.names=FALSE)
+			}
+			
+			message("\nGenerating report.........")
+			# report
+			dir.create(file.path(args.htmlReportFile.files_path), showWarnings = FALSE, recursive = TRUE)
+			html <- "<html><body><h1>Summary of annotation results:</h1>" 
+			nrTotalFeatures <- nrow(LC$PeakTable)
+			nrAnnotatedFeatures <- nrow(LC$Annotation$annotation.table)
+			html <- paste(html,"<p>Total nr of features: ", nrTotalFeatures,"</p>", sep="") 
+			html <- paste(html,"<p>Total nr of annotated features: ", nrAnnotatedFeatures,"</p>", sep="")
+			
+			html <- paste(html,"</body><html>")
+			message("finished generating report")
+			write(html,file=args.htmlReportFile)
+			# unlink(args.htmlReportFile)
+			cat("\nWarnings================:\n")
+			str( warnings() ) 
+		},
+        error=function(cond) {
+            sink(NULL, type="message") # default setting
+			sink(stderr(), type="output")
+            message("\nERROR: ===========\n")
+            print(cond)
+        }
+    ) 
--- a/metaMS_cmd_interface.r	Wed Nov 19 15:11:45 2014 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,99 +0,0 @@
-## read args:
-args <- commandArgs(TRUE)
-## the constructed DB, e.g. "E:/Rworkspace/metaMS/data/LCDBtest.RData"
-args.constructedDB <- args[1]
-## data files, e.g. "E:/Rworkspace/metaMS/data/data.zip" (with e.g. .CDF files) and unzip output dir, e.g. "E:/"
-args.dataZip <- args[2]
-args.zipExtrDir <- paste(args[2],"dir/")
-## settings file, e.g. "E:/Rworkspace/metaMS/data/settings.r", should contain assignment to an object named "customMetaMSsettings" 
-args.settings <- args[3]
-
-## output file names, e.g. "E:/Rworkspace/metaMS/data/out.txt"
-args.outAnnotationTable <- args[4]
-args.outLogFile <- args[5]
-args.xsetOut <- args[6]
-
-## report files
-args.htmlReportFile <- args[7]
-args.htmlReportFile.files_path <- args[8]
-
-# Send all STDERR to STDOUT using sink() see http://mazamascience.com/WorkingWithData/?p=888
-msg <- file(args.outLogFile, open="wt")
-sink(msg, type="message") 
-sink(msg, type="output")
-
-cat("\nSettings used===============:\n")
-cat(readChar(args.settings, 1e5))
-
-
-tryCatch(
-        {
-	        library(metaMS)
-	
-			## load the constructed DB :
-			tempEnv <- new.env()
-			testDB <- load(args.constructedDB, envir=tempEnv)
-			
-			## load the data files from a zip file
-			files <- unzip(args.dataZip, exdir=args.zipExtrDir)
-			
-			## load settings "script" into "customMetaMSsettings" 
-			source(args.settings, local=tempEnv)
-			message(paste(" loaded : ", args.settings))
-			
-			# Just to highlight: if you want to use more than one 
-			# trigger runLC: 
-			LC <- runLC(files, settings = tempEnv[["customMetaMSsettings"]], DB = tempEnv[[testDB[1]]]$DB, nSlaves=20, returnXset = TRUE)
-			
-			# write out runLC annotation results:
-			write.table(LC$Annotation$annotation.table, args.outAnnotationTable, sep="\t", row.names=FALSE)
-			
-			# the used constructed DB (write to log):
-			cat("\nConstructed DB info===============:\n")
-			str(tempEnv[[testDB[1]]]$Info)
-			cat("\nConstructed DB table===============:\n") 
-			write.table(tempEnv[[testDB[1]]]$DB, args.outLogFile, append=TRUE, row.names=FALSE)
-			write.table(tempEnv[[testDB[1]]]$Reftable, args.outLogFile, sep="\t", append=TRUE, row.names=FALSE)
-			# save xset as rdata:
-			xsetData <- LC$xset@xcmsSet
-			saveRDS(xsetData, file=args.xsetOut)
-			
-			message("\nGenerating report.........")
-			# report
-			dir.create(file.path(args.htmlReportFile.files_path), showWarnings = FALSE)
-			setwd(file.path(args.htmlReportFile.files_path))
-			html <- "<html><body><h1>Extracted Ion Chromatograms of groups with more than 3 peaks</h1>" 
-			
-			LC$xset@xcmsSet
-			gt <- groups(LC$xset@xcmsSet)
-			colnames(gt)
-			groupidx1 <- which(gt[,"rtmed"] > 0 & gt[,"rtmed"] < 3000 & gt[,"npeaks"] > 3)
-			if (length(groupidx1) > 0)
-			{
-				eiccor <- getEIC(LC$xset@xcmsSet, groupidx = c(groupidx1))
-				eicraw <- getEIC(LC$xset@xcmsSet, groupidx = c(groupidx1), rt = "raw")
-				for (i in 1:length(groupidx1)) 
-				{
-					figureName <- paste(args.htmlReportFile.files_path, "/figure", i,".png", sep="")
-					html <- paste(html,"<img src='", "figure", i,".png' />", sep="") 
-					png( figureName, type="cairo" ) 
-					plot(eiccor, LC$xset@xcmsSet, groupidx = i)
-					devname = dev.off()
-				}
-			}
-			
-			
-			html <- paste(html,"</body><html>")
-			message("finished generating report")
-			write(html,file=args.htmlReportFile)
-			# unlink(args.htmlReportFile)
-			cat("\nWarnings================:\n")
-			str( warnings() ) 
-		},
-        error=function(cond) {
-            sink(NULL, type="message") # default setting
-			sink(stderr(), type="output")
-            message("\nERROR: ===========\n")
-            print(cond)
-        }
-    ) 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metaMS_cmd_pick_and_group.r	Wed Dec 10 22:03:27 2014 +0100
@@ -0,0 +1,89 @@
+## read args:
+args <- commandArgs(TRUE)
+## data files, e.g. "E:/Rworkspace/metaMS/data/data.zip" (with e.g. .CDF files) and unzip output dir, e.g. "E:/"
+args.dataZip <- args[1]
+args.zipExtrDir <- sub("\\.","_",paste(args[1],"dir", sep=""))
+dir.create(file.path(args.zipExtrDir), showWarnings = FALSE, recursive = TRUE)
+## settings file, e.g. "E:/Rworkspace/metaMS/data/settings.r", should contain assignment to an object named "customMetaMSsettings" 
+args.settings <- args[2]
+
+## output file names, e.g. "E:/Rworkspace/metaMS/data/out.txt"
+args.outPeakTable <- args[3]
+args.xsetOut <- args[4]
+
+## report files
+args.htmlReportFile <- args[5]
+args.htmlReportFile.files_path <- args[6]
+
+
+if (length(args) == 7)
+{
+	args.outLogFile <- args[7]
+	# suppress messages:
+	# Send all STDERR to STDOUT using sink() see http://mazamascience.com/WorkingWithData/?p=888
+	msg <- file(args.outLogFile, open="wt")
+	sink(msg, type="message") 
+	sink(msg, type="output")
+}
+
+cat("\nSettings used===============:\n")
+cat(readChar(args.settings, 1e5))
+
+
+tryCatch(
+        {
+	        library(metaMS)
+	
+			## load the data files from a zip file
+			files <- unzip(args.dataZip, exdir=args.zipExtrDir)
+			
+			## load settings "script" into "customMetaMSsettings"
+			tempEnv <- new.env() 
+			source(args.settings, local=tempEnv)
+			message(paste(" loaded : ", args.settings))
+			allSettings <- tempEnv[["customMetaMSsettings"]] 
+			
+			# trigger runLC: 
+			LC <- runLC(files, settings = allSettings, nSlaves=20, returnXset = TRUE)
+			
+			# write out runLC annotation results:
+			write.table(LC$PeakTable, args.outPeakTable, sep="\t", row.names=FALSE)
+			
+			# save xset as rdata:
+			xsAnnotatePreparedData <- LC$xset
+			saveRDS(xsAnnotatePreparedData, file=args.xsetOut)
+			
+			message("\nGenerating report.........")
+			# report
+			dir.create(file.path(args.htmlReportFile.files_path), showWarnings = FALSE, recursive = TRUE)
+			html <- "<html><body><h1>Info on alignment quality </h1>" 
+			# TODO add (nr and mass error) and group size
+			
+			message("\nPlotting figures... ")
+			figureName <- paste(args.htmlReportFile.files_path, "/figure_retcor.png", sep="")
+			html <- paste(html,"<img src='figure_retcor.png' /><br/>", sep="") 
+			png( figureName, type="cairo", width=1100,height=600 ) 
+			retcor(LC$xset@xcmsSet, method="peakgroups", plottype = "mdevden")
+			html <- paste(html,"<a>*NB: retention time correction plot based on 'peakgroups' option with default settings. This is not the plot matching the exact settings used in the run, 
+									but just intended to give a rough estimate of the retention time shifts present in the data. A more accurate plot will be available once
+                                    this option is added in metaMS API. </a><br/>", sep="")
+			devname = dev.off()
+			
+			
+			gt <- groups(LC$xset@xcmsSet)
+			groupidx1 <- which(gt[,"rtmed"] > 0 & gt[,"rtmed"] < 3000 & gt[,"npeaks"] > 3)
+			
+			html <- paste(html,"</body><html>")
+			message("finished generating report")
+			write(html,file=args.htmlReportFile)
+			# unlink(args.htmlReportFile)
+			cat("\nWarnings================:\n")
+			str( warnings() ) 
+		},
+        error=function(cond) {
+            sink(NULL, type="message") # default setting
+			sink(stderr(), type="output")
+            message("\nERROR: ===========\n")
+            print(cond)
+        }
+    ) 
--- a/metams_lcms_annotate.xml	Wed Nov 19 15:11:45 2014 +0100
+++ b/metams_lcms_annotate.xml	Wed Dec 10 22:03:27 2014 +0100
@@ -1,58 +1,28 @@
-<tool id="metams_lcms_annotate" name="METAMS-LC/MS Annotate"  version="0.0.3">
-	<description> Runs metaMS process for LC/MS feature grouping and annotation</description>
+<tool id="metams_lcms_annotate" name="METAMS-LC/MS Annotate"  version="0.0.4">
+	<description> Runs metaMS process for LC/MS feature annotation</description>
 	<requirements>
 		<requirement type="package" version="3.1.1">R_bioc_metams</requirement>
 	</requirements>	
 	<command interpreter="Rscript">
-		metaMS_cmd_interface.r 
+		metaMS_cmd_annotate.r 
 	    $constructed_db
-	    $data_files
+	    $xsetData
 	    $customMetaMSsettings
 	    $outputFile 
-	    $outputLog
-	    $xsetOut
 	    $htmlReportFile
 	    $htmlReportFile.files_path
+	    $outputLog
 	</command>
 <inputs>
 	<param name="constructed_db" type="select" label="Constructed DB" help="Reference annotation database generated from matching measurements of a mixture of chemical standards
 	against a manually validated reference table which contains the key analytical information for each standard." 
       		 dynamic_options='get_directory_files("tool-data/shared/PRIMS-metabolomics/metaMS")'/>
 	
