# HG changeset patch
# User lecorguille
# Date 1487177126 18000
# Node ID f24b9c360a60ff35ae9a73727627ea212a9aa64a
# Parent  9541ba588de1529a5abbbdacd8fd2df09a2fa937
planemo upload commit dc4b1363a3fe83f195167f1f0b25c9728006e364

diff -r 9541ba588de1 -r f24b9c360a60 ProbMetab.xml
--- a/ProbMetab.xml	Mon Jul 04 11:58:12 2016 -0400
+++ b/ProbMetab.xml	Wed Feb 15 11:45:26 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="Probmetab" name="ProbMetab Tool" version="1.0.1">
+<tool id="Probmetab" name="ProbMetab Tool" version="1.1.0">
 
     <description>Wrapper function for ProbMetab R package.</description>
 
@@ -12,186 +12,214 @@
     <command>
         @COMMAND_CAMERA_SCRIPT@
         #if $acquisition_options.mode == "one":
-            mode_acquisition $acquisition_options.mode xa $acquisition_options.xa
+            mode_acquisition $acquisition_options.mode
+            image '$acquisition_options.image'
             ##if $acquisition_options.xsetnofill_options.option == "show":
-	            ##xsetnofill $acquisition_options.xsetnofill_options.xsetnofill
-     	    ##end if	
+                ##xsetnofill $acquisition_options.xsetnofill_options.xsetnofill
+            ##end if
+
+            @COMMAND_FILE_LOAD_ONE@
+
         #else
-            mode_acquisition $acquisition_options.mode inputs_mode $acquisition_options.input_mode.option
+            mode_acquisition $acquisition_options.mode
+            inputs_mode $acquisition_options.input_mode.option
             #if $acquisition_options.input_mode.option== "two":
 
-	            image_pos $acquisition_options.input_mode.image_pos image_neg $acquisition_options.input_mode.image_neg
-	            ##if $acquisition_options.input_mode.xsetnofill_options.option == "show":
-		            ##xsetPnofill $acquisition_options.input_mode.xsetnofill_options.xsetPnofill xsetNnofill $acquisition_options.input_mode.xsetnofill_options.xsetNnofill
-         		##end if		
+                image_pos '$acquisition_options.input_mode.image_pos'
+                image_neg '$acquisition_options.input_mode.image_neg'
+                ##if $acquisition_options.input_mode.xsetnofill_options.option == "show":
+                    ##xsetPnofill $acquisition_options.input_mode.xsetnofill_options.xsetPnofill
+                    ##xsetNnofill $acquisition_options.input_mode.xsetnofill_options.xsetNnofill
+                ##end if
+
+                @COMMAND_FILE_LOAD_POSITIVE@
+                @COMMAND_FILE_LOAD_NEGATIVE@
             ##else
-	            ##image_combinexsannos $acquisition_options.input_mode.image_combinexsannos image_pos $acquisition_options.input_mode.image_pos
+                ##image_combinexsannos $acquisition_options.input_mode.image_combinexsannos
+                ##image_pos $acquisition_options.input_mode.image_pos
             #end if
 
         #end if
 
         #if $option_toexclude.option == "show":
-        	toexclude $option_toexclude.toexclude
+            toexclude $option_toexclude.toexclude
         #end if
-        allowMiss $allowMiss html $html kegg_db $kegg_db ppm_tol $ppm_tol
-        opt $opt corths $corths corprob $corprob pcorprob $pcorprob prob $prob
-        
-        @COMMAND_ZIPFILE_LOAD@
+        allowMiss $allowMiss
+        html $html
+        kegg_db $kegg_db
+        ppm_tol $ppm_tol
+        opt $opt
+        corths $corths
+        corprob $corprob
+        pcorprob $pcorprob
+        prob $prob
+
+        @COMMAND_LOG_EXIT@
 
     </command>
 
     <inputs>
 
         <conditional name="acquisition_options">
-	        <param name="mode" type="select" label="Choose your acquisition mode" >
-		        <option value="one" selected="true"  >One acquisition charge mode</option>
-            	<option value="two"  >Two acquisition charge mode (positif and negatif)</option>
-	        </param>
-
-	        <!-- One acquisition mode-->
-	        <when value="one">
-		        <param name="xa" type="data" label="Annotate RData" format="rdata.camera.positive,rdata.camera.negative,rdata" help="Output file from annotate step " />
-		        <!--
-		        <conditional name="xsetnofill_options">
-            			<param name="option" type="select" label="RData group step" help="xcmsSet xcms object after missing data replacement, to retrieve SNR to isotopic peaks." >
-             				<option value="show">show</option>
-             				<option value="hide" selected="true">hide</option>
-             			</param>
-             			<when value="show">
-	          			<param name="xsetnofill" type="data" label="Positive or Negative RData from group step before fillpeaks " format="rdata" help=" output from group step" />
-             			</when>
-		
-          			</conditional>
-		        -->
-	        </when>
-	        <!-- Two acquisition modes-->
-	        <when value="two">
+            <param name="mode" type="select" label="Choose your acquisition mode" >
+                <option value="one" selected="true"  >One acquisition charge mode</option>
+                <option value="two"  >Two acquisition charge mode (positif and negatif)</option>
+            </param>
 
