# HG changeset patch
# User lecorguille
# Date 1518514944 18000
# Node ID e93153c07be004fee79cfcc7af0c2113f8f17c90
# Parent  d71827ecd22c751f72107426dbe0aa4526a82823
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298

diff -r d71827ecd22c -r e93153c07be0 README.rst
--- a/README.rst	Thu Oct 26 11:14:49 2017 -0400
+++ b/README.rst	Tue Feb 13 04:42:24 2018 -0500
@@ -22,9 +22,9 @@
 Changelog/News
 --------------
 
-**Version 2.2.0 - 19/10/2017**
+**Version 2.1.1 - 29/11/2017**
 
-- NEW: The TIC and BPC is new exported as tabular files to be visualized using MultiQC.
+- BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C
 
 **Version 2.1.0 - 22/02/2017**
 
diff -r d71827ecd22c -r e93153c07be0 abims_xcms_xcmsSet.xml
--- a/abims_xcms_xcmsSet.xml	Thu Oct 26 11:14:49 2017 -0400
+++ b/abims_xcms_xcmsSet.xml	Tue Feb 13 04:42:24 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.2.0">
+<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.1.1">
     <description>Filtration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis </description>
 
     <macros>
@@ -21,6 +21,9 @@
 
         xsetRdataOutput '$xsetRData'
         sampleMetadataOutput '$sampleMetadata'
+        ticspdf '$ticsRawPdf'
+        bicspdf '$bpcsRawPdf'
+
 
         #if $options_scanrange.option == "show":
             scanrange "c($options_scanrange.scanrange)"
@@ -56,13 +59,7 @@
             scales "c($methods.scales)"
             SNR.method "$methods.SNR_method"
         #end if
-
-        #if $input.is_of_type("mzxml") or $input.is_of_type("mzml") or $input.is_of_type("mzdata") or $input.is_of_type("netcdf"):
-            && mv *-TIC_mqc.out $ticsRawTab
-            && mv *-BPC_mqc.out $bpcsRawTab
-        #end if
-
-        @COMMAND_LOG_EXIT@;
+        @COMMAND_LOG_EXIT@
     ]]></command>
 
     <inputs>
@@ -158,47 +155,39 @@
                 <param name="SNR_method" type="text" value="data.mean" label="SNR (Signal to Noise Ratio) method" help="[SNR.method] Method to estimate noise level. Currently, only 95 percentage quantile is supported." />
             </when>
         </conditional>
-
-
-        <expand macro="input_tic_bpc_pdf"/>
     </inputs>
 
     <outputs>
         <data name="xsetRData" format="rdata.xcms.raw" label="${input.name.rsplit('.',1)[0]}.xset.RData" />
-        <data name="log" format="txt" label="${input.name.rsplit('.',1)[0]}.xset.log.txt" />
-
-        <!-- SINGLE MODE -->
-        <data name="ticsRawTab" format="tabular" label="${input.name.rsplit('.',1)[0]}.xset.TICs_raw.tabular">
-            <filter>input.extension in ["mzxml","mzml","mzdata","netcdf"]</filter>
-        </data>
-        <data name="bpcsRawTab" format="tabular" label="${input.name.rsplit('.',1)[0]}.xset.BPCs_raw.tabular">
-            <filter>input.extension in ["mzxml","mzml","mzdata","netcdf"]</filter>
-        </data>
-
-        <!-- ZIP MODE -->
         <data name="sampleMetadata" format="tabular" label="${input.name.rsplit('.',1)[0]}.sampleMetadata.tsv">
             <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter>
         </data>
-        <data name="ticsRawPdf" format="pdf" from_work_dir="TICs.pdf" label="${input.name.rsplit('.',1)[0]}.xset.TICs_raw.pdf">
-            <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter>
-            <filter>tic_bpc_pdf</filter>
-        </data>
-        <data name="bpcsRawPdf" format="pdf" from_work_dir="BPCs.pdf" label="${input.name.rsplit('.',1)[0]}.xset.BPCs_raw.pdf">
-            <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter>
-            <filter>tic_bpc_pdf</filter>
-        </data>
-        <collection name="ticsRawTabCollection" type="list" label="TIC raw tabular">
-            <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter>
-           <discover_datasets pattern="(?P&lt;designation&gt;.+)-TIC_mqc\.out" ext="tabular" />
-        </collection>
-        <collection name="bpcsRawTabCollection" type="list" label="BPC raw tabular">
-            <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter>
-           <discover_datasets pattern="(?P&lt;designation&gt;.+)-BPC_mqc\.out" ext="tabular" />
-        </collection>
+        <data name="ticsRawPdf"   format="pdf" label="${input.name.rsplit('.',1)[0]}.xset.TICs_raw.pdf" />
+        <data name="bpcsRawPdf"   format="pdf" label="${input.name.rsplit('.',1)[0]}.xset.BPCs_raw.pdf" />
+        <data name="log" format="txt" label="${input.name.rsplit('.',1)[0]}.xset.log.txt" />
     </outputs>
 