-	<param name="data_files" type="data" format="prims.fileset.zip" label="Data files (.zip file with CDFs)" help=".zip file containing the CDF files of the new measurements"/>
-	
-	
+	<param name="xsetData" type="data" format="rdata" label="xcmsSet data file (xset RDATA)" help="E.g. output data file resulting from METAMS 'feature picking, aligning and grouping' run"/>
 	
 	<param name="protocolName" type="text" size="30" label="protocolName" value="Synapt.QTOF.RP" help="protocolName"/>
 	
-	<param name="method" type="select" size="30" label="PEAK PICKING method =====================================================">
-		<option value="matchedFilter" selected="true">matchedFilter</option>
-	</param>
-	<param name="step" type="float" size="10" value="0.05" label="step" help="step"/>
-	<param name="fwhm" type="integer" size="10" value="20" label="fwhm" help="fwhm" />
-	<param name="snthresh" type="integer" size="10" value="4" label="snthresh" help="snthresh" />
-	<param name="max" type="integer" size="10" value="50" label="max" help="max" />
-	
-	<param name="min_class_fraction" type="float" size="10" value="0.3" label="ALIGNMENT min.class.fraction =====================================================" help="min.class.fraction"/>
-	<param name="min_class_size" type="integer" size="10" value="3" label="min.class.size" help="min.class.size" />
-	<param name="mzwid" type="float" size="10" value="0.1" label="mzwid" help="mzwid"/>
-	<param name="bws" type="text" size="10" value="30,10" label="bws" help="bws"/>
-	<param name="missingratio" type="float" size="10" value="0.2" label="missingratio" help="missingratio"/>
-	<param name="extraratio" type="float" size="10" value="0.1" label="extraratio" help="extraratio"/>
-	<param name="retcormethod" type="select" size="30" label="retcormethod" help="retcormethod">
-		<option value="linear" selected="true">linear</option>
-	</param>
-	<param name="retcorfamily" type="select" size="30" label="retcorfamily" help="retcorfamily">
-		<option value="symmetric" selected="true">symmetric</option>
-	</param>
-	<param name="fillPeaks" type="select" size="30" label="fillPeaks" help="fillPeaks">
-		<option value="TRUE" selected="true">Yes</option>
-		<option value="FALSE">No</option>
-	</param>
-	<param name="perfwhm" type="float" size="10" value="0.6" label="CAMERA perfwhm =====================================================" help="perfwhm"/>
-	<param name="cor_eic_th" type="float" size="10" value="0.7" label="cor_eic_th" help="cor_eic_th" />
-	<param name="ppm" type="float" size="10" value="5.0" label="ppm" help="ppm" />
-	<param name="rtdiff" type="float" size="10" value="1.5" label="MATCH2DB rtdiff =====================================================" help="rtdiff"/>
+	<param name="rtdiff" type="float" size="10" value="1.5" label="rtdiff" help="rtdiff"/>
 	<param name="rtval" type="float" size="10" value="0.1" label="rtval" help="rtval" />
 	<param name="mzdiff" type="float" size="10" value="0.005" label="mzdiff" help="mzdiff" />
 	<param name="match2DB_ppm" type="float" size="10" value="5.0" label="ppm" help="ppm" />
@@ -64,27 +34,7 @@
 <configfile name="customMetaMSsettings">## start comment
 		## metaMS process settings
 		customMetaMSsettings &lt;- metaMSsettings(protocolName = "${protocolName}",
-                            chrom = "LC",
-                            PeakPicking = list(
-                              method = "${method}",
-                              step = ${step},
-                              fwhm = ${fwhm},
-                              snthresh = ${snthresh},
-                              max = ${max}),
-                            Alignment = list(
-                              min.class.fraction = ${min_class_fraction},
-                              min.class.size = ${min_class_size},
-                              mzwid = ${mzwid},
-                              bws = c(${bws}),
-                              missingratio = ${missingratio},
-                              extraratio = ${extraratio},
-                              retcormethod = "${retcormethod}",
-                              retcorfamily = "${retcorfamily}",            
-                              fillPeaks = ${fillPeaks}),
-                            CAMERA = list(
-                              perfwhm = ${perfwhm},
-                              cor_eic_th = ${cor_eic_th},
-                              ppm= ${ppm}))
+                            chrom = "LC")
 metaSetting(customMetaMSsettings, "match2DB") &lt;- list(
             rtdiff = ${rtdiff},
             rtval = ${rtval},
@@ -96,8 +46,7 @@
 
 <outputs>
 	<data name="outputFile" format="tabular" label="${tool.name} on ${on_string} - metaMS annotated file (TSV)"/>
-	<data name="outputLog" format="txt" label="${tool.name} on ${on_string} - metaMS LOG"/>
-	<data name="xsetOut" format="rdata" label="${tool.name} on ${on_string} - metaMS xcmsSet (RDATA)"/>
+	<data name="outputLog" format="txt" label="${tool.name} on ${on_string} - metaMS LOG" hidden="True"/>
 	<data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - metaMS report (HTML)"/>
 </outputs>
 <tests>
@@ -109,12 +58,17 @@
 
 .. class:: infomark
   
-Runs metaMS process for LC/MS feature grouping and annotation. Parts of the metaMS process also make use of the XCMS and CAMERA tools and algorithms.
-The figure below shows the main parts of the metaMS process. 
+Runs metaMS process for LC/MS feature annotation. 
+The figure below shows the main parts of the metaMS process.
+This tool related to the last step of this process. 
 