-		
-		        <conditional name="input_mode">
-			        <param name="option" type="select" label="Choose your input type method:" >
-				        <!-- Bug combinexsannos TODO <option value="one">Input from combinexsAnnos step</option> -->
-                		<option value="two" selected="true">Rdata inputs from annotate</option>
-			        </param>
-			        <!--
-			        <when value="one">
-				        <param name="image_combinexsannos" type="data" label="RData output from combinexsAnnos step" format="rdata" help="output file from combinexAnnos step " /> 
-				        <param name="image_pos" type="data" label="Positive RData ion mode from annotatediffreport step" format="rdata" help="output file from annotatediffreport step " />
-			        </when>
-			        -->
-			        <when value="two">
-				        <param name="image_pos" type="data" label="Positive annotate RData" format="rdata.camera.positive,rdata" help="output file from annotate step " />
-				        <param name="image_neg" type="data" label="Negative annotate RData" format="rdata.camera.negative,rdata" help="output file from annotate step" />
-				        <!--
-				        <conditional name="xsetnofill_options">
-					        <param name="option" type="select" label="Two RData group step (positive and negative)" help="xcmsSet xcms objects after missing data replacement from your two acquisition modes, to retrieve SNR to isotopic peaks." >
-			         			<option value="show">show</option>
-			         			<option value="hide" selected="true">hide</option>
-			         		</param>
-					        <when value="show">
-						        <param name="xsetPnofill" type="data" label="Positive RData from group step before fillpeaks " format="rdata.xcms.group,rdata" help="" />
-						        <param name="xsetNnofill" type="data" label="Negative RData from group step before fillpeaks" format="rdata.xcms.group,rdata" help="" />
-					        </when>
-				        </conditional>
-				        -->
-			        </when>
-		        </conditional>
-	        </when>	
-	
+            <!-- One acquisition mode-->
+            <when value="one">
+                <param name="image" type="data" label="Annotate RData" format="rdata.camera.positive,rdata.camera.negative,rdata" help="Output file from annotate step " />
+                <!--
+                <conditional name="xsetnofill_options">
+                    <param name="option" type="select" label="RData group step" help="xcmsSet xcms object after missing data replacement, to retrieve SNR to isotopic peaks." >
+                        <option value="show">show</option>
+                        <option value="hide" selected="true">hide</option>
+                    </param>
+                    <when value="show">
+                        <param name="xsetnofill" type="data" label="Positive or Negative RData from group step before fillpeaks " format="rdata" help=" output from group step" />
+                    </when>
+                </conditional>
+                -->
+            </when>
+            <!-- Two acquisition modes-->
+            <when value="two">
+                <conditional name="input_mode">
+                    <param name="option" type="select" label="Choose your input type method:" >
+                        <!-- Bug combinexsannos TODO <option value="one">Input from combinexsAnnos step</option> -->
+                        <option value="two" selected="true">Rdata inputs from annotate</option>
+                    </param>
+                    <!--
+                    <when value="one">
+                        <param name="image_combinexsannos" type="data" label="RData output from combinexsAnnos step" format="rdata" help="output file from combinexAnnos step " />
+                        <param name="image_pos" type="data" label="Positive RData ion mode from annotatediffreport step" format="rdata" help="output file from annotatediffreport step " />
+                    </when>
+                    -->
+                    <when value="two">
+                        <param name="image_pos" type="data" label="Positive annotate RData" format="rdata.camera.positive,rdata" help="output file from annotate step " />
+                        <param name="image_neg" type="data" label="Negative annotate RData" format="rdata.camera.negative,rdata" help="output file from annotate step" />
+                        <!--
+                        <conditional name="xsetnofill_options">
+                            <param name="option" type="select" label="Two RData group step (positive and negative)" help="xcmsSet xcms objects after missing data replacement from your two acquisition modes, to retrieve SNR to isotopic peaks." >
+                                 <option value="show">show</option>
+                                 <option value="hide" selected="true">hide</option>
+                             </param>
+                            <when value="show">
+                                <param name="xsetPnofill" type="data" label="Positive RData from group step before fillpeaks " format="rdata.xcms.group,rdata" help="" />
+                                <param name="xsetNnofill" type="data" label="Negative RData from group step before fillpeaks" format="rdata.xcms.group,rdata" help="" />
+                            </when>
+                        </conditional>
+                        -->
+                    </when>
+                </conditional>
+            </when>
         </conditional>
 
-
-	    <param name="allowMiss" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Retrieves peaks with no eviendence of adduct or isotope" help=" [allowMiss] (ionAnnot function) Logical, annotate also the peaks as single charged molecules [M+/-H]." />
+        <param name="allowMiss" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Retrieves peaks with no eviendence of adduct or isotope" help=" [allowMiss] (ionAnnot function) Logical, annotate also the peaks as single charged molecules [M+/-H]." />
         <conditional name="option_toexclude">
-    		<param name="option" type="select" label="Exclude samples" >
-     			<option value="show">show</option>
-     			<option value="hide" selected="true">hide</option>
-     		</param>
-     		<when value="show">
-       		    <param name="toexclude" type="text" value="blank,medium,QC" label="samples to be excluded of peak counting to non-annotated peak selection." help="" />
-     		</when>
+            <param name="option" type="select" label="Exclude samples" >
+                <option value="show">show</option>
+                <option value="hide" selected="true">hide</option>
+            </param>
+            <when value="show">
+                <param name="toexclude" type="text" value="blank,medium,QC" label="samples to be excluded of peak counting to non-annotated peak selection." help="" />
+            </when>
             <when value="hide" />
-  		</conditional>
+        </conditional>
         <!--
         <conditional name="useIso_options">
-	        <param name="option" type="select" label="Calculates the relative isotopic abundance ratio (Carbon 13)" >
-     			<option value="show">Yes</option>
-     			<option value="hide" selected="true">No</option>
-     		</param>
-	        <when value="show">
-           		<param name="var" type="select" label="var (incorporate.isotopes)" help="1 to use standard mean/sd estimators to carbon number prediction, 2 for median/mad estimators." >
-			        <option value="1">1</option>
-     				<option value="2" selected="true">2</option>
-     			</param>
-     		</when>
+            <param name="option" type="select" label="Calculates the relative isotopic abundance ratio (Carbon 13)" >
+                <option value="show">Yes</option>
+                <option value="hide" selected="true">No</option>
+            </param>
+            <when value="show">
+                <param name="var" type="select" label="var (incorporate.isotopes)" help="1 to use standard mean/sd estimators to carbon number prediction, 2 for median/mad estimators." >
+                    <option value="1">1</option>
+                    <option value="2" selected="true">2</option>
+                </param>
+            </when>
         </conditional>
         -->
         <param name="html" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Logical, check if you want to generate a HTML ProbMetab report" help=" [html] (export.class.table function).This parameter uses the raw data to plot EICs and may be time consuming." />
 
         <param name="kegg_db" type="text" size="40" label="Search on KEGG database or multiple organisms "  help="Search on all KEGG organisms or multiple organisms (id1,id2,id3,...).By default,the value is KEGG which means searching on all KEGG organism. The list of KEGG IDs are available at http://rest.kegg.jp/list/organism" value="KEGG" >
-	        <validator type="empty_field"/>
+            <validator type="empty_field"/>
         </param>
         <param name="ppm_tol" type="integer" value="8" label="Parts per million mass tolerance allowed in the mass search" help="[ppm.tol] (create.reactionMfunction) " />
 
-
         <param name="opt" type="select" label="Correlation option" help="[opt] (reac2cor function) cor for correlation, and pcor for partial correlation." >
-	        <option value="cor" selected="true">cor</option>
-	        <option value="pcor">pcor</option>
+            <option value="cor" selected="true">cor</option>
+            <option value="pcor">pcor</option>
         </param>
 
-
-        <param name="corprob" type="float" value="0.8" label="Probability that the correlation is considered significant" help="[corprob] (reac2cor function) " /> 
-
+        <param name="corprob" type="float" value="0.8" label="Probability that the correlation is considered significant" help="[corprob] (reac2cor function) " />
 
         <param name="pcorprob" type="float" value="0.8" label="Probability that the partial correlation is considered significant." help="[pcorprob](reac2cor function)" />
         <param name="corths" type="float" value="0.75" label="Correlation intensity threshold" help="[corths] (reac2cor function)" />
 