     <tests>
-        <!--
+        <!--<test>
+            <param name="input" value="sacuri_dir_root.zip"  ftype="zip" />
+            <param name="methods|method" value="matchedFilter" />
+            <param name="methods|step" value="0.01" />
+            <param name="methods|fwhm" value="4" />
+            <param name="methods|options_m|option" value="show" />
+            <param name="methods|options_m|max" value="50" />
+            <param name="methods|options_m|snthresh" value="1" />
+            <param name="methods|options_m|steps" value="2" />
+            <output name="log">
+                <assert_contents>
+                    <has_text text="object with 4 samples" />
+                    <has_text text="Time range: 0.7-1139.7 seconds (0-19 minutes)" />
+                    <has_text text="Mass range: 50.0021-999.9863 m/z" />
+                    <has_text text="Peaks: 59359 (about 14840 per sample)" />
+                    <has_text text="Peak Groups: 0" />
+                    <has_text text="Sample classes: bio, blank" />
+                </assert_contents>
+            </output>
+        </test>
         <test>
             <param name="input" value="sacuri_current_root.zip"  ftype="zip" />
             <param name="methods|method" value="centWave" />
@@ -230,21 +219,56 @@
                     <has_text text="Sample classes: KO, WT" />
                 </assert_contents>
             </output>
-            <output_collection name="ticsRawTabCollection" type="list">
-                <element name="ko15" value="ko15-TIC_mqc.out" />
-                <element name="ko16" value="ko16-TIC_mqc.out" />
-                <element name="wt15" value="wt15-TIC_mqc.out" />
-                <element name="wt16" value="wt16-TIC_mqc.out" />
-            </output_collection>
-            <output_collection name="bpcsRawTabCollection" type="list">
-                <element name="ko15" value="ko15-BPC_mqc.out" />
-                <element name="ko16" value="ko16-BPC_mqc.out" />
-                <element name="wt15" value="wt15-BPC_mqc.out" />
-                <element name="wt16" value="wt16-BPC_mqc.out" />
-            </output_collection>
         </test>
         <!-- Passed but disable to save time for Travis" -->
-        <!--
+        <!--<test>
+            <param name="input" value="ko15.CDF"  ftype="netcdf" />
+            <param name="methods|method" value="centWave" />
+            <param name="methods|ppm" value="25" />
+            <param name="methods|peakwidth" value="20,50" />
+            <output name="log">
+                <assert_contents>
+                    <has_text text="object with 1 samples" />
+                    <has_text text="Time range: 2506.1-4471.7 seconds (41.8-74.5 minutes)" />
+                    <has_text text="Mass range: 200.2-600 m/z" />
+                    <has_text text="Peaks: 2262 (about 2262 per sample)" />
+                    <has_text text="Peak Groups: 0" />
+                    <has_text text="Sample classes: ." />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input" value="ko16.CDF"  ftype="netcdf" />
+            <param name="methods|method" value="centWave" />
+            <param name="methods|ppm" value="25" />
+            <param name="methods|peakwidth" value="20,50" />
+            <output name="log">
+                <assert_contents>
+                    <has_text text="object with 1 samples" />
+                    <has_text text="Time range: 2521.7-4477.9 seconds (42-74.6 minutes)" />
+                    <has_text text="Mass range: 200.1-600 m/z" />
+                    <has_text text="Peaks: 2408 (about 2408 per sample)" />
+                    <has_text text="Peak Groups: 0" />
+                    <has_text text="Sample classes: ." />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input" value="wt15.CDF"  ftype="netcdf" />
+            <param name="methods|method" value="centWave" />
+            <param name="methods|ppm" value="25" />
+            <param name="methods|peakwidth" value="20,50" />
+            <output name="log">
+                <assert_contents>
+                    <has_text text="object with 1 samples" />
+                    <has_text text="Time range: 2517-4473.2 seconds (42-74.6 minutes)" />
+                    <has_text text="Mass range: 200.2-599.8 m/z" />
+                    <has_text text="Peaks: 2278 (about 2278 per sample)" />
+                    <has_text text="Peak Groups: 0" />
+                    <has_text text="Sample classes: ." />
+                </assert_contents>
+            </output>
+        </test>
         <test>
             <param name="inputs|input" value="single_file" />
             <param name="inputs|single_file" value="wt16.CDF"  ftype="netcdf" />
@@ -277,8 +301,6 @@
                     <has_text text="Sample classes: ." />
                 </assert_contents>
             </output>
-            <output name="ticsRawTab" value="HU_neg_017-TIC_mqc.out" />
-            <output name="bpcsRawTab" value="HU_neg_017-BPC_mqc.out" />
         </test>
         <test>
             <param name="input" value="MM14.mzML"  ftype="mzxml" />
@@ -295,8 +317,6 @@
                     <has_text text="Sample classes: ." />
                 </assert_contents>
             </output>
-            <output name="ticsRawTab" value="MM14-TIC_mqc.out" />
-            <output name="bpcsRawTab" value="MM14-BPC_mqc.out" />
         </test>
     </tests>
 
@@ -308,6 +328,7 @@
 Xcms.xcmsSet
 ============
 
+-----------
 Description
 -----------
 
@@ -317,16 +338,18 @@
 .. _here: http://web11.sb-roscoff.fr/download/w4m/howto/w4m_HowToPerformXcmsPreprocessing_v02.pdf
 
 
+-----------------
 Workflow position
 -----------------
 
 **Upstream tools**
 
-+------------------------+--------------------+-----------------------------+-----------+
-| Name                   | output file        | format                      | parameter |
-+------------------------+--------------------+-----------------------------+-----------+
-| Upload File            | Dataset Collection | mzXML, mzML, mzData, netCDF | NA        |
-+------------------------+--------------------+-----------------------------+-----------+
+========================= ================= ======= =========
+Name                      output file       format  parameter
+========================= ================= ======= =========
+NA                        NA                zip     NA
+========================= ================= ======= =========
+
 
 **Downstream tools**
 
@@ -335,89 +358,90 @@
 +===========================+====================+=================+
 |xcms.group                 | xset.RData         | rdata.xcms.raw  |
 +---------------------------+--------------------+-----------------+
+|PCA ellipsoid by factors   | sampleMetadata.tsv | Tabular         |
++---------------------------+--------------------+-----------------+
+|Anova                      | sampleMetadata.tsv | Tabular         |
++---------------------------+--------------------+-----------------+
 
 
 **Example of a metabolomic workflow**
 
 .. image:: xcms_xcmsset_workflow.png
 
+
+------
+
+.. class:: infomark
+
+The output file is an xset.RData file. You can continue your analysis using it in **xcms.group** tool.
+
 ---------------------------------------------------
 