 .. image:: $PATH_TO_IMAGES/metaMS.png 
 
 
+From CAMERA documentation: 
+
+.. image:: $PATH_TO_IMAGES/CAMERA_results.png 
+
 **References**
 
 If you use this Galaxy tool in work leading to a scientific publication please
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metams_lcms_pick_and_group.xml	Wed Dec 10 22:03:27 2014 +0100
@@ -0,0 +1,296 @@
+<tool id="metams_lcms_pick_and_group" name="METAMS-LC/MS Pick, Align and Group"  version="0.0.4">
+	<description> Runs metaMS process for LC/MS feature picking, aligning and grouping</description>
+	<requirements>
+		<requirement type="package" version="3.1.1">R_bioc_metams</requirement>
+	</requirements>	
+	<command interpreter="Rscript">
+		metaMS_cmd_pick_and_group.r 
+	    $data_files
+	    $customMetaMSsettings
+	    $outputFile 
+	    $xsetOut
+	    $htmlReportFile
+	    $htmlReportFile.files_path
+	    $outputLog
+	</command>
+<inputs>
+	<param name="data_files" type="data" format="prims.fileset.zip" label="Data files (.zip file with CDF, mzML or mzXML files)" help=".zip file containing the CDF, mzML or mzXML files of the new measurements"/>
+	
+	<param name="protocolName" type="text" size="30" label="protocolName" value="e.g. Synapt.QTOF.RP" 
+		help="Choose a name to give for the specific settings in the parameters below"/><!-- TODO - let user choose this -->
+	
+	
+	<!-- ===========NB : if peak picking, alignment OR CAMERA settings have to be reused for runGC wrapper in the future, we can use Galaxy macro expansions here
+	                     to avoid defining these parameters again in the runGC wrapper ========================= -->
+	<conditional name="peakPicking">
+		<param name="method" type="select" size="30" label="PEAK PICKING method ====================================================="
+		help="matchedFilter=Feature detection in the chromatographic time domain ; centWave=Feature detection for high resolution LC/MS data">
+			<option value="matchedFilter" selected="true">matchedFilter</option>
+			<option value="centWave" >centWave</option>
+		</param>
+		<when value="matchedFilter">	
+			<param name="fwhm" type="integer" size="10" value="20" label="fwhm" 
+			help="full width at half maximum of matched filtration gaussian model peak. Only used to calculate the actual sigma" />
+			<param name="sigma_denom" type="float" size="10" value="2.3548" label="sigma_denominator" 
+			help="denominator for standard deviation (width) of matched filtration model peak (e.g. sigma = fwhm/2.3548)" />
+			<param name="max" type="integer" size="10" value="50" label="max" 
+			help="maximum number of peaks per extracted ion chromatogram" />
+			<param name="snthresh" type="integer" size="10" value="4" label="snthresh" 
+			help="signal to noise ratio cutoff" />
+			<param name="step" type="float" size="10" value="0.05" label="step" 
+			help="step size to use for profile generation"/>
+			<param name="steps" type="integer" size="10" value="2" label="steps" 
+			help="number of steps to merge prior to filtration"/>
+			<param name="mzdiff" type="float" size="10" value="0.8" label="mzdiff" 
+			help="minimum difference in m/z for peaks with overlapping retention times"/>
+		</when>
+		<when value="centWave">
+			<param name="ppm" type="integer" size="10" value="25" label="ppm" 
+			help="maxmial tolerated m/z deviation in consecutive scans, in ppm" />
+			<param name="peakwidth" type="text" size="10" value="20,50" label="peakwidth" 
+			help="Chromatographic peak width, given as range (min,max) in seconds" />
+			<param name="snthresh" type="integer" size="10" value="10" label="snthresh" 
+			help="signal to noise ratio cutoff" />			
+			<param name="prefilter" type="text" size="10" value="3,100" label="prefilter=c(k,I)" 
+				help="Prefilter step for the first phase. Mass traces are only retained if 
+				they contain at least k peaks with intensity &gt; = I" />			
+			<param name="mzCenterFun" type="select" size="30" label="mzCenterFun" 
+				help="Function to calculate the m/z center of the feature: wMean intensity weighted mean of the 
+				feature m/z values, mean mean of the feature m/z values, apex use m/z value at peak apex, 
+				wMeanApex3 intensity weighted mean of the m/z value at peak apex and the m/z value left and 
+				right of it, meanApex3 mean of the m/z value at peak apex and the m/z value left and right of it">
+				<option value="wMean" selected="true">wMean</option>
+				<option value="mean" >mean</option>
+				<option value="apex" >apex</option>
+				<option value="wMeanApex3" >wMeanApex3</option>
+				<option value="meanApex3" >meanApex3</option>
+			</param>
+			<param name="integrate" type="select" size="30" label="integrate" 
+				help="Integration method. If =1 peak limits are found through descent 
+				on the mexican hat filtered data, if =2 the descent is done on the real data. 
+				Method 2 is very accurate but prone to noise, while method 1 is more robust to noise but less exact">
+				<option value="1" selected="true">1</option>
+				<option value="2" >2</option>
+			</param>
+			<param name="mzdiff" type="float" size="10" value="-0.001" label="mzdiff" 
+				help="minimum difference in m/z for peaks with overlapping retention times, can be negative to allow overlap" />
+			<param name="fitgauss" type="integer" size="10" value="20" label="fitgauss" 
+				help="logical, if Yes: a Gaussian is fitted to each peak" >
+				<option value="TRUE" selected="true">Yes</option>
+				<option value="FALSE" >No</option>
+			</param>
+			<param name="noise" type="integer" size="10" value="0" label="noise" 
+				help="optional argument which is useful for data that was centroided without any intensity
+				 threshold, centroids with intensity &lt; noise are omitted from ROI detection" />
+		</when>
+	</conditional>
+
+	
+	<param name="min_class_fraction" type="float" size="10" value="0.3" label="ALIGNMENT min.class.fraction =====================================================" 
+		    help="Minimum fraction of samples necessary in the alignment to make it a valid alignment/group"/>
+	<param name="min_class_size" type="integer" size="10" value="3" label="min.class.size" 
+			help="Minimum number of samples necessary in the alignment to make it a valid alignment/group. The lowest criteria
+			between this and min.class.fraction will be used." />
+	<param name="mzwid" type="float" size="10" value="0.1" label="mzwid" 
+			help="width of overlapping m/z slices to use for creating peak density chromatograms and grouping peaks across samples"/>
+	<param name="bws" type="text" size="10" value="30,10" label="bws" 
+			help="bandwidth (standard deviation or half width at half maximum) of gaussian smoothing kernel 
+			to apply to the peak density chromatogram. Fill in two values separated by comma. First value is used for 
+			first grouping round, seccond value is used for last grouping/alignment round after retention time
+			correction. "/>
+	
+	<conditional name="retcor">
+		<param name="retcormethod" type="select" size="30" label="retcormethod" 
+			help="retention time correction method. 'peakgroups' is the default density based approach, 'obiwarp' is 
+			  alignment data by Ordered Bijective Interpolated Warping ">
+			<option value="peakgroups" selected="true">peakgroups</option>
+			<option value="obiwarp" >obiwarp</option>
+		</param>
+		<when value="peakgroups">
+			<param name="retcorfamily" type="select" size="30" label="retcorfamily" 
+				help="retention time correction method type/family">
+				<option value="symmetric" selected="true">symmetric</option>
+				<option value="gaussian">gaussian</option>
+			</param>
+			<param name="smooth" type="select" size="30" label="smooth" 
+				help="either 'loess' for non-linear alignment or 'linear' for linear alignment">
+				<option value="linear" selected="true">linear</option>
+				<option value="loess">loess (TODO - waiting for metaMS to add/parse this option)</option>
+			</param>
+			<param name="missingratio" type="float" size="10" value="0.2" label="missingratio" 
+				help="ratio of missing samples to allow in retention time correction groups"/>
+			<param name="extraratio" type="float" size="10" value="0.1" label="extraratio" 
+				help="ratio of extra peaks to allow in retention time correction correction groups"/>
+		</when>
+		<when value="obiwarp">
+			<param name="profStep" type="integer" size="10" value="1" label="profStep" 