         <param name="prob" type="select" label=" Calculation of the probability to attribute a mass to a compound" help="[prob] (export.class.table function). Default is 'count'. See the tool help for more details." >
-	        <option value="count" selected="true">Count</option>
-    		<option value="mean">Mean</option>
+            <option value="count" selected="true">Count</option>
+            <option value="mean">Mean</option>
         </param>
         <!--
-            <param name="organismId" type="text" size="40" value="NULL" label="organismIdorganismId" help="(create.pathway.node.attributes function) KEGG organism id (http://www.kegg.jp/kegg/catalog/org_list.html) to filter possible pathways for known pathways for that organism. Only works for KEGG database for now. Default is NULL (all KEGG organisms).
+        <param name="organismId" type="text" size="40" value="NULL" label="organismIdorganismId" help="(create.pathway.node.attributes function) KEGG organism id (http://www.kegg.jp/kegg/catalog/org_list.html) to filter possible pathways for known pathways for that organism. Only works for KEGG database for now. Default is NULL (all KEGG organisms).
 " />
+        -->
 
-         -->
-        
-        <expand macro="zipfile_load"/>
+        <expand macro="input_file_load"/>
+        <expand macro="input_file_load" polarity="Positive"/>
+        <expand macro="input_file_load" polarity="Negative"/>
     </inputs>
 
     <outputs>
         <!-- <data name="output_image" format="rdata" from_work_dir="probmetab.RData" label="Probmetab.RData" /> -->
         <data name="html_output" format="html" from_work_dir="AnalysisExample.html" label="Probmetab.Analysis_Report_html" >
-	         <filter>(html)</filter>
+             <filter>(html)</filter>
         </data>
         <data name="tsv_output" format="tabular" from_work_dir="Analysis_Report.tsv" label="Probmetab.CytoScape_output_Attribute_List.tsv" />
         <data name="eics" format="zip" from_work_dir="Analysis_Report.zip" label="Probmetab.Analysis_Report_EICs_plots.zip" >
             <filter>(html)</filter>
         </data>
         <data name="sif_output" format="tabular" from_work_dir="sif.tsv" label="Probmetab.CytoScape_output.sif" />
-        <data name="log" format="txt" from_work_dir="probmetab.log" label="Probmetab.log" />
+        <data name="log" format="txt" label="Probmetab.log" />
         <data name="variableMetadata" format="tabular" from_work_dir="variableMetadata.tsv" label="variableMetadata.tsv" >
-	        <filter>(acquisition_options['mode'] == 'one')</filter>
+            <filter>(acquisition_options['mode'] == 'one')</filter>
         </data>
 
         <data name="CombineMolIon" format="tabular" from_work_dir="CombineMolIon.tsv" label="CombineMolIon.tsv" >
-	        <filter>(acquisition_options['mode'] == 'two')</filter>
+            <filter>(acquisition_options['mode'] == 'two')</filter>
         </data>
         <data name="variableMetadata_Positive" format="tabular" from_work_dir="variableMetadata_Positive.tsv" label="variableMetadata_Positive.tsv" >
-	        <filter>(acquisition_options['mode'] == 'two')</filter>
+            <filter>(acquisition_options['mode'] == 'two')</filter>
         </data>
         <data name="variableMetadata_Negative" format="tabular" from_work_dir="variableMetadata_Negative.tsv" label="variableMetadata_Negative.tsv" >
-	        <filter>(acquisition_options['mode'] == 'two')</filter>
+            <filter>(acquisition_options['mode'] == 'two')</filter>
         </data>
 
     </outputs>
 
     <tests>
         <test>
-            <param name="acquisition_options|mode" value="one" />
-            <param name="acquisition_options|xa" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.negative.Rdata" />
-            <param name="zipfile_load_conditional|zipfile_load_select" value="yes" />
-            <param name="zipfile_load_conditional|zip_file" value="faahKO_reduce.zip"  ftype="zip" />
+            <conditional name="acquisition_options">
+                <param name="mode" value="one" />
+                <param name="image" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.negative.Rdata" />
+            </conditional>
+            <expand macro="test_file_load_zip"/>
+            <output name="log">
+                <assert_contents>
+                    <has_text text="ko15 ko16 wt15 wt16" />
+                    <has_text text="Step 1... determine cutoff point" />
+                    <has_text text="Step 2... estimate parameters of null distribution and eta0" />
+                    <has_text text="Step 3... compute p-values and estimate empirical PDF/CDF" />
+                    <has_text text="Step 4... compute q-values and local fdr" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <conditional name="acquisition_options">
+                <param name="mode" value="one" />
+                <param name="image" value="faahOK-single.xset.merged.group.retcor.group.fillPeaks.annotate.negative.Rdata" />
+            </conditional>
+            <expand macro="test_file_load_single"/>
             <output name="log">
                 <assert_contents>
                     <has_text text="ko15 ko16 wt15 wt16" />
@@ -206,7 +234,7 @@
 
 
     <help>
-	
+
 @HELP_AUTHORS@
 
 =========
@@ -225,7 +253,7 @@
 **Details**
 
 ProbMetab assumes peak detection, retention time correction and peak grouping [4, 5] in order to
-perform mass peak to compound assignment. 
+perform mass peak to compound assignment.
 
 Once the initial annotation for different forms of the same ion (adducts and isotopes), is defined,
 one can seek for a non-redundant set of putative molecules (after charge and possible adduct
@@ -235,7 +263,7 @@
 experimental condition. In order to address this issue, a flexible workflow, which allows users to
 integrate different methods, would improve true molecular ions recovery.
 
-The ion annotation table has the following core information: exact mass of putative molecule with experimental error; isotopic pattern associated; adduct form associated, and the original reference to raw data. 
+The ion annotation table has the following core information: exact mass of putative molecule with experimental error; isotopic pattern associated; adduct form associated, and the original reference to raw data.
 
 
 
@@ -250,9 +278,9 @@
 ========================= ========================================== ======= ==========
 Name                      Output file                                Format  Parameter
 ========================= ========================================== ======= ==========
-xcms.annotate             xset.annotate_POS (or NEG).RData RData     RData   file            			
+xcms.annotate             xset.annotate_POS (or NEG).RData RData     RData   file
 ========================= ========================================== ======= ==========
-  
+
 
 **General schema of the metabolomic workflow**
 
@@ -295,7 +323,7 @@
 
 **Calculate**
 
-**intervals** 
+**intervals**
 A vector of SNR numerical intervals, to which different carbon offset should be added to predicted C-number.
 
 **offset**
@@ -309,7 +337,7 @@
 
 Which noise model to use, "erfc" to complementary error function, or "gaussian" to standard gaussian with two sd corresponding to the given p.p.m precision.
 