+
+
 -----------
 Input files
 -----------
 
-Choose your inputs
-------------------
-
 +---------------------------+----------------------------------+
-| Parameter                 |   Format                         |
+| Parameter : num + label   |   Format                         |
 +===========================+==================================+
+| OR : Zip file             |   zip                            |
++---------------------------+----------------------------------+
 | OR : Single file          |   mzXML, mzML, mzData, netCDF    |
 +---------------------------+----------------------------------+
-| OR : Zip file             |   zip                            |
-+---------------------------+----------------------------------+
+
+**Choose your inputs**
 
 You have two methods for your inputs:
 
-* Single file (recommended): You can put a single file as input. That way, you will be able to launch several xcmsSet in parallel and use "xcms.xcmsSet Merger" before "xcms.group"
-
-* Zip file: You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).
-
-Single file
------------
-
-This method is recommended because:
-
-* Since files are uploaded indivudially, they are smaller. And so they should be able to be uploaded using the Get Data tools.
+    | Single file (recommended): You can put a single file as input. That way, you will be able to launch several xcmsSet in parallel and use "xcms.xcmsSet Merger" before "xcms.group"
+    | Zip file: You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).
 
-* It allow you to launch your xcmsSet in parallele.
-
-You just have to create a Dataset Collection as explain in this video_
-
-.. _video: http://download.workflow4metabolomics.org/docs/170510_galaxy_xcms_dataset_collection.m4v
-
-
-Zip file
---------
-
-This method isn't recommended because zip file aren't really well integrated
-
-Steps for creating the zip file
+Zip file: Steps for creating the zip file
+-----------------------------------------
 
 **Step1: Creating your directory and hierarchize the subdirectories**
 
 
-    | **VERY IMPORTANT**: If you zip your files under Windows, you must use the 7Zip software (http://www.7-zip.org/), otherwise your zip will not be well unzipped on the platform W4M (zip corrupted bug).
-    | Your zip should contain all your conditions as sub-directories. For example, two conditions (mutant and wild):
-    | - arabidopsis/wild/01.raw
-    | - arabidopsis/mutant/01.raw
+VERY IMPORTANT: If you zip your files under Windows, you must use the 7Zip software (http://www.7-zip.org/), otherwise your zip will not be well unzipped on the platform W4M (zip corrupted bug).
+
+Your zip should contain all your conditions as sub-directories. For example, two conditions (mutant and wild):
+arabidopsis/wild/01.raw
+arabidopsis/mutant/01.raw
 
 **Step2: Creating a zip file**
 
-    | Create your zip file (e.g.: arabidopsis.zip).
+Create your zip file (e.g.: arabidopsis.zip).
 
 **Step 3 : Uploading it to our Galaxy server**
 
-    | If your zip file is less than 2Gb, you get use the Get Data tool to upload it.
-    | Otherwise if your zip file is larger than 2Gb, please refer to the HOWTO on workflow4metabolomics.org (http://application.sb-roscoff.fr/download/w4m/howto/galaxy_upload_up_2Go.pdf).
-    | For more informations, don't hesitate to send us an email at supportATworkflow4metabolomics.org).
-    | Advices for converting your files for the XCMS input
+If your zip file is less than 2Gb, you get use the Get Data tool to upload it.
+
+Otherwise if your zip file is larger than 2Gb, please refer to the HOWTO on workflow4metabolomics.org (http://application.sb-roscoff.fr/download/w4m/howto/galaxy_upload_up_2Go.pdf).
 
-Raw file format
----------------
+For more informations, don't hesitate to send us an email at supportATworkflow4metabolomics.org).
 
-We recommend you to convert your raw files to **mzXML** in centroid mode (smaller files) and the files will be compatible with the xcms centWave method.
+Advices for converting your files for the XCMS input
+----------------------------------------------------
+
+We recommend you to convert your raw files to **mzXML** in centroid mode (smaller files) and the files will be compatible with the xmcs centWave method.
 
 **We recommend you the following parameters:**
 
-    | **Use Filtering**: True
-    | **Use Peak Picking**: True
-    | **Peak Peaking**: -Apply to MS Levels: All Levels (1-) : Centroid Mode
-    | **Use zlib**: 64
-    | **Binary Encoding**: 64
-    | **m/z Encoding**: 64
-    | **Intensity Encoding**: 64
+Use Filtering: **True**
+
+Use Peak Picking: **True**
+
+Peak Peaking -Apply to MS Levels: **All Levels (1-)** : Centroid Mode
+
+Use zlib: **64**
+
+Binary Encoding: **64**
+
+m/z Encoding: **64**
+
+Intensity Encoding: **64**
 
 
 ----------
@@ -451,16 +475,28 @@
 Output files
 ------------
 
+xset.TICs_raw.pdf
+
+    | "Total Ion Chromatograms" graph in pdf format.
+
+xset.BPCs_raw.pdf
+
+    | "Base Peak Chromatograms" graph in pdf format with each class samples opposed.
+
+sampleMetadata.tsv
+
+    | Tabular file that contains for each sample, it's associated class and polarity (positive,negative and mixed).
+    | This file is necessary in the Anova and PCA step of the workflow.
+
 xset.RData: rdata.xcms.raw format
 
     | Rdata file that is necessary in the second step of the workflow "xcms.group".
 
-@HELP_BCP_TIC@
+------
 
-sampleMetadata.tsv [if using zip]
+.. class:: infomark
 
-    | Tabular file that contains for each sample, it's associated class and polarity (positive,negative and mixed).
-    | This file is necessary in the Batch correction and statictics steps of the workflow.
+The output file is an xset.RData file. You can continue your analysis using it in **xcms.group** tool.
 