+				help="step size (in m/z) to use for profile generation from the raw data files" />
+		</when>
+	</conditional>
+		
+	<param name="fillPeaks" type="select" size="30" label="fillPeaks" 
+		help="Fill missing peaks in peak groups/alignments that do not include peaks from every sample. 
+		This method produces intensity values for those missing samples by integrating raw data in peak group region.">
+		<option value="TRUE" selected="true">Yes</option>
+		<option value="FALSE">No</option>
+	</param>
+	<param name="perfwhm" type="float" size="10" value="0.6" label="CAMERA perfwhm =====================================================" 
+		help="percentage of FWHM width"/>
+	<param name="cor_eic_th" type="float" size="10" value="0.7" label="cor_eic_th" 
+		help="correlation threshold (0..1)" />
+	<param name="ppm" type="float" size="10" value="5.0" label="ppm" 
+		help="General ppm error" />
+	
+	<param name="groupCorr_graphMethod" type="select" size="30" label="(groupCorr)graphMethod" 
+		help="Method selection for grouping peaks after correlation analysis into pseudospectra.">
+		<option value="hcs" selected="true">hcs</option>
+	</param>
+		
+	<param name="groupCorr_pval" type="float" size="10" value="0.05" label="(groupCorr)pval" 
+		help="significant correlation threshold" />	
+
+	<param name="groupCorr_calcCiS" type="select" size="30" label="(groupCorr)calcCiS" 
+		help="Use correlation inside samples for peak grouping">
+		<option value="TRUE" selected="true">Yes</option>
+		<option value="FALSE">No</option>
+	</param>
+	
+	<param name="groupCorr_calcIso" type="select" size="30" label="(groupCorr)calcIso" 
+		help="Use isotopic relationship for peak grouping">
+		<option value="TRUE" >Yes</option>
+		<option value="FALSE" selected="true">No</option>
+	</param>
+	
+	<param name="groupCorr_calcCaS" type="select" size="30" label="(groupCorr)calcCaS" 
+		help="Use correlation across samples for peak grouping">
+		<option value="TRUE" >Yes</option>
+		<option value="FALSE" selected="true">No</option>
+	</param>
+	
+	
+	<param name="findIsotopes_maxcharge" type="integer" size="10" value="3" label="(findIsotopes)maxcharge" 
+			help="max. ion charge" />
+			
+	<param name="findIsotopes_maxiso" type="integer" size="10" value="4" label="(findIsotopes)maxiso" 
+			help="max. number of expected isotopes" />	
+			
+	<param name="findIsotopes_minfrac" type="float" size="10" value="0.5" label="(findIsotopes)minfrac" 
+		help="The ratio for the number of samples, which must satisfy the C12/C13 rule for isotope annotation" />					
+	
+	<param name="findAdducts_polarity" type="select" size="30" label="(findAdducts)polarity" 
+		help="Which polarity mode was used for measuring of the ms sample">
+		<option value="positive" selected="true">positive</option>
+		<option value="negative" >negative</option>
+	</param>
+
+	<param name="findAdducts_multiplier" type="integer" size="10" value="3" label="(findAdducts)multiplier" 
+			help="If no ruleset is provided, calculate ruleset with max. number n of [nM+x] clusterions" />
+
+
+	
+</inputs>
+<configfiles>
+
+<configfile name="customMetaMSsettings">## ====================================
+		## metaMS process settings
+		customMetaMSsettings &lt;- metaMSsettings(protocolName = "${protocolName}",
+                            chrom = "LC",
+                            PeakPicking = list(
+                              method = "${peakPicking.method}",
+							#if $peakPicking.method == "matchedFilter"  
+								fwhm = ${peakPicking.fwhm},
+								sigma = ${peakPicking.fwhm}/${peakPicking.sigma_denom},
+								max = ${peakPicking.max},
+								snthresh = ${peakPicking.snthresh},
+								step = ${peakPicking.step},
+								steps = ${peakPicking.steps},
+								mzdiff = ${peakPicking.mzdiff}),
+							#else 
+								ppm = ${peakPicking.ppm},
+								peakwidth = c(${peakPicking.peakwidth}),
+								snthresh = ${peakPicking.snthresh},
+								prefilter = c(${peakPicking.prefilter}),
+								mzCenterFun = "${peakPicking.mzCenterFun}",
+								integrate = ${peakPicking.integrate},
+								mzdiff = ${peakPicking.mzdiff},
+								fitgauss = ${peakPicking.fitgauss},
+								noise = ${peakPicking.noise}),
+							#end if
+                            Alignment = list(
+                              min.class.fraction = ${min_class_fraction},
+                              min.class.size = ${min_class_size},
+                              mzwid = ${mzwid},
+                              bws = c(${bws}),
+                              retcormethod = "${retcor.retcormethod}",
+							#if $retcor.retcormethod == "peakgroups"
+                           		smooth = "${retcor.smooth}",
+                            	missingratio = ${retcor.missingratio},
+                            	extraratio = ${retcor.extraratio},
+                            	retcorfamily = "${retcor.retcorfamily}",            
+							#else
+								##repeating the method as workaround/ backwards compatibility (can remove this one after fix from metaMS):
+								method = "${retcor.retcormethod}", 
+								profStep = ${retcor.profStep},
+							#end if								                             
+                              fillPeaks = ${fillPeaks}),
+                            CAMERA = list(
+                              perfwhm = ${perfwhm},
+                              cor_eic_th = ${cor_eic_th},
+                              ppm= ${ppm},
+                              graphMethod= "${groupCorr_graphMethod}",
+                              pval= ${groupCorr_pval},
+                              calcCiS= ${groupCorr_calcCiS},
+                              calcIso= ${groupCorr_calcIso},
+                              calcCaS= ${groupCorr_calcCaS},
+                              maxcharge= ${findIsotopes_maxcharge},
+                              maxiso= ${findIsotopes_maxiso},
+                              minfrac= ${findIsotopes_minfrac},
+                              polarity= "${findAdducts_polarity}",
+                              multiplier= ${findAdducts_multiplier}
+                              ))</configfile>
+
+</configfiles>
+
+<outputs>
+	<data name="outputFile" format="tabular" label="${tool.name} on ${on_string} - peaks table (TSV)"/>
+	<data name="outputLog" format="txt" label="${tool.name} on ${on_string} - LOG" hidden="True"/>
+	<data name="xsetOut" format="rdata" label="${tool.name} on ${on_string} - xcmsSet (RDATA)"/>
+	<data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - report (HTML)"/>
+</outputs>
+<tests>
+	<test>
+	</test>
+</tests>
+<help>
+
+.. class:: infomark
+  
+Runs metaMS process for LC/MS feature feature picking, aligning and grouping. 
+This part of the metaMS process makes use of the XCMS and CAMERA tools and algorithms.
+CAMERA is used for automatic deconvolution/annotation of LC/ESI-MS data.
+The figure below shows the main parts of the metaMS process. 
+
+.. image:: $PATH_TO_IMAGES/metaMS.png 
+
+
+**References**
+
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following papers:
+
+Wehrens, R.; Weingart, G.; Mattivi, F. (2014). 
+metaMS: an open-source pipeline for GC-MS-based untargeted metabolomics. 
+Journal of chromatography B: biomedical sciences and applications, 996 (1): 109-116. 
+doi: 10.1016/j.jchromb.2014.02.051 
+handle: http://hdl.handle.net/10449/24012
+
+Wrapper by Pieter Lukasse.
+
+
+  </help>
+  <citations>
+        <citation type="doi">10.1016/j.jchromb.2014.02.051</citation> <!-- example 
+        see also https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set
+        -->
+   </citations>
+</tool>
\ No newline at end of file
--- a/msclust.xml	Wed Nov 19 15:11:45 2014 +0100
+++ b/msclust.xml	Wed Dec 10 22:03:27 2014 +0100
@@ -1,4 +1,4 @@
-<tool name="MsClust" id="msclust2" version="2.0.6">
+<tool name="MsClust" id="msclust2" version="2.0.7">
 	<description>Extracts fragmentation spectra from aligned data</description>
 	<!-- 
 	   For remote debugging start you listener on port 8000 and use the following as command interpreter:
@@ -15,7 +15,7 @@
         #if $imputationMethod.type == "valueRange"
         	-rangeUpperLimit $imputationMethod.rangeUpperLimit
         #end if
-		-plInputFormat "metalign" 
+		-plInputFormat $plInputFormat 
 		-potDensFuncType $potDensFuncType.type 
 		-centerSelectionType $centerSelectionType.type 
 		-clusteringType $clusteringType.type 
@@ -68,11 +68,15 @@
 	</command>
 	<inputs>
 