-**precision** 
+**precision**
 
 Equipment mass accuracy, usually the same used in exact mass search.
 
@@ -384,6 +412,10 @@
 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
@@ -393,10 +425,8 @@
 
 - NEW: ProbMetab first version
 
- 
+
     </help>
 
     <expand macro="citation" />
 </tool>
- 
- 
diff -r 9541ba588de1 -r f24b9c360a60 README.txt
--- a/README.txt	Mon Jul 04 11:58:12 2016 -0400
+++ b/README.txt	Wed Feb 15 11:45:26 2017 -0500
@@ -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 -r 9541ba588de1 -r f24b9c360a60 lib.r
--- a/lib.r	Mon Jul 04 11:58:12 2016 -0400
+++ b/lib.r	Wed Feb 15 11:45:26 2017 -0500
@@ -5,204 +5,204 @@
 
 ##Main probmetab function launch by the Galaxy ProbMetab wrapper
 probmetab = function(xa, xaP, xaN, variableMetadata, variableMetadataP, variableMetadataN, listArguments){
-	##ONE MODE ACQUISITION##
-	if(listArguments[["mode_acquisition"]]=="one") {
-		comb=NULL
+    ##ONE MODE ACQUISITION##
+    if(listArguments[["mode_acquisition"]]=="one") {
+        comb=NULL
 
-		#Get the polarity from xa object
-		polarity=xa@polarity
-		#SNR option
-		if ("xsetnofill" %in% names(listArguments)) {
-			load(listArguments[["xsetnofill"]])
-			xsetnofill=xset
-		}
-		else{
-			xsetnofill=NULL
-		}
-		#Exclude samples
-		if ("toexclude" %in% names(listArguments)) {
-			toexclude=listArguments[["toexclude"]]
-		}
-		else {
-			toexclude=NULL
-		}
-		ionAnnot=get.annot(xa, polarity=polarity, allowMiss=listArguments[["allowMiss"]],xset=xsetnofill,toexclude=toexclude)
-		comb=NULL
-	}
+        #Get the polarity from xa object
+        polarity=xa@polarity
+        #SNR option
+        if ("xsetnofill" %in% names(listArguments)) {
+            load(listArguments[["xsetnofill"]])
+            xsetnofill=xset
+        }
+        else{
+            xsetnofill=NULL
+        }
+        #Exclude samples
+        if ("toexclude" %in% names(listArguments)) {
+            toexclude=listArguments[["toexclude"]]
+        }
+        else {
+            toexclude=NULL
+        }
+        ionAnnot=get.annot(xa, polarity=polarity, allowMiss=listArguments[["allowMiss"]],xset=xsetnofill,toexclude=toexclude)
+        comb=NULL
+    }
 
-	##TWO MODES ACQUISITION##
-	#Mode annotatediffreport
-	else if(listArguments[["inputs_mode"]]=="two"){
-		##Prepare the objects that will be used for the get.annot function
-		comb=1
-		
+    ##TWO MODES ACQUISITION##
+    #Mode annotatediffreport
+    else if(listArguments[["inputs_mode"]]=="two"){
+        ##Prepare the objects that will be used for the get.annot function
+        comb=1
+
 
-		xsetPnofill=NULL
-		xsetNnofill=NULL
-		# TODO: a reactiver		
-		#if ("xsetPnofill" %in% names(listArguments)) {
-		#	load(listArguments[["xsetPnofill"]])
-		#	xsetPnofill=xset
-		#}
-		#if ("xsetNnofill" %in% names(listArguments)) {
-		#	load(listArguments[["xsetNnofill"]])
-		#	xsetNnofill=xset
-		#}
-		# include CAMERA non-annotated compounds, and snr retrieval 
-		# comb 2+ - used on Table 1	
-		ionAnnotP2plus = get.annot(axP, allowMiss=listArguments[["allowMiss"]], xset=xsetPnofill,toexclude=listArguments[["toexclude"]]) 
-		ionAnnotN2plus = get.annot(axN, polarity="negative", allowMiss=listArguments[["allowMiss"]], xset=xsetNnofill,toexclude=listArguments[["toexclude"]])
-		ionAnnot = combineMolIon(ionAnnotP2plus, ionAnnotN2plus)
-		print(sum(ionAnnot$molIon[,3]==1))
-		print(sum(ionAnnot$molIon[,3]==0))
-		write.table(ionAnnot[1], sep="\t", quote=FALSE, row.names=FALSE, file="CombineMolIon.tsv")
-		#Merge variableMetadata Negative and positive acquisitions mode
-		
+        xsetPnofill=NULL
+        xsetNnofill=NULL
+        # TODO: a reactiver
+        #if ("xsetPnofill" %in% names(listArguments)) {
+        #    load(listArguments[["xsetPnofill"]])
+        #    xsetPnofill=xset
+        #}
+        #if ("xsetNnofill" %in% names(listArguments)) {
+        #    load(listArguments[["xsetNnofill"]])
+        #    xsetNnofill=xset
+        #}
+        # include CAMERA non-annotated compounds, and snr retrieval
+        # comb 2+ - used on Table 1
+        ionAnnotP2plus = get.annot(axP, allowMiss=listArguments[["allowMiss"]], xset=xsetPnofill,toexclude=listArguments[["toexclude"]])
+        ionAnnotN2plus = get.annot(axN, polarity="negative", allowMiss=listArguments[["allowMiss"]], xset=xsetNnofill,toexclude=listArguments[["toexclude"]])
+        ionAnnot = combineMolIon(ionAnnotP2plus, ionAnnotN2plus)
+        print(sum(ionAnnot$molIon[,3]==1))
+        print(sum(ionAnnot$molIon[,3]==0))
+        write.table(ionAnnot[1], sep="\t", quote=FALSE, row.names=FALSE, file="CombineMolIon.tsv")
+        #Merge variableMetadata Negative and positive acquisitions mode
 
-		#Mode combinexsannos TODO bug avec tableau issus de combinexsannos
-		#else {
-			#load(listArguments[["image_combinexsannos"]])
-			#image_combinexsannos=cAnnot
-			##Prepare the objects that will be used for the combineMolIon function
-			#load(listArguments[["image_pos"]])
-			#image_pos=xa
-			#ionAnnot=combineMolIon(peaklist=cAnnot, cameraobj=image_pos, polarity="pos")
-		#}
-		
-	}
+
+        #Mode combinexsannos TODO bug avec tableau issus de combinexsannos
+        #else {
+            #load(listArguments[["image_combinexsannos"]])
+            #image_combinexsannos=cAnnot
+            ##Prepare the objects that will be used for the combineMolIon function
+            #load(listArguments[["image_pos"]])
+            #image_pos=xa
+            #ionAnnot=combineMolIon(peaklist=cAnnot, cameraobj=image_pos, polarity="pos")
+        #}
+
+    }
 