 ---------------------------------------------------
 
@@ -471,20 +507,49 @@
 Input files
 -----------
 
-    | Dataset Collection -> build using this dataset_
-
-.. _dataset: http://download.workflow4metabolomics.org/datasets/sacurine-neg-subset_mzXML.zip
+    | zip_file -> **sacuri.zip**
 
 Parameters
 ----------
 
-    | **Method**: centWave
-    | **Max tolerated ppm m/z deviation in consecutive scans in ppm**: 25
-    | **Min,Max peak width in seconds**: 10,40
-    | **Advanced option**: show
-    | **Signal/Noise threshold**: 50
-    | **Minimum difference in m/z for peaks with overlapping retention times**: 1
-    | **Prefilter step for the first phase**: 3,100
+    | Method -> **matchedFilter**
+    | step   -> **0.01**
+    | fwhm   -> **4**
+    | Advanced option -> **show**
+    | max: -> **50**
+    | snthresh -> **1**
+    | steps -> **2**
+
+
+Output files
+------------
+
+    | **1) xset.RData: RData file**
+
+    | **2) Example of a sampleMetadata.tsv  :**
+
+
++---------------------------+------------+---------+
+| sampleMetadata            |   class    | polarity|
++===========================+============+=========+
+|HU_neg_017                 |   bio      |negative |
++---------------------------+------------+---------+
+|HU_neg_028                 |   bio      |negative |
++---------------------------+------------+---------+
+|HU_neg_034                 |   bio      |negative |
++---------------------------+------------+---------+
+|Blanc04                    |   blank    |negative |
++---------------------------+------------+---------+
+|Blanc06                    |   blank    |negative |
++---------------------------+------------+---------+
+|Blanc09                    |   blank    |negative |
++---------------------------+------------+---------+
+
+
+
+    | **3) Example of xset.TICs_raw.pdf (Total Ion Chromatograms) :**
+
+.. image:: xcms_tics.png
 
 
 ---------------------------------------------------
@@ -492,9 +557,9 @@
 Changelog/News
 --------------
 
-**Version 2.2.0 - 19/10/2017**
+**Version 2.1.1 - 29/11/2017**
 
-- NEW: The TIC and BPC is new exported as tabular files to be visualized using MultiQC.
+- BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C
 
 **Version 2.1.0 - 22/02/2017**
 
diff -r d71827ecd22c -r e93153c07be0 destinations_input_type.py
--- a/destinations_input_type.py	Thu Oct 26 11:14:49 2017 -0400
+++ b/destinations_input_type.py	Tue Feb 13 04:42:24 2018 -0500
@@ -16,8 +16,11 @@
     inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] )
     inp_data.update( [ ( da.name, da.dataset ) for da in job.input_library_datasets ] )
     input_extension = inp_data[ "input" ].extension
-    log.debug("The input extension is %s" % input_extension)
-    if input_extension in ["mzxml","mzml","mzdata","netcdf"]:
-        return 'thread1-mem_free10'
-    else: # zip file
-        return 'thread4-men_free10'
+    if 'input' in inp_data:
+        input_extension = inp_data[ "input" ].extension
+        log.debug("The input extension is %s" % input_extension)
+        if input_extension in ["mzxml","mzml","mzdata","netcdf"]:
+            return 'thread1-mem_free8'
+    # zip file
+    return 'thread9-mem_free8'
+
diff -r d71827ecd22c -r e93153c07be0 lib.r
--- a/lib.r	Thu Oct 26 11:14:49 2017 -0400
+++ b/lib.r	Tue Feb 13 04:42:24 2018 -0500
@@ -51,42 +51,6 @@
     write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
 }
 
-#@author G. Le Corguille
-exportTicBpcTabular <- function(dataset, filenameBase, ticORbpc, rt='raw') {
-
-        rawORcorrected = ''
-        title = ''
-        if (rt=='corrected') {
-            rawORcorrected = '_corrected'
-            title = ' corrected by retcor'
-        }
-
-        if (ticORbpc == "TIC") {
-            section_name = paste0('TIC',rawORcorrected)
-            title = paste0('Total Ion Current (TIC) chromatogram',title)
-            description = 'Sum of intensity (Y) of all ions detected at each retention time(X)'
-        } else if (ticORbpc == "BPC") {
-            section_name = paste0('BPC',rawORcorrected)
-            title = paste0('Base Peak Chromatogram (BPC)',title)
-            description = 'Sum of intensity (Y) of the most intense peaks at each retention time(X)'
-        }
-
-        filename=paste0(basename(file_path_sans_ext(filenameBase)),"-",ticORbpc,rawORcorrected,"_mqc.out")
-
-        # Headers for MultiQC
-        cat("# file_format: 'tsv'\n", sep="", file = filename)
-        cat("# section_name: '",section_name,"'\n", sep="", file = filename, append = T)
-        cat("# title: '",title,"'\n", sep="", file = filename, append = T)
-        cat("# description: '",description,"'\n", sep="", file = filename, append = T)
-        cat("# plot_type: 'linegraph'\n", sep="", file = filename, append = T)
-        cat("# pconfig:\n", sep="", file = filename, append = T)
-        cat("#     id: '",ticORbpc,rawORcorrected,"_lineplot'\n", sep="", file = filename, append = T)
-        cat("#     ylab: 'Base Peak Intensity'\n", sep="", file = filename, append = T)
-        cat("#     xlab: 'Retention Time'\n", sep="", file = filename, append = T)
-        cat("Intensity\tRT\n", file = filename, append = T)
-        write.table(dataset, filename ,row.names = F, col.names = F, sep = "\t", append = T, quote = F)
-}
-
 #@author Y. Guitton
 getBPC <- function(file,rtcor=NULL, ...) {
     object <- xcmsRaw(file)
@@ -130,9 +94,6 @@
             rtcor <- NULL
 
         TIC[[j]] <- getBPC(files[j],rtcor=rtcor)
-
-        exportTicBpcTabular(TIC[[j]], files[j], "BPC", rt=rt)
-
         # TIC[[j]][,1]<-rtcor
     }
 