-	 	<param name="inputPeaks" type="data" format="txt" label="Ion-wise aligned data (e.g. MetAlign output data)" />
+	 	<param name="inputPeaks" type="data" format="txt" label="Ion-wise aligned data (e.g. MetAlign or XCMS/metaMS output data)" />
+	 	<param name="plInputFormat" type="select" size="30" label="Data format">
+			<option value="metalign"  selected="true">MetAlign</option>
+			<option value="xcms">XCMS/metaMS (beta)</option>
+		</param>
 		<param name="dataType" type="select" size="30" label="Data type">
-				<option value="gcms"  selected="true">GC-MS</option>
-				<option value="lcms">LC-MS</option>
-			</param>
+			<option value="gcms"  selected="true">GC-MS</option>
+			<option value="lcms">LC-MS</option>
+		</param>
 	 	<conditional name="imputationMethod">
 			<param name="type" type="select" size="30" label="Select the approach used for imputing missing values (optional)" help="select how you generated the values to fill in the data gaps">
 				<option value="none" >none</option>
@@ -95,8 +99,9 @@
 		      <param name="pdf_neighborhoodWindowSize" type="integer" size="10" value="200" label="Effective Peaks"  />
 		      <conditional name="rt_dist_tol_unit">
 		      	<param name="type" type="select" size="30" label="Peak time unit">
-		      		<option value="1" selected="true">scan nr</option>
-		      		<option value="2" >(average) micro minutes</option>
+		      		<option value="1" selected="true">scan nr (MetAlign)</option>
+		      		<option value="2" >(average) micro minutes (MetAlign)</option>
+		      		<option value="3" >(average) minutes (XCMS)</option>
 		      	</param>
 		      	<when value="1">
 		      		<param name="pdf_rt_toler" type="float" size="10" value="10" label="Peak Width, in scans"  />
@@ -104,6 +109,9 @@
 		      	<when value="2">
 		      		<param name="pdf_rt_toler" type="float" size="10" value="100000" label="Peak Width, in micro minutes" help="e.g. 100,000=6 seconds" />
 		      	</when>
+		      	<when value="3">
+		      		<param name="pdf_rt_toler" type="float" size="10" value="0.1" label="Peak Width, in minutes" help="e.g. 0.1=6 seconds" />
+		      	</when>
 		      </conditional>
 		      <param name="pdf_scan_conf" type="float" size="10" value="80" label="Peak Width confidence (0.0 to 99.99)" help="example: 0[no confidence]...50[good guess]...99.9[quite certain])" />
 		      <param name="pdf_pears_treshold" type="float" size="10" value="0.8" label="Correlation threshold (0.0 - 1.0)" />
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/next.r	Wed Dec 10 22:03:27 2014 +0100
@@ -0,0 +1,4 @@
+# next script, useful for plotting the CAMERA groups pseudo-spectra:
+plotPsSpectrum( LC$xset,320,maxlabel=10)
+320 is group id
+plotEICs( LC$xset,35,maxlabel=5)
\ No newline at end of file
Binary file static/images/CAMERA_results.png has changed
Binary file static/images/massEIC.png has changed
--- a/xcms_differential_analysis.r	Wed Nov 19 15:11:45 2014 +0100
+++ b/xcms_differential_analysis.r	Wed Dec 10 22:03:27 2014 +0100
@@ -14,19 +14,23 @@
 #cat(paste("args.topcount <- ", args[4], "\n", sep=""))
 
 args.outTable <- args[5]
-args.outLogFile <- args[6]
-#cat(paste("args.outLogFile <- \"", args[6], "\"\n", sep=""))
 
 ## report files
-args.htmlReportFile <- args[7]
-args.htmlReportFile.files_path <- args[8]
-#cat(paste("args.htmlReportFile <- \"", args[7], "\"\n", sep=""))
-#cat(paste("args.htmlReportFile.files_path <- \"", args[8], "\"\n", sep=""))
+args.htmlReportFile <- args[6]
+args.htmlReportFile.files_path <- args[7]
+#cat(paste("args.htmlReportFile <- \"", args[6], "\"\n", sep=""))
+#cat(paste("args.htmlReportFile.files_path <- \"", args[7], "\"\n", sep=""))
+
 
-# Send all STDERR to STDOUT using sink() see http://mazamascience.com/WorkingWithData/?p=888
-msg <- file(args.outLogFile, open="wt")
-sink(msg, type="message") 
-sink(msg, type="output")
+if (length(args) == 8)
+{
+	args.outLogFile <- args[8]
+	# suppress messages:
+	# Send all STDERR to STDOUT using sink() see http://mazamascience.com/WorkingWithData/?p=888
+	msg <- file(args.outLogFile, open="wt")
+	sink(msg, type="message") 
+	sink(msg, type="output")
+}
 
 tryCatch(
         {
@@ -34,12 +38,18 @@
         	library(xcms)
 	        #library("R2HTML")
 	
-			## load the constructed DB :
-			xcmsSet <- readRDS(args.xsetData)
+			# load the xset data :
+			xsetData <- readRDS(args.xsetData)
+			# if here to support both scenarios:
+			if ("xcmsSet" %in% slotNames(xsetData) )
+			{
+				xsetData <- xsetData@xcmsSet
+			}
+			
 			