-	##DATABASE MATCHING##
-	if (listArguments[["kegg_db"]]=="KEGG"){		
-		DB=build.database.kegg(orgID = NULL)
-	}
-	else{	
-		table_list <<- NULL
-		ids=strsplit(listArguments[["kegg_db"]],",")
-		ids=ids[[1]]
-		if(length(ids)>1){
-			for(i in 1:length(ids)){
-				 table_list[[i]] <- build.database.kegg(ids[i])
-			}
-			db_table=do.call("rbind",table_list)
-			DB=unique(db_table)
-		}
-		else{
-			DB=build.database.kegg(listArguments[["kegg_db"]])
-		}
-	}	
-	#Matching des mass exactes mesurees avec les masses des compounds KEGG (pas M+H ou M-H)
-	reactionM = create.reactionM(DB, ionAnnot, ppm.tol=listArguments[["ppm_tol"]])
-	##PROBABILITY RANKING##
-	# number of masses with candidates inside the fixed mass window
-	# and masses with more than one candidate
-	length(unique(reactionM[reactionM[,"id"]!="unknown",1])) 
-	sum(table(reactionM[reactionM[,"id"]!="unknown",1])>1)
-	#if (listArguments[["useIso"]]){
-		#BUG TODO
-		# Calculate the ratio between observed and theoretical isotopic patterns.
-		# If you don't have an assessment of carbon offset to carbon number prediction 
-		# skip this step and use the reactionM as input to weigthM function. 
-		#isoPatt < incorporate.isotopes(comb2plus, reactionM, , samp=12:23, DB=DB)  
-		#  calculate   the   likelihood   of   each   mass   to   compound   assignment   using   mass   accuracy,and isotopic pattern, when present
-		#wl < weightM(isoPatt,intervals=seq(0,1000,by=500), offset=c(3.115712, 3.434146, 2.350798))
-		
-			#isoPatt=incorporate.isotopes(ionAnnot, reactionM,comb=comb,var=listArguments[["var"]],DB=DB)
+    ##DATABASE MATCHING##
+    if (listArguments[["kegg_db"]]=="KEGG"){
+        DB=build.database.kegg(orgID = NULL)
+    }
+    else{
+        table_list <<- NULL
+        ids=strsplit(listArguments[["kegg_db"]],",")
+        ids=ids[[1]]
+        if(length(ids)>1){
+            for(i in 1:length(ids)){
+                 table_list[[i]] <- build.database.kegg(ids[i])
+            }
+            db_table=do.call("rbind",table_list)
+            DB=unique(db_table)
+        }
+        else{
+            DB=build.database.kegg(listArguments[["kegg_db"]])
+        }
+    }
+    #Matching des mass exactes mesurees avec les masses des compounds KEGG (pas M+H ou M-H)
+    reactionM = create.reactionM(DB, ionAnnot, ppm.tol=listArguments[["ppm_tol"]])
+    ##PROBABILITY RANKING##
+    # number of masses with candidates inside the fixed mass window
+    # and masses with more than one candidate
+    length(unique(reactionM[reactionM[,"id"]!="unknown",1]))
+    sum(table(reactionM[reactionM[,"id"]!="unknown",1])>1)
+    #if (listArguments[["useIso"]]){
+        #BUG TODO
+        # Calculate the ratio between observed and theoretical isotopic patterns.
+        # If you don't have an assessment of carbon offset to carbon number prediction
+        # skip this step and use the reactionM as input to weigthM function.
+        #isoPatt < incorporate.isotopes(comb2plus, reactionM, , samp=12:23, DB=DB)
+        #  calculate   the   likelihood   of   each   mass   to   compound   assignment   using   mass   accuracy,and isotopic pattern, when present
+        #wl < weightM(isoPatt,intervals=seq(0,1000,by=500), offset=c(3.115712, 3.434146, 2.350798))
 
-		#wl = weightM(reactionM, useIso=true)
-	#}
-	#else {
-		#wl = weightM(reactionM, useIso=FALSE)
-	#}
-	wl =weightM(reactionM, useIso=FALSE)	
-	w = design.connection(reactionM)
-	# Probability calculations
-	x = 1:ncol(wl$wm)
-	y = 1:nrow(wl$wm)
-	conn = gibbs.samp(x, y, 5000, w, wl$wm)
-	ansConn = export.class.table(conn, reactionM, ionAnnot, DB=DB,html=listArguments[["html"]],filename="AnalysisExample",prob=listArguments[["prob"]])
-	if(listArguments[["html"]]){
-		#Zip the EICS plot
-		system(paste('zip -r "Analysis_Report.zip" "AnalysisExample_fig"'))
-	}
-	
-	# calculate the correlations and partial correlations and cross reference then with reactions
-	mw=which(w==1,arr.ind=TRUE)
-	#reac2cor function : Use the intensity of putative molecules in repeated samples to calculate correlations and partial
-	#correlation in a user defined threshold of false discovery rate for significance testing. After the
-	#correlation test the function also overlay significant correlations with all putative reactions between
-	#two masses.
-	#It generates a list of estimated correlations and reactions.
-	corList=reac2cor(mw,ansConn$classTable,listArguments[["opt"]],listArguments[["corths"]],listArguments[["corprob"]],listArguments[["pcorprob"]])
-	ans=list("ansConn"=ansConn,"corList"=corList)
-	#Generate the siff table for CytoScape
-	cytoscape_output(corList,ansConn)
+            #isoPatt=incorporate.isotopes(ionAnnot, reactionM,comb=comb,var=listArguments[["var"]],DB=DB)
+
+        #wl = weightM(reactionM, useIso=true)
+    #}
+    #else {
+        #wl = weightM(reactionM, useIso=FALSE)
+    #}
+    wl =weightM(reactionM, useIso=FALSE)
+    w = design.connection(reactionM)
+    # Probability calculations
+    x = 1:ncol(wl$wm)
+    y = 1:nrow(wl$wm)
+    conn = gibbs.samp(x, y, 5000, w, wl$wm)
+    ansConn = export.class.table(conn, reactionM, ionAnnot, DB=DB,html=listArguments[["html"]],filename="AnalysisExample",prob=listArguments[["prob"]])
+    if(listArguments[["html"]]){
+        #Zip the EICS plot
+        system(paste('zip -r "Analysis_Report.zip" "AnalysisExample_fig"'))
+    }
+
+    # calculate the correlations and partial correlations and cross reference then with reactions
+    mw=which(w==1,arr.ind=TRUE)
+    #reac2cor function : Use the intensity of putative molecules in repeated samples to calculate correlations and partial
+    #correlation in a user defined threshold of false discovery rate for significance testing. After the
+    #correlation test the function also overlay significant correlations with all putative reactions between
+    #two masses.
+    #It generates a list of estimated correlations and reactions.
+    corList=reac2cor(mw,ansConn$classTable,listArguments[["opt"]],listArguments[["corths"]],listArguments[["corprob"]],listArguments[["pcorprob"]])
+    ans=list("ansConn"=ansConn,"corList"=corList)
+    #Generate the siff table for CytoScape
+    cytoscape_output(corList,ansConn)
 