@@ -260,8 +221,6 @@
             rtcor <- xcmsSet@rt$corrected[[i]] else
         rtcor <- NULL
         TIC[[i]] <- getTIC(files[i],rtcor=rtcor)
-
-        exportTicBpcTabular(TIC[[i]], files[i], "TIC", rt=rt)
     }
 
     pdf(pdfname,w=16,h=10)
@@ -517,7 +476,7 @@
 
 
 # This function get the raw file path from the arguments
-getRawfilePathFromArguments <- function(singlefile, zipfile, listArguments) {
+getRawfilePathFromArguments <- function(singlefile, zipfile, listArguments) {    
     if (!is.null(listArguments[["zipfile"]]))           zipfile = listArguments[["zipfile"]]
     if (!is.null(listArguments[["zipfilePositive"]]))   zipfile = listArguments[["zipfilePositive"]]
     if (!is.null(listArguments[["zipfileNegative"]]))   zipfile = listArguments[["zipfileNegative"]]
diff -r d71827ecd22c -r e93153c07be0 macros.xml
--- a/macros.xml	Thu Oct 26 11:14:49 2017 -0400
+++ b/macros.xml	Tue Feb 13 04:42:24 2018 -0500
@@ -12,7 +12,6 @@
             <requirement type="package" version="1.46.0">bioconductor-xcms</requirement>
         </requirements>
     </xml>
-
     <xml name="stdio">
         <stdio>
             <exit_code range="1" level="fatal" />
@@ -20,7 +19,7 @@
     </xml>
 
     <token name="@COMMAND_XCMS_SCRIPT@">
-        LANG=C Rscript $__tool_directory__/xcms.r
+        LC_ALL=C Rscript $__tool_directory__/xcms.r
     </token>
 
     <token name="@COMMAND_LOG_EXIT@">
@@ -117,55 +116,14 @@
         </data>
     </xml>
 
-    <xml name="input_tic_bpc_pdf">
-        <param name="tic_bpc_pdf" type="boolean" checked="False" label="Do you want TIC and BCP in PDF Format" help="Whatever, you will be able to use MultiQC tools on the tabular files" />
-    </xml>
-
-    <xml name="test_retcor_param">
-        <param name="methods|method" value="peakgroups"/>
-        <param name="methods|smooth" value="loess"/>
-        <param name="methods|extra" value="1"/>
-        <param name="methods|missing" value="1"/>
-        <param name="methods|options|option" value="show"/>
-        <param name="methods|options|span" value="0.2"/>
-        <param name="methods|options|family" value="gaussian"/>
-        <param name="methods|options|plottype" value="deviation"/>
-    </xml>
-
-    <xml name="test_retcor_output" token_raworcorrected="">
-        <output name="log">
-            <assert_contents>
-                <has_text text="object with 4 samples" />
-                <has_text text="Time range: 2507.7-4481.7 seconds (41.8-74.7 minutes)" />
-                <has_text text="Mass range: 200.1-600 m/z" />
-                <has_text text="Peaks: 9251 (about 2313 per sample)" />
-                <has_text text="Peak Groups: 0" />
-                <has_text text="Sample classes: KO, WT" />
-            </assert_contents>
-        </output>
-        <output_collection name="ticsCorrectedTabCollection" type="list">
-            <element name="ko15" value="ko15-TIC@RAWORCORRECTED@_mqc.out" />
-            <element name="ko16" value="ko16-TIC@RAWORCORRECTED@_mqc.out" />
-            <element name="wt15" value="wt15-TIC@RAWORCORRECTED@_mqc.out" />
-            <element name="wt16" value="wt16-TIC@RAWORCORRECTED@_mqc.out" />
-        </output_collection>
-        <output_collection name="bpcsCorrectedTabCollection" type="list">
-            <element name="ko15" value="ko15-BPC@RAWORCORRECTED@_mqc.out" />
-            <element name="ko16" value="ko16-BPC@RAWORCORRECTED@_mqc.out" />
-            <element name="wt15" value="wt15-BPC@RAWORCORRECTED@_mqc.out" />
-            <element name="wt16" value="wt16-BPC@RAWORCORRECTED@_mqc.out" />
-        </output_collection>
-    </xml>
-
     <token name="@HELP_AUTHORS@">
-
 .. class:: infomark
 
 **Authors**  Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu
 
 .. class:: infomark
 
-**Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station Biologique de Roscoff and Yann Guitton yann.guitton@oniris-nantes.fr - part of Workflow4Metabolomics.org [W4M]
+**Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@oniris-nantes.fr - part of Workflow4Metabolomics.org [W4M]
 
  | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
 
@@ -173,57 +131,6 @@
 
     </token>
 
-    <token name="@HELP_BCP_TIC@">
-
-BPCs and TICs: tabular
-
-    | "Base Peak Chromatograms" and "Total Ion Chromatograms" graphs
-    | Import BPC and TIC from xcmsSet and retcor [at once] within MultiQC_ (in or outside Galaxy) to display and navigate in the graphs.
-    | - In MultiQC: as tool, use the Custom Content
-
-.. _MultiQC: http://multiqc.info/
-
-BPCs and TICs: pdf [if using zip]
-
-    | "Base Peak Chromatograms" and "Total Ion Chromatograms" graphs in pdf format.
-
-    </token>
-
-    <token name="@HELP_GET_PEAK_LIST@">
-
-Get a Peak List
----------------
-
-If 'true', the module generates two additional files corresponding to the peak list:
-- the variable metadata file (corresponding to information about extracted ions such as mass or retention time)
-- the data matrix (corresponding to related intensities)
-
-**decimal places for [mass or retention time] values in identifiers**
-
-    | Ions' identifiers are constructed as MxxxTyyy where 'xxx' is the ion median mass and 'yyy' the ion median retention time.
-    | Two parameters are used to adjust the number of decimal places wanted in identifiers for mass and retention time respectively.
-    | Theses parameters do not affect decimal places in columns other than the identifier one.
-
-**Reported intensity values**
-
-    | This parameter determines which values should be reported as intensities in the dataMatrix table; it correspond to xcms 'intval' parameter:
-    | - into: integrated area of original (raw) peak
-    | - maxo: maximum intensity of original (raw) peak
-    | - intb: baseline corrected integrated peak area (only available if peak detection was done by ‘findPeaks.centWave’)
-
-    </token>
-
-    <token name="@HELP_GET_PEAK_LIST_OUTPUTS@">
-
-xset.variableMetadata.tsv : tabular format [If Get a Peak List == Yes]
-
-    | Table containing information about ions - Can be used in **Normalisation/Generic_filter** and **Statitics** tools.
-
-xset.dataMatrix.tsv : tabular format
-
-    | Table containing ions' intensities - Can be used **Normalisation/Generic_filter** and **Statitics** tools.
-
-    </token>
 