 			# info: levels(xcmsSet@phenoData$class) also gives access to the class names
-			dir.create(file.path(args.htmlReportFile.files_path), showWarnings = FALSE)
-			reporttab <- diffreport(xcmsSet, args.class1, args.class2, paste(args.htmlReportFile.files_path,"/fig", sep=""), args.topcount, metlin = 0.15, h=480, w=640)
+			dir.create(file.path(args.htmlReportFile.files_path), showWarnings = FALSE, recursive = TRUE)
+			reporttab <- diffreport(xsetData, args.class1, args.class2, paste(args.htmlReportFile.files_path,"/fig", sep=""), args.topcount, metlin = 0.15, h=480, w=640)
 			
 			# write out tsv table:
 			write.table(reporttab, args.outTable, sep="\t", row.names=FALSE)
--- a/xcms_differential_analysis.xml	Wed Nov 19 15:11:45 2014 +0100
+++ b/xcms_differential_analysis.xml	Wed Dec 10 22:03:27 2014 +0100
@@ -1,4 +1,4 @@
-<tool id="xcms_differential_analysis" name="XCMS Differential Analsysis"  version="0.0.1">
+<tool id="xcms_differential_analysis" name="XCMS Differential Analsysis"  version="0.0.4">
 	<description> Runs xcms diffreport function for differential Analsysis</description>
 	<requirements>
 		<requirement type="package" version="3.1.1">R_bioc_metams</requirement>
@@ -6,13 +6,13 @@
 	<command interpreter="Rscript">
 		xcms_differential_analysis.r 
 	    $xsetData
-		$class1
-		$class2
+		"$class1"
+		"$class2"
 		$topcount
 		$outTable 
-		$outLogFile
 		$htmlReportFile
 		$htmlReportFile.files_path
+		$outLogFile
 	</command>
 <inputs>
 	