 
-	#Execute the merge_probmetab function to merge the variableMetadata table and annotations from ProbMetab results
-	
-	if(listArguments[["mode_acquisition"]]=="one") {
-		#Retrocompatibility with previous annotateDiffreport variableMetadata dataframe (must replace mzmed column by mz, and rtmed by rt)
-		names(variableMetadata)[names(variableMetadata)=="mzmed"] <- "mz"
-		names(variableMetadata)[names(variableMetadata)=="rtmed"] <- "rt"
-		variableM=merge_probmetab(variableMetadata, ansConn)
-		write.table(variableM, sep="\t", quote=FALSE, row.names=FALSE, file="variableMetadata.tsv")
-	} else if (listArguments[["mode_acquisition"]]=="two") {
-		#Retrocompatibility with previous annotateDiffreport variableMetadata dataframe (must replace mzmed column by mz, and rtmed by rt)
-		names(variableMetadataP)[names(variableMetadata)=="mzmed"] <- "mz"
-		names(variableMetadataP)[names(variableMetadata)=="rtmed"] <- "rt"
-		names(variableMetadataN)[names(variableMetadata)=="mzmed"] <- "mz"
-		names(variableMetadataN)[names(variableMetadata)=="rtmed"] <- "rt"
-		variableMP=merge_probmetab(variableMetadataP, ansConn)
-		write.table(variableMP, sep="\t", quote=FALSE, row.names=FALSE, file="variableMetadata_Positive.tsv")
-		variableMN=merge_probmetab(variableMetadataN, ansConn)
-		write.table(variableMN, sep="\t", quote=FALSE, row.names=FALSE, file="variableMetadata_Negative.tsv")
-	}
+    #Execute the merge_probmetab function to merge the variableMetadata table and annotations from ProbMetab results
+
+    if(listArguments[["mode_acquisition"]]=="one") {
+        #Retrocompatibility with previous annotateDiffreport variableMetadata dataframe (must replace mzmed column by mz, and rtmed by rt)
+        names(variableMetadata)[names(variableMetadata)=="mzmed"] <- "mz"
+        names(variableMetadata)[names(variableMetadata)=="rtmed"] <- "rt"
+        variableM=merge_probmetab(variableMetadata, ansConn)
+        write.table(variableM, sep="\t", quote=FALSE, row.names=FALSE, file="variableMetadata.tsv")
+    } else if (listArguments[["mode_acquisition"]]=="two") {
+        #Retrocompatibility with previous annotateDiffreport variableMetadata dataframe (must replace mzmed column by mz, and rtmed by rt)
+        names(variableMetadataP)[names(variableMetadata)=="mzmed"] <- "mz"
+        names(variableMetadataP)[names(variableMetadata)=="rtmed"] <- "rt"
+        names(variableMetadataN)[names(variableMetadata)=="mzmed"] <- "mz"
+        names(variableMetadataN)[names(variableMetadata)=="rtmed"] <- "rt"
+        variableMP=merge_probmetab(variableMetadataP, ansConn)
+        write.table(variableMP, sep="\t", quote=FALSE, row.names=FALSE, file="variableMetadata_Positive.tsv")
+        variableMN=merge_probmetab(variableMetadataN, ansConn)
+        write.table(variableMN, sep="\t", quote=FALSE, row.names=FALSE, file="variableMetadata_Negative.tsv")
+    }
 
-	return(ans)
+    return(ans)
 
 }
 
 ##Function that generates a siff table for CytoScape
 cytoscape_output=function(corList,ansConn){
-	signif_cor=as.data.frame(corList$signif.cor)
-	classTable=as.data.frame(ansConn$classTable)
-	#Siff table
-	siff_table=cbind(signif_cor["node1"],signif_cor["cor"],signif_cor["node2"])
-	#attribute table output for Cytoscape
+    signif_cor=as.data.frame(corList$signif.cor)
+    classTable=as.data.frame(ansConn$classTable)
+    #Siff table
+    siff_table=cbind(signif_cor["node1"],signif_cor["cor"],signif_cor["node2"])
+    #attribute table output for Cytoscape
 
-	## START  Code part from the export2cytoscape function of ProbMetab written by Ricardo R. Silva 
-	for (i in 1:nrow(classTable)) if (classTable[i, 1] == ""){
-		classTable[i, c(1, 4, 6, 7)] <- classTable[i - 1, c(1, 4, 6, 7)]
-	}
- 	msel <- as.matrix(classTable[, 1:7])
- 	msel <- cbind(msel[, 6], msel[,-6])
- 	colnames(msel)[1] <- "Id"
- 	msel[, 1] <- sub("^\\s+", "", msel[, 1])
- 	colnames(msel)[1] <- "Id"
-	ids <- unique(msel[, 1])
- 	attrMatrix <- matrix("", nrow = length(ids), ncol = ncol(msel)-1)
-	for (i in 1:length(ids)) {
-		    attrMatrix[i, 1] <- unique(msel[msel[, 1] == ids[i], 
-		        2])
-		    attrMatrix[i, 2] <- paste("[", paste(msel[msel[, 
-		        1] == ids[i], 3], collapse = ", "), "]", sep = "")
-		    attrMatrix[i, 3] <- paste("[", paste(msel[msel[, 
-		        1] == ids[i], 4], collapse = ", "), "]", sep = "")
-		    attrMatrix[i, 4] <- unique(msel[msel[, 1] == ids[i], 
-		        5])
-		    attrMatrix[i, 5] <- paste("[", paste(msel[msel[, 
-		        1] == ids[i], 6], collapse = ", "), "]", sep = "")
-		    attrMatrix[i, 6] <- unique(msel[msel[, 1] == ids[i], 
-		        7])
+    ## START  Code part from the export2cytoscape function of ProbMetab written by Ricardo R. Silva
+    for (i in 1:nrow(classTable)) if (classTable[i, 1] == ""){
+        classTable[i, c(1, 4, 6, 7)] <- classTable[i - 1, c(1, 4, 6, 7)]
+    }
+     msel <- as.matrix(classTable[, 1:7])
+     msel <- cbind(msel[, 6], msel[,-6])
+     colnames(msel)[1] <- "Id"
+     msel[, 1] <- sub("^\\s+", "", msel[, 1])
+     colnames(msel)[1] <- "Id"
+    ids <- unique(msel[, 1])
+     attrMatrix <- matrix("", nrow = length(ids), ncol = ncol(msel)-1)
+    for (i in 1:length(ids)) {
+            attrMatrix[i, 1] <- unique(msel[msel[, 1] == ids[i],
+                2])
+            attrMatrix[i, 2] <- paste("[", paste(msel[msel[,
+                1] == ids[i], 3], collapse = ", "), "]", sep = "")
+            attrMatrix[i, 3] <- paste("[", paste(msel[msel[,
+                1] == ids[i], 4], collapse = ", "), "]", sep = "")
+            attrMatrix[i, 4] <- unique(msel[msel[, 1] == ids[i],
+                5])
+            attrMatrix[i, 5] <- paste("[", paste(msel[msel[,
+                1] == ids[i], 6], collapse = ", "), "]", sep = "")
+            attrMatrix[i, 6] <- unique(msel[msel[, 1] == ids[i],
+                7])
         }
-	ids <- as.numeric(unique(msel[, 1]))
-	attrMatrix <- cbind(ids, attrMatrix)
-	colnames(attrMatrix) <- colnames(msel)
-	## END Code part from the export2cytoscape function of ProbMetab writieen by Ricardo R. Silva 
-	write.table(attrMatrix, sep="\t", quote=FALSE, row.names=FALSE, file="Analysis_Report.tsv")
-	write.table(siff_table, sep="\t", quote=FALSE, row.names=FALSE, file="sif.tsv")
+    ids <- as.numeric(unique(msel[, 1]))
+    attrMatrix <- cbind(ids, attrMatrix)
+    colnames(attrMatrix) <- colnames(msel)
+    ## END Code part from the export2cytoscape function of ProbMetab writieen by Ricardo R. Silva
+    write.table(attrMatrix, sep="\t", quote=FALSE, row.names=FALSE, file="Analysis_Report.tsv")
+    write.table(siff_table, sep="\t", quote=FALSE, row.names=FALSE, file="sif.tsv")
 