     <xml name="citation">
         <citations>
diff -r d71827ecd22c -r e93153c07be0 test-data/HU_neg_017-BPC_mqc.out
--- a/test-data/HU_neg_017-BPC_mqc.out	Thu Oct 26 11:14:49 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2042 +0,0 @@
-# file_format: 'tsv'
-# section_name: 'BPC'
-# title: 'Base Peak Chromatogram (BPC)'
-# description: 'Sum of intensity (Y) of the most intense peaks at each retention time(X)'
-# plot_type: 'linegraph'
-# pconfig:
-#     id: 'BPC_lineplot'
-#     ylab: 'Base Peak Intensity'
-#     xlab: 'Retention Time'
-Intensity	RT
-0.7297	7404300
-0.8794	5418759
-1.3837	4575903.5
-1.9176	3957671
-2.4696	5267160.5
-2.9744	5155556.5
-3.4938	6381890.5
-3.9999	6118589
-4.5139	5505080
-5.0289	4391217
-5.5646	4989254.5
-6.0832	5969857.5
-6.5894	5898433
-7.1015	4330695.5
-7.6362	5400559.5
-8.1449	5462957
-8.6613	5332687.5
-9.1776	6422903.5
-9.6809	5603778
-10.2005	6161521
-10.7068	5751687
-11.2194	4525409.5
-11.757	6346037.5
-12.2632	5758794
-12.7805	6500522
-13.281	5887984
-13.7899	5703498.5
-14.2969	5103971.5
-14.814	5842016
-15.3243	6282516.5
-15.8325	5519839
-16.3465	5516280.5
-16.8642	4256555
-17.3977	4321544
-17.9404	5829238
-18.4534	6367631.5
-18.9636	6108155
-19.4767	5312623.5
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-27.1922	5773508
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-40.2381	5040457
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-41.2835	4107465.25
-41.8198	4822950
-42.336	5317510
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-44.3992	4773695
-44.9086	3555183.25
-45.4508	5295598
-45.9695	4186214.75
-46.4884	3734517.75
-47.0371	4856365
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-48.5481	3911497
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-50.0636	3269102.75
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-51.5752	1379332.25
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-52.5935	1362738
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-96.31	5937568
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diff -r d71827ecd22c -r e93153c07be0 test-data/HU_neg_017-TIC_mqc.out
--- a/test-data/HU_neg_017-TIC_mqc.out	Thu Oct 26 11:14:49 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2042 +0,0 @@
-# file_format: 'tsv'
-# section_name: 'TIC'
-# title: 'Total Ion Current (TIC) chromatogram'
-# description: 'Sum of intensity (Y) of all ions detected at each retention time(X)'
-# plot_type: 'linegraph'
-# pconfig:
-#     id: 'TIC_lineplot'
-#     ylab: 'Base Peak Intensity'
-#     xlab: 'Retention Time'
-Intensity	RT
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diff -r d71827ecd22c -r e93153c07be0 test-data/MM14-BPC_mqc.out
--- a/test-data/MM14-BPC_mqc.out	Thu Oct 26 11:14:49 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,122 +0,0 @@
-# file_format: 'tsv'
-# section_name: 'BPC'
-# title: 'Base Peak Chromatogram (BPC)'
-# description: 'Sum of intensity (Y) of the most intense peaks at each retention time(X)'
-# plot_type: 'linegraph'
-# pconfig:
-#     id: 'BPC_lineplot'
-#     ylab: 'Base Peak Intensity'
-#     xlab: 'Retention Time'
-Intensity	RT
-270.334	1685
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-304.65	1489
-304.986	1258
-305.323	1146
-305.659	1371
-305.995	1294
-306.332	1200
-306.668	1350
-307.004	1327
-307.34	1973
-307.678	2404
diff -r d71827ecd22c -r e93153c07be0 test-data/MM14-TIC_mqc.out
--- a/test-data/MM14-TIC_mqc.out	Thu Oct 26 11:14:49 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,122 +0,0 @@
-# file_format: 'tsv'
-# section_name: 'TIC'
-# title: 'Total Ion Current (TIC) chromatogram'
-# description: 'Sum of intensity (Y) of all ions detected at each retention time(X)'
-# plot_type: 'linegraph'
-# pconfig:
-#     id: 'TIC_lineplot'
-#     ylab: 'Base Peak Intensity'
-#     xlab: 'Retention Time'
-Intensity	RT
-270.334	64989
-270.671	67476
-271.007	77870
-271.343	105126
-271.68	155634
-272.016	212782
-272.353	268032
-272.689	316565
-273.025	340331
-273.362	338131
-273.698	335301
-274.034	307674
-274.371	271946
-274.707	234750
-275.043	195146
-275.38	161970
-275.716	136385
-276.052	128592
-276.389	123558
-276.725	121014
-277.061	127507
-277.399	126646
-277.735	130228
-278.072	132416
-278.408	132485
-278.744	124922
-279.081	125163
-279.417	124318
-279.753	123363
-280.089	120277
-280.426	118986
-280.762	113485
-281.098	107102
-281.435	101458
-281.771	90191
-282.107	83128
-282.444	77062
-282.78	75613
-283.116	71773
-283.453	67160
-283.789	66865
-284.126	65476
-284.463	65096
-284.799	65391
-285.135	64007
-285.476	67614
-285.812	67987
-286.148	71023
-286.485	74579
-286.821	76881
-287.157	80532
-287.495	84444
-287.832	82377
-288.168	84165
-288.505	85163
-288.841	83033
-289.177	76825
-289.514	75184
-289.85	69372
-290.186	68449
-290.523	67203
-290.859	67735
-291.195	65109
-291.531	62919
-291.868	62332
-292.204	61394
-292.54	63670
-292.877	63974
-293.213	63777
-293.549	66847