@@ -27,7 +27,7 @@
 </inputs>
 <outputs>
 	<data name="outTable" format="tabular" label="${tool.name} on ${on_string} - Top differential items (TSV)"/>
-	<data name="outLogFile" format="txt" label="${tool.name} on ${on_string} - differential log (LOG)"/>
+	<data name="outLogFile" format="txt" label="${tool.name} on ${on_string} - log (LOG)" hidden="True"/>
 	<data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - differential report (HTML)"/>
 </outputs>
 <tests>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/xcms_get_alignment_eic.r	Wed Dec 10 22:03:27 2014 +0100
@@ -0,0 +1,153 @@
+# shows all alignment results in a rt region
+## read args:
+args <- commandArgs(TRUE)
+# xset data:
+args.xsetData <- args[1]
+
+args.rtStart  <- strtoi(args[2])
+args.rtEnd <- strtoi(args[3])
+
+# limit max diff to 600 and minNrSamples to at least 2 :
+if (args.rtEnd - args.rtStart > 600)
+	stop("The RT window should be <= 600")
+
+args.minNrSamples <- strtoi(args[4]) #min nr samples
+if (args.minNrSamples < 2)
+	stop("Set 'Minimum number of samples' to 2 or higher")
+
+
+args.sampleNames <- strsplit(args[5], ",")[[1]]
+# trim leading and trailing spaces:
+args.sampleNames <- gsub("^\\s+|\\s+$", "", args.sampleNames)
+
+## report files
+args.htmlReportFile <- args[6]
+args.htmlReportFile.files_path <- args[7]
+
+
+if (length(args) == 8) 
+{
+	args.outLogFile <- args[8]
+	# suppress messages:
+	# Send all STDERR to STDOUT using sink() see http://mazamascience.com/WorkingWithData/?p=888
+	msg <- file(args.outLogFile, open="wt")
+	sink(msg, type="message") 
+	sink(msg, type="output")
+}
+
+
+
+tryCatch(
+        {
+	        library(metaMS)
+	
+			# load the xset data :
+			xsetData <- readRDS(args.xsetData)
+			# if here to support both scenarios:
+			if ("xcmsSet" %in% slotNames(xsetData) )
+			{
+				xsetData <- xsetData@xcmsSet
+			}
+			
+			# report
+			dir.create(file.path(args.htmlReportFile.files_path), showWarnings = FALSE, recursive = TRUE)
+			message(paste("\nGenerating report.........in ", args.htmlReportFile.files_path))
+			
+			write(paste("<html><body><h1>Extracted Ion Chromatograms (EIC) of alignments with peaks in ",args.minNrSamples, " or more samples</h1>"),
+			      file=args.htmlReportFile)
+			
+			gt <- groups(xsetData)
+			message("\nParsed groups... ")
+			groupidx1 <- which(gt[,"rtmed"] > args.rtStart & gt[,"rtmed"] < args.rtEnd & gt[,"npeaks"] >= args.minNrSamples)  # this should be only on samples selected
+			
+			if (length(groupidx1) > 0)
+			{
+				message("\nGetting EIC... ")
+				eiccor <- getEIC(xsetData, groupidx = c(groupidx1), sampleidx=args.sampleNames)
+				#eicraw <- getEIC(xsetData, groupidx = c(groupidx1), sampleidx=args.sampleNames, rt = "raw")
+				
+				#sampleNamesIdx <- which(sampnames(LC$xset@xcmsSet) %in% args.sampleNames, arr.ind = TRUE)
+				#or (from bioconductor code for getEIC):  NB: this is assuming sample indexes used in data are ordered after the order of sample names!!
+				sampNames <- sampnames(xsetData)
+				sampleNamesIdx <- match( args.sampleNames, sampNames)
+				message(paste("Samples: ", sampleNamesIdx))
+				
+				#TODO html <- paste(html, "<table><tbody>")
+				message(paste("\nPlotting figures... "))
+				
+				#get the mz list (interestingly, this [,"mz"] is relatively slow):
+				peakMzList <- xsetData@peaks[,"mz"]
+				peakSampleList <- xsetData@peaks[,"sample"]
+				#signal to noise list:
+				peakSnList <- xsetData@peaks[,"sn"]
+				
+				message(paste("Total nr of peaks: ", length(peakMzList)))
+				
+				for (i in 1:length(groupidx1)) 
+				{
+					groupMembers <- xsetData@groupidx[[groupidx1[i]]]
+					
+					groupMzList <- ""
+					groupSampleList <- ""
+					finalGroupSize <- 0
+					
+					for (j in 1:length(groupMembers))
+					{
+						#get only the peaks from the selected samples:
+						memberSample <- peakSampleList[groupMembers[j]]
+						memberSn <- peakSnList[groupMembers[j]]
+						if (!is.na(memberSn) && memberSample %in% sampleNamesIdx)
+						{
+							message(paste("Group: ", groupidx1[i], " / Member sample: ", memberSample))
+							memberMz <- peakMzList[groupMembers[j]]
+							
+							
+							if (finalGroupSize == 0)
+							{
+								groupMzList <- memberMz
+								groupSampleList <- sampNames[memberSample]
+							} else {
+								groupMzList <- paste(groupMzList,",",memberMz, sep="")
+								groupSampleList <- paste(groupSampleList,",",sampNames[memberSample], sep="")
+							}
+							
+							finalGroupSize <- finalGroupSize +1	
+						}
+					}
+					# here we do the real check on group size and only the groups that have enough
+					# members with signal to noise > 0 will be plotted here:
+					if (finalGroupSize >= args.minNrSamples)
+					{
+						message(paste("Plotting figure ",i, " of max ", length(groupidx1)," figures... "))
+						
+						figureName <- paste(args.htmlReportFile.files_path, "/figure", i,".png", sep="")
+						write(paste("<img src='", "figure", i,".png' />", sep="") ,
+			      				file=args.htmlReportFile, append=TRUE)
+			
+						png( figureName, type="cairo" ) 
+						plot(eiccor, xsetData, groupidx = i)
+						devname = dev.off()
+						
+						write(paste("<p>Alignment id: [", groupidx1[i], "]. m/z list of peaks in alignment with signal/noise <> NA:<br/>", groupMzList,"</p>", sep="") ,
+			      				file=args.htmlReportFile, append=TRUE)
+			      		write(paste("<p>m/z values found in the following samples respectively: <br/>", groupSampleList,"</p>", sep="") ,
+			      				file=args.htmlReportFile, append=TRUE)
+					}
+				}
+				
+			}
+			
+			write("</body><html>",
+			      	file=args.htmlReportFile, append=TRUE)
+			message("finished generating report")
+			# unlink(args.htmlReportFile)
+			cat("\nWarnings================:\n")
+			str( warnings() ) 
+		},
+        error=function(cond) {
+            sink(NULL, type="message") # default setting
+			sink(stderr(), type="output")
+            message("\nERROR: ===========\n")
+            print(cond)
+        }
+    ) 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/xcms_get_alignment_eic.xml	Wed Dec 10 22:03:27 2014 +0100
@@ -0,0 +1,72 @@
+<tool id="xcms_get_alignment_eic" name="XCMS Get Alignment EICs"  version="0.0.4">
+	<description> Extracts alignment EICs from feature alignment data</description>
+	<requirements>
+		<requirement type="package" version="3.1.1">R_bioc_metams</requirement>
+	</requirements>	
+	<command interpreter="Rscript">
+		xcms_get_alignment_eic.r 
+	    $xsetData
+		$rtStart
+		$rtEnd
+		$minNrSamples
+		"$sampleNames" 
+		$htmlReportFile
+		$htmlReportFile.files_path
+		$outLogFile
+	</command>
+<inputs>
+	
+	<param name="xsetData" type="data" format="rdata" label="xset xcms data file" help="E.g. output data file resulting from METAMS run"/>
+	
+	
+	<param name="rtStart" type="integer" value="" size="10" label="RT start" help="Start of Retention Time region to plot" />
+	<param name="rtEnd" type="integer" value="" size="10"  label="RT end" help="End of Retention Time region to plot" />
+	
+	<param name="minNrSamples" type="integer" size="10" value="10" label="Minimum number of samples in which aligned feature should be found" help="Can also read this as: Minimum 
+	number of features in alignment. E.g. if set to 10, it means the alignment should consist of at least 10 peaks from 10 different samples aligned together." />
+	
+	<param name="sampleNames" type="text" area="true" size="10x70" label="List of sample names" 
+	value="sampleName1,sampleName2,etc"
+	help="Comma or line-separated list of sample names. Optional field where you can specify the subset of samples
+	to use for the EIC plots. NB: if your dataset has many samples, specifying a subset here can significantly speed up the processing time." >
+		<sanitizer>
+			<!-- this translates from line-separated to comma separated list -->
+			<valid/>
+			<mapping initial="none">
+		    	<add source="&#10;" target=","/>
+		    	<add source="&#13;" target=""/>
+ 			</mapping>
+		</sanitizer>	
+	</param>
+	
+	
+</inputs>
+<outputs>
+	<data name="outLogFile" format="txt" label="${tool.name} on ${on_string} - log (LOG)" hidden="True"/>
+	<data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - EIC(s) report (HTML)"/>
+</outputs>
+<tests>
+	<test>
+	</test>
+</tests>
+<help>
+
+.. class:: infomark
+ 
+This tool finds the alignments in the specified RT window and extracts alignment EICs from feature alignment data using XCMS's getEIC method. 
+It produces a HTML report showing the EIC plots and the mass list of each alignment. The figure below shows an example of such an EIC plot, showing also the difference between 
+two classes, with extra alignment information beneath it.
+ 
+.. image:: $PATH_TO_IMAGES/diffreport.png 
+
+Alignment id: 1709. m/z list of peaks in alignment:
+614.002922098482,613.998019830021,614.000382307519,613.998229980469,613.998229980469
+
+
+  </help>
+  <citations>
+        <citation type="doi">10.1021/ac051437y</citation> <!-- example 
+        see also https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set
+        -->
+   </citations>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/xcms_get_mass_eic.r	Wed Dec 10 22:03:27 2014 +0100
@@ -0,0 +1,162 @@
+## read args:
+args <- commandArgs(TRUE)
+# xset data:
+args.xsetData <- args[1]
+
+args.rtStart  <- strtoi(args[2])
+args.rtEnd <- strtoi(args[3])
+
+args.mzStart <- as.double(args[4])
+args.mzEnd <- as.double(args[5])
+# there are 2 options: specify a mz range or a mz list:
+if (args.mzStart < 0) 
+{
+	args.mzList <- as.double(strsplit(args[6], ",")[[1]])
+	cat(typeof(as.double(strsplit(args[6], ",")[[1]])))
+	args.mzTolPpm <- as.double(args[7])
+	# calculate mzends based on ppm tol:
+	mzListEnd <- c()
+	mzListStart <- c()
+	for (i in 1:length(args.mzList))
+	{