-	return(attrMatrix)
+    return(attrMatrix)
 }
 
 ##Functions written by Jean-Francois Martin
@@ -211,55 +211,55 @@
 {
   # determine ionisation in ProbMetab result file, used in function merge_probmetab
   # input : for 1 ion, aninfo = string with m/z rt and CAMERA annotation from ProbMetab result file
-  # if the difference between m/z and the probmetab proposed mass is ~1 we use the sign (positive or negative) of this diference 
+  # if the difference between m/z and the probmetab proposed mass is ~1 we use the sign (positive or negative) of this diference
   # to define the type of ionisation
-  # If adduct or fragment was detected, therefore diff >>1 and so, we search for substring "+" ou "2+" ou "3+" ou "-"... 
+  # If adduct or fragment was detected, therefore diff >>1 and so, we search for substring "+" ou "2+" ou "3+" ou "-"...
   # to define the type of ionisation
   # aninfo : vecteur of character resulting of the parsing(sep="#") of the probmetab annotation
   if (round(abs(as.numeric(aninfo[1]) - pm),0) ==1) {
     if (as.numeric(aninfo[1]) - pm <0) {esi <- "n"} else {esi <- "p"}
-  } else 
+  } else
     if (!is.na(aninfo[4])) {
       anstr <- aninfo[4]
       # cat(anstr)
       if ((grepl("]+",anstr,fixed=T)==T) || (grepl("]2+",anstr,fixed=T)==T) || (grepl("]3+",anstr,fixed=T)==T)) { esi <- "p"}
-      else 
+      else
         if ((grepl("]-",anstr,fixed=T)==T) || (grepl("]2-",anstr,fixed=T)==T) || (grepl("]3-",anstr,fixed=T)==T)) { esi <- "n"}
       # cat(" ioni ",esi,"\n")
     } else
-    { esi <- "u"} 
-  
+    { esi <- "u"}
+
   return(esi)
 }
 
 
 merge_probmetab <- function(metaVar,ansConn) {
   ## Parse ProbMetab information result file and merge in variable_metaData initial file
-  ##  inputs : 
+  ##  inputs :
   ##      metaVar : data.frame of metadataVariable input of probmetab function
   ##     ansConn  : data.frame of ProbMetab result
   ## output : dataframe with Probmetab results merge with variableMetadata
   ## Constante
   ## iannot : indice de la colonne annotation dans le resultat de probMetab
   iannot <- 4
-  
-  ## definition of an unique identification of ions mz with 3 decimals and rt(sec) with 1 decimal to avoid 
+
+  ## definition of an unique identification of ions mz with 3 decimals and rt(sec) with 1 decimal to avoid
   ## duplicate ions name in the diffreport result file
   ions <- paste ("M",round(metaVar$mz,3),"T",round(metaVar$rt,1),sep="")
   metaVar <- data.frame(ions,metaVar)
-  
+
   ###### Result data.frame from ProbMetab result list
   an_ini <- ansConn$classTable
-  
+
   ## Suppression of rows without  mz and rt or unknown and columns of intensities
-  ## COLUMNS SUBSCRIPTS HAVE TO BE CHECKED WITh DIFFERENT RESULTS FILES 
+  ## COLUMNS SUBSCRIPTS HAVE TO BE CHECKED WITh DIFFERENT RESULTS FILES
   an <- an_ini[(an_ini[,2]!="unknown"),c(1,2,3,7)]
-  ## initialisation of vectors receiving the result of the parse of the column annotation (subscrip iannot) 
+  ## initialisation of vectors receiving the result of the parse of the column annotation (subscrip iannot)
   mz <- rep(0,dim(an)[1])
   rt <- rep(0,dim(an)[1])
   propmz <- rep(0,dim(an)[1])
   ioni <- rep("u",dim(an)[1])
-  
+
   ## parse the column annotation and define ionisation mode
   for (i in 1:dim(an)[1]) {
     if (an[i,1] != "") {
@@ -276,12 +276,12 @@
       ioni[i] <- ioni[i-1]
     }
   }
-  
+
   ## definition of an unique identification of ions : mz with 3 decimals and rt(sec) with 1 decimal
   ## The same as for the metadataVariable data.frame to match with.
   ions <- paste ("M",round(mz,3),"T",round(rt,1),sep="")
   an <- data.frame(ions,ioni,propmz,mz,rt,an)
-  
+
   ## transposition of the different probmetab annotations which are in different rows in the initial result data.frame
   ## on only 1 row separated with a ";"
   li <- as.matrix(table(an$propmz))
@@ -298,26 +298,105 @@
     ions[c]   <- as.character(suban[1,1])
     propmz[c] <- as.numeric(suban[1,3])
     mpc[c]    <- paste(suban[,7],collapse=";")
-    proba[c]  <- paste(as.character(suban[,8]),collapse=";") 
+    proba[c]  <- paste(as.character(suban[,8]),collapse=";")
   }
-  
+
   ## Creation of the data.frame with 1 row per ions
   anc <- data.frame(ions,propmz,mpc,proba)
   anc <- anc[order(anc[,1]),]
-  
+
   metaVarFinal <- merge(metaVar, anc, by.x=1, by.y=1, all.x=T, all.y=T)
   metaVarFinal <- metaVarFinal[,-1]
   #write.table(metaVarFinal,file="res.txt", sep="\t", row.names=F, quote=F)
-  
+
   return (metaVarFinal)
 }
 