-293.886	69879
-294.222	67201
-294.558	68828
-294.895	70897
-295.231	69083
-295.567	68382
-295.903	66991
-296.24	67648
-296.576	65762
-296.912	63895
-297.249	62145
-297.586	62027
-297.923	64304
-298.259	67216
-298.595	73178
-298.932	75116
-299.268	78789
-299.604	87023
-299.941	88688
-300.277	87898
-300.613	88769
-300.95	86435
-301.286	82923
-301.622	75966
-301.958	71102
-302.295	69901
-302.631	67821
-302.968	63912
-303.304	64266
-303.641	65557
-303.977	65430
-304.314	66124
-304.65	65862
-304.986	68685
-305.323	68801
-305.659	67658
-305.995	68467
-306.332	67208
-306.668	67104
-307.004	68460
-307.34	70357
-307.678	75178
diff -r d71827ecd22c -r e93153c07be0 test-data/ko15-BPC_mqc.out
--- a/test-data/ko15-BPC_mqc.out	Thu Oct 26 11:14:49 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1288 +0,0 @@
-# file_format: 'tsv'
-# section_name: 'BPC'
-# title: 'Base Peak Chromatogram (BPC)'
-# description: 'Sum of intensity (Y) of the most intense peaks at each retention time(X)'
-# plot_type: 'linegraph'
-# pconfig:
-#     id: 'BPC_lineplot'
-#     ylab: 'Base Peak Intensity'
-#     xlab: 'Retention Time'
-Intensity	RT
-2501.378	43888
-2502.943	43960
-2504.508	43392
-2506.073	42632
-2507.638	42200
-2509.203	42288
-2510.768	42664
-2512.333	42480
-2513.898	42320
-2515.463	42528
-2517.028	43376
-2518.593	44240
-2520.158	44696
-2521.722	44560
-2523.287	44112
-2524.852	43936
-2526.417	43736
-2527.982	42912
-2529.547	42360
-2531.112	43128
-2532.677	43880
-2534.242	44104
-2535.807	44256
-2537.372	44664
-2538.937	44600
-2540.502	44224
-2542.067	44120
-2543.632	44328
-2545.197	44536
-2546.762	44872
-2548.327	44592
-2549.892	43600
-2551.457	42872
-2553.022	43528
-2554.586	44072
-2556.151	43360
-2557.716	41632
-2559.281	40752
-2560.846	40472
-2562.411	39792
-2563.976	39096
-2565.541	39696
-2567.106	41152
-2568.671	41896
-2570.236	41568
-2571.801	41448
-2573.366	42336
-2574.931	43432
-2576.496	43720
-2578.061	43352
-2579.626	43528
-2581.191	55720
-2582.756	74184
-2584.321	91992
-2585.886	105888
-2587.451	114512
-2589.015	120272
-2590.58	123640
-2592.145	122024
-2593.71	115504
-2595.275	106736
-2596.84	97864
-2598.405	87640
-2599.97	77312
-2601.535	67952
-2603.1	59464
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diff -r d71827ecd22c -r e93153c07be0 test-data/ko15-TIC_mqc.out
--- a/test-data/ko15-TIC_mqc.out	Thu Oct 26 11:14:49 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1288 +0,0 @@
-# file_format: 'tsv'
-# section_name: 'TIC'
-# title: 'Total Ion Current (TIC) chromatogram'
-# description: 'Sum of intensity (Y) of all ions detected at each retention time(X)'
-# plot_type: 'linegraph'
-# pconfig:
-#     id: 'TIC_lineplot'
-#     ylab: 'Base Peak Intensity'
-#     xlab: 'Retention Time'
-Intensity	RT
-2501.378	621512
-2502.943	628280
-2504.508	631958
-2506.073	628012
-2507.638	631396
-2509.203	641593
-2510.768	647566
-2512.333	647653
-2513.898	655215
-2515.463	650586
-2517.028	652966
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-2520.158	649768
-2521.722	655132
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-2531.112	638449
-2532.677	638841
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-2538.937	635962
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-2556.151	611652
-2557.716	613707
-2559.281	609318
-2560.846	601736
-2562.411	597967
-2563.976	594325
-2565.541	592978
-2567.106	591391
-2568.671	593893
-2570.236	598743
-2571.801	604232
-2573.366	612288
-2574.931	616854
-2576.496	632732
-2578.061	666622
-2579.626	690549
-2581.191	733387
-2582.756	774636
-2584.321	813394
-2585.886	848164
-2587.451	875137
-2589.015	892787
-2590.58	901174
-2592.145	896042
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-2603.1	792693
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-2690.737	1968639
-2692.302	1841448
-2693.867	1709988
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-4499.824	7237
diff -r d71827ecd22c -r e93153c07be0 test-data/ko16-BPC_mqc.out
--- a/test-data/ko16-BPC_mqc.out	Thu Oct 26 11:14:49 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1288 +0,0 @@
-# file_format: 'tsv'
-# section_name: 'BPC'
-# title: 'Base Peak Chromatogram (BPC)'
-# description: 'Sum of intensity (Y) of the most intense peaks at each retention time(X)'
-# plot_type: 'linegraph'
-# pconfig:
-#     id: 'BPC_lineplot'
-#     ylab: 'Base Peak Intensity'
-#     xlab: 'Retention Time'
-Intensity	RT
-2501.378	8078
-2502.943	8202
-2504.508	8123
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diff -r d71827ecd22c -r e93153c07be0 test-data/ko16-TIC_mqc.out
--- a/test-data/ko16-TIC_mqc.out	Thu Oct 26 11:14:49 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1288 +0,0 @@
-# file_format: 'tsv'
-# section_name: 'TIC'
-# title: 'Total Ion Current (TIC) chromatogram'
-# description: 'Sum of intensity (Y) of all ions detected at each retention time(X)'
-# plot_type: 'linegraph'
-# pconfig:
-#     id: 'TIC_lineplot'