+		mzEnd <- args.mzList[i] + args.mzList[i]*args.mzTolPpm/1000000.0
+		mzStart <- args.mzList[i] - args.mzList[i]*args.mzTolPpm/1000000.0
+		mzListEnd <- c(mzListEnd, mzEnd)
+		mzListStart <- c(mzListStart, mzStart)
+	} 
+	str(mzListStart)
+	str(mzListEnd)
+} else {
+	mzListEnd <- c(args.mzEnd)
+	mzListStart <- c(args.mzStart)
+} 
+
+args.sampleNames <- strsplit(args[8], ",")[[1]]
+# trim leading and trailing spaces:
+args.sampleNames <- gsub("^\\s+|\\s+$", "", args.sampleNames)
+
+args.combineSamples <- args[9]
+args.rtPlotMode <- args[10]
+
+## report files
+args.htmlReportFile <- args[11]
+args.htmlReportFile.files_path <- args[12]
+
+
+if (length(args) == 13) 
+{
+	args.outLogFile <- args[13]
+	# suppress messages:
+	# Send all STDERR to STDOUT using sink() see http://mazamascience.com/WorkingWithData/?p=888
+	msg <- file(args.outLogFile, open="wt")
+	sink(msg, type="message") 
+	sink(msg, type="output")
+}
+
+# TODO - add option to do masses in same plot (if given in same line oid) or in separate plots
+# TODO2 - let it run in parallel 
+
+tryCatch(
+        {
+	        library(metaMS)
+	
+			# load the xset data :
+			xsetData <- readRDS(args.xsetData)
+			# if here to support both scenarios:
+			if ("xcmsSet" %in% slotNames(xsetData) )
+			{
+				xsetData <- xsetData@xcmsSet
+			}
+			
+			# report
+			dir.create(file.path(args.htmlReportFile.files_path), showWarnings = FALSE, recursive = TRUE)
+			message(paste("\nGenerating report.........in ", args.htmlReportFile.files_path))
+			
+			html <- "<html><body><h1>Extracted Ion Chromatograms (EIC) matching criteria</h1>" 
+			
+			if (args.combineSamples == "No")
+			{
+				if (length(args.sampleNames) > 1 && length(mzListStart) > 1 && length(args.sampleNames) != length(mzListStart))
+					stop(paste("The number of sample names should match the number of m/z values in the list. Found ", length(mzListStart), 
+					          " masses while ",  length(args.sampleNames), " sample names were given."))
+				
+		  		iterSize <- length(args.sampleNames)
+				# these can be set to 1 or 0 just as a trick to iterate OR not over the items. If the respective list is of length 1, only the first item should be used 
+				fixSampleIdx <- 1
+				fixMzListIdx <- 1
+				if (length(args.sampleNames) == 1)
+				{
+					fixSampleIdx <- 0
+					iterSize <- length(mzListStart)
+				}
+				if (length(mzListStart) == 1)
+				{
+					fixMzListIdx <- 0
+				}
+				lineColors <- rainbow(iterSize)
+				for (i in 0:(iterSize-1))
+				{
+					message("\nGetting EIC... ")
+					eiccor <- getEIC(xsetData, 
+										mzrange=matrix(c(mzListStart[i*fixMzListIdx+1],mzListEnd[i*fixMzListIdx+1]),nrow=1,ncol=2,byrow=TRUE),
+										rtrange=matrix(c(args.rtStart,args.rtEnd),nrow=1,ncol=2,byrow=TRUE), 
+										sampleidx=c(args.sampleNames[i*fixSampleIdx+1]), rt=args.rtPlotMode)
+					
+					message("\nPlotting figures... ")
+					figureName <- paste(args.htmlReportFile.files_path, "/figure", i,".png", sep="")
+					html <- paste(html,"<img src='", "figure", i,".png' /><br/>", sep="") 
+					png( figureName, type="cairo", width=1100,height=250 ) 
+					#plot(eiccor, col=lineColors[i+1])
+					# black is better in this case:
+					plot(eiccor)
+					legend('topright', # places a legend at the appropriate place 
+							legend=c(args.sampleNames[i*fixSampleIdx+1]), # puts text in the legend 
+							lty=c(1,1), # gives the legend appropriate symbols (lines)
+							lwd=c(2.5,2.5))
+							
+					devname = dev.off()
+				}
+			
+			} else {
+				for (i in 1:length(mzListStart))
+				{
+					message("\nGetting EIC... ")
+					eiccor <- getEIC(xsetData, 
+										mzrange=matrix(c(mzListStart[i],mzListEnd[i]),nrow=1,ncol=2,byrow=TRUE), 
+										rtrange=matrix(c(args.rtStart,args.rtEnd),nrow=1,ncol=2,byrow=TRUE), 
+										sampleidx=args.sampleNames, rt = args.rtPlotMode)
+										
+										#set size, set option (plot per sample, plot per mass)
+					
+					message("\nPlotting figures... ")
+					figureName <- paste(args.htmlReportFile.files_path, "/figure", i,".png", sep="")
+					html <- paste(html,"<img src='", "figure", i,".png' />", sep="") 
+					png( figureName, type="cairo", width=1100,height=450 ) 
+					lineColors <- rainbow(length(args.sampleNames))
+					plot(eiccor, col=lineColors)
+					legend('topright', # places a legend at the appropriate place 
+						  legend=args.sampleNames, # puts text in the legend 
+						  lty=c(1,1), # gives the legend appropriate symbols (lines)
+						  lwd=c(2.5,2.5),
+				          col=lineColors)
+					devname = dev.off()
+				}
+			}
+			if (args.rtPlotMode == "corrected")
+			{
+				html <- paste(html,"<p>*rt values are corrected ones</p></body><html>")
+			}
+			html <- paste(html,"</body><html>")
+			message("finished generating report")
+			write(html,file=args.htmlReportFile)
+			# unlink(args.htmlReportFile)
+			cat("\nWarnings================:\n")
+			str( warnings() ) 
+		},
+        error=function(cond) {
+            sink(NULL, type="message") # default setting
+			sink(stderr(), type="output")
+            message("\nERROR: ===========\n")
+            print(cond)
+        }
+    ) 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/xcms_get_mass_eic.xml	Wed Dec 10 22:03:27 2014 +0100
@@ -0,0 +1,114 @@
+<tool id="xcms_get_mass_eic" name="XCMS Get EICs"  version="0.0.4">
+	<description> Extracts EICs for a given list of masses</description>
+	<requirements>
+		<requirement type="package" version="3.1.1">R_bioc_metams</requirement>
+	</requirements>	
+	<command interpreter="Rscript">
+		xcms_get_mass_eic.r 
+	    $xsetData
+		$rtStart
+		$rtEnd
+		#if $massParameters.massParametersType == "window"
+			$massParameters.mzStart 
+			$massParameters.mzEnd
+			-1
+			"."
+		#else
+			-1
+			-1
+			$massParameters.mzList
+			$massParameters.mzTolPpm
+		#end if  
+		"$sampleNames" 
+		$combineSamples
+		$rtPlotMode
+		$htmlReportFile
+		$htmlReportFile.files_path
+		$outLogFile
+	</command>
+<inputs>
+	
+	<param name="xsetData" type="data" format="rdata" label="xset xcms data file" help="E.g. output data file resulting from METAMS run"/>
+	
+	
+	<param name="rtStart" type="integer" value="" size="10" label="RT start" help="Start of Retention Time region to plot" />
+	<param name="rtEnd" type="integer" value="" size="10"  label="RT end" help="End of Retention Time region to plot" />
+	
+	<conditional name="massParameters">
+		<param name="massParametersType" type="select" size="50" label="Give masses as" >
+			<option value="list" selected="true">m/z list</option>
+			<option value="window" >m/z window</option>
+		</param>
+		<when value="list">
+			<param name="mzList" type="text" area="true" size="7x70" label="m/z list" 
+				help="Comma or line-separated list of m/z values for which to plot an EIC. One EIC will be plotted for each m/z given here.">
+				<sanitizer>
+					<!-- this translates from line-separated to comma separated list -->
+					<valid/>
+					<mapping initial="none">
+				    	<add source="&#10;" target=","/>
+				    	<add source="&#13;" target=""/>
+		 			</mapping>
+				</sanitizer>
+			</param>
+			<param name="mzTolPpm" type="integer" size="10" value="5" label="m/z tolerance (ppm)"  />
+		</when>
+		<when value="window">
+			<param name="mzStart" type="float" value="" size="10" label="m/z start" help="Start of m/z window" />
+			<param name="mzEnd" type="float" value="" size="10"  label="m/z end" help="End of m/z window" />
+   		</when>
+	</conditional>		 
+	
+
+	<param name="sampleNames" type="text" area="true" size="10x70" label="List of sample names" 
+		value="sampleName1,sampleName2,etc"
+		help="Comma or line-separated list of sample names. Here you can specify the subset of samples
+		to use for the EIC plots. NB: if your dataset has many samples, specifying a subset here can significantly speed up the processing time." >
+		<sanitizer>
+			<valid/>
+			<mapping initial="none">
+		    	<add source="&#10;" target=","/>
+		    	<add source="&#13;" target=""/>
+ 			</mapping>
+		</sanitizer>	
+	</param>
+	
+	<param name="combineSamples" type="select" size="50" label="Combine samples in EIC" 
+	       help="Combining samples means plot contains the combined EIC of a m/z in the different samples. When NOT combining, each plot 
+	       only contains the EIC of the m/z in the respectively given sample (the sample name from the sample list in the same position as the
+	       m/z in the m/z list.). Tip: use Yes for visualizing EIC of grouped masses (MsClust or CAMERA groups), use No for visualizing EICs of the same mass in 
+	       the different samples.">
+		<option value="No" selected="true">No</option>
+		<option value="Yes" >Yes</option>
+	</param>
+	<param name="rtPlotMode" type="select" size="50" label="RT plot mode" 
+	       help="Select whether EIC should be on original or raw Retention Time">
+		<option value="raw" selected="true">Raw</option>
+		<option value="corrected" >Corrected</option>
+	</param>
+</inputs>
+<outputs>
+	<data name="outLogFile" format="txt" label="${tool.name} on ${on_string} - log (LOG)" hidden="True"/>
+	<data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - EIC(s) report (HTML)"/>
+</outputs>
+<tests>
+	<test>
+	</test>
+</tests>
+<help>
+
+.. class:: infomark
+ 
+This tool will plot EICs for a given list of masses (or a mass window) using XCMS's getEIC method. 
+It produces a HTML report showing the EIC plots, one for each given mass. The figure below shows an example of such an EIC plot.
+ 
+.. image:: $PATH_TO_IMAGES/massEIC.png 
+
+
+  </help>
+  <citations>
+        <citation type="doi">10.1021/ac051437y</citation> <!-- example 
+        see also https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set
+        -->
+   </citations>
+</tool>
\ No newline at end of file