 # RETROCOMPATIBILITE avec ancienne version de annotate
 getVariableMetadata = function(xa) {
-	# --- variableMetadata ---
-	peakList=getPeaklist(xa)
-	peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name");
-	variableMetadata=peakList[,!(colnames(peakList) %in% c(sampnames(xa@xcmsSet)))]
-	variableMetadata$name= paste("M",round(variableMetadata$mz),"T",round(variableMetadata$rt),sep="")
-	return (variableMetadata)
+    # --- variableMetadata ---
+    peakList=getPeaklist(xa)
+    peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name");
+    variableMetadata=peakList[,!(colnames(peakList) %in% c(sampnames(xa@xcmsSet)))]
+    variableMetadata$name= groupnames(xa@xcmsSet)
+    return (variableMetadata)
+}
+
+
+# This function get the raw file path from the arguments
+getRawfilePathFromArguments <- function(listArguments) {
+    zipfile = NULL
+    singlefile = NULL
+    if (!is.null(listArguments[["zipfile"]]))           zipfile = listArguments[["zipfile"]]
+    if (!is.null(listArguments[["zipfilePositive"]]))   zipfile = listArguments[["zipfilePositive"]]
+    if (!is.null(listArguments[["zipfileNegative"]]))   zipfile = listArguments[["zipfileNegative"]]
+
+    if (!is.null(listArguments[["singlefile_galaxyPath"]])) {
+        singlefile_galaxyPaths = listArguments[["singlefile_galaxyPath"]];
+        singlefile_sampleNames = listArguments[["singlefile_sampleName"]]
+    }
+    if (!is.null(listArguments[["singlefile_galaxyPathPositive"]])) {
+        singlefile_galaxyPaths = listArguments[["singlefile_galaxyPathPositive"]];
+        singlefile_sampleNames = listArguments[["singlefile_sampleNamePositive"]]
+    }
+    if (!is.null(listArguments[["singlefile_galaxyPathNegative"]])) {
+        singlefile_galaxyPaths = listArguments[["singlefile_galaxyPathNegative"]];
+        singlefile_sampleNames = listArguments[["singlefile_sampleNameNegative"]]
+    }
+    if (exists("singlefile_galaxyPaths")){
+        singlefile_galaxyPaths = unlist(strsplit(singlefile_galaxyPaths,","))
+        singlefile_sampleNames = unlist(strsplit(singlefile_sampleNames,","))
+
+        singlefile=NULL
+        for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
+            singlefile_galaxyPath=singlefile_galaxyPaths[singlefile_galaxyPath_i]
+            singlefile_sampleName=singlefile_sampleNames[singlefile_galaxyPath_i]
+            singlefile[[singlefile_sampleName]] = singlefile_galaxyPath
+        }
+    }
+    return(list(zipfile=zipfile, singlefile=singlefile))
 }
+
+
+# This function retrieve the raw file in the working directory
+#   - if zipfile: unzip the file with its directory tree
+#   - if singlefiles: set symlink with the good filename
+retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
+
+    if(!is.null(singlefile) && (length("singlefile")>0)) {
+        for (singlefile_sampleName in names(singlefile)) {
+            singlefile_galaxyPath = singlefile[[singlefile_sampleName]]
+            if(!file.exists(singlefile_galaxyPath)){
+                error_message=paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
+                print(error_message); stop(error_message)
+            }
+
+            file.symlink(singlefile_galaxyPath,singlefile_sampleName)
+        }
+        directory = "."
+
+    }
+    if(!is.null(zipfile) && (zipfile!="")) {
+        if(!file.exists(zipfile)){
+            error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
+            print(error_message)
+            stop(error_message)
+        }
+
+        #list all file in the zip file
+        #zip_files=unzip(zipfile,list=T)[,"Name"]
+
+        #unzip
+        suppressWarnings(unzip(zipfile, unzip="unzip"))
+
+        #get the directory name
+        filesInZip=unzip(zipfile, list=T);
+        directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])));
+        directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
+        directory = "."
+        if (length(directories) == 1) directory = directories
+
+        cat("files_root_directory\t",directory,"\n")
+
+    }
+}
diff -r 9541ba588de1 -r f24b9c360a60 macros.xml
--- a/macros.xml	Mon Jul 04 11:58:12 2016 -0400
+++ b/macros.xml	Wed Feb 15 11:45:26 2017 -0500
@@ -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>
+
+    <token name="@COMMAND_FILE_LOAD_NEGATIVE@">
+        #set file_load_section_selected = $file_load_sectionNegative
+        #set polarity="Negative"
+        @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>
+
+    <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 -r 9541ba588de1 -r f24b9c360a60 probmetab.r
--- a/probmetab.r	Mon Jul 04 11:58:12 2016 -0400
+++ b/probmetab.r	Wed Feb 15 11:45:26 2017 -0500
@@ -4,7 +4,7 @@
 
 
 # ----- LOG -----
-log_file=file("probmetab.log", open = "wt")
+log_file=file("log.txt", open = "wt")
 sink(log_file)
 sink(log_file, type = "out")
 
@@ -12,8 +12,8 @@
 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(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 @@
 # ----- 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
+
+    # 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
 
-	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
+    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 @@
 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 -r 9541ba588de1 -r f24b9c360a60 test-data/faahOK-single.xset.merged.group.retcor.group.fillPeaks.annotate.negative.Rdata
Binary file test-data/faahOK-single.xset.merged.group.retcor.group.fillPeaks.annotate.negative.Rdata has changed
diff -r 9541ba588de1 -r f24b9c360a60 test-data/ko15.CDF
Binary file test-data/ko15.CDF has changed
diff -r 9541ba588de1 -r f24b9c360a60 test-data/ko16.CDF
Binary file test-data/ko16.CDF has changed
diff -r 9541ba588de1 -r f24b9c360a60 test-data/wt15.CDF
Binary file test-data/wt15.CDF has changed
diff -r 9541ba588de1 -r f24b9c360a60 test-data/wt16.CDF
Binary file test-data/wt16.CDF has changed