-#     ylab: 'Base Peak Intensity'
-#     xlab: 'Retention Time'
-Intensity	RT
-2501.378	440346
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-4499.823	6682
diff -r d71827ecd22c -r e93153c07be0 test-data/wt15-BPC_mqc.out
--- a/test-data/wt15-BPC_mqc.out	Thu Oct 26 11:14:49 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1288 +0,0 @@
-# file_format: 'tsv'
-# section_name: 'BPC'
-# title: 'Base Peak Chromatogram (BPC)'
-# description: 'Sum of intensity (Y) of the most intense peaks at each retention time(X)'
-# plot_type: 'linegraph'
-# pconfig:
-#     id: 'BPC_lineplot'
-#     ylab: 'Base Peak Intensity'
-#     xlab: 'Retention Time'
-Intensity	RT
-2501.378	44464
-2502.943	44632
-2504.508	45232
-2506.073	46200
-2507.638	46592
-2509.203	46376
-2510.768	45760
-2512.333	45632
-2513.898	45152
-2515.463	44280
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-2523.287	44528
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-2527.982	42520
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-2531.112	41312
-2532.677	40832
-2534.242	40624
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-2540.502	40488
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-2553.021	41936
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-2559.281	41400
-2560.846	40752
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-2565.541	41488
-2567.106	42928
-2568.671	44352
-2570.236	44968
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-2576.496	42184
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-2579.626	52312
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-2584.321	102376
-2585.885	115304
-2587.45	125384
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-2593.71	120840
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-2631.269	39456
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diff -r d71827ecd22c -r e93153c07be0 test-data/wt15-TIC_mqc.out
--- a/test-data/wt15-TIC_mqc.out	Thu Oct 26 11:14:49 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1288 +0,0 @@
-# file_format: 'tsv'
-# section_name: 'TIC'
-# title: 'Total Ion Current (TIC) chromatogram'
-# description: 'Sum of intensity (Y) of all ions detected at each retention time(X)'
-# plot_type: 'linegraph'
-# pconfig:
-#     id: 'TIC_lineplot'
-#     ylab: 'Base Peak Intensity'
-#     xlab: 'Retention Time'
-Intensity	RT
-2501.378	679705
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-4430.966	4891
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-4491.999	12909
-4493.564	12855
-4495.129	12894
-4496.694	13644
-4498.259	14440
-4499.824	15502
diff -r d71827ecd22c -r e93153c07be0 test-data/wt16-BPC_mqc.out
--- a/test-data/wt16-BPC_mqc.out	Thu Oct 26 11:14:49 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1288 +0,0 @@
-# file_format: 'tsv'
-# section_name: 'BPC'
-# title: 'Base Peak Chromatogram (BPC)'
-# description: 'Sum of intensity (Y) of the most intense peaks at each retention time(X)'
-# plot_type: 'linegraph'
-# pconfig:
-#     id: 'BPC_lineplot'
-#     ylab: 'Base Peak Intensity'
-#     xlab: 'Retention Time'
-Intensity	RT
-2501.378	7215
-2502.943	6822
-2504.508	6494
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-2507.637	6170
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diff -r d71827ecd22c -r e93153c07be0 test-data/wt16-TIC_mqc.out
--- a/test-data/wt16-TIC_mqc.out	Thu Oct 26 11:14:49 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1288 +0,0 @@
-# file_format: 'tsv'
-# section_name: 'TIC'
-# title: 'Total Ion Current (TIC) chromatogram'
-# description: 'Sum of intensity (Y) of all ions detected at each retention time(X)'
-# plot_type: 'linegraph'
-# pconfig:
-#     id: 'TIC_lineplot'
-#     ylab: 'Base Peak Intensity'
-#     xlab: 'Retention Time'
-Intensity	RT
-2501.378	364122
-2502.943	368599
-2504.508	366635
-2506.073	370143
-2507.637	367549
-2509.202	369586
-2510.767	372421
-2512.332	378793
-2513.897	385235
-2515.462	388989
-2517.027	390943
-2518.592	392489
-2520.157	391143
-2521.722	397327
-2523.287	401857
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-2529.547	394008
-2531.112	387712
-2532.677	381245
-2534.242	376619
-2535.807	380812
-2537.372	381306
-2538.937	382864
-2540.502	381995
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-2549.891	387231
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-2553.021	387460
-2554.586	385045
-2556.151	380493
-2557.716	377481
-2559.281	372247
-2560.846	370866
-2562.411	369468
-2563.976	371630
-2565.541	375503
-2567.106	370641
-2568.671	363606
-2570.236	357730
-2571.801	361033
-2573.366	364745
-2574.93	366085
-2576.495	371134
-2578.06	371185
-2579.625	375571
-2581.19	385929
-2582.755	399199
-2584.32	424021
-2585.885	452459
-2587.45	489418
-2589.015	527449
-2590.58	564825
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-2623.444	452525
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diff -r d71827ecd22c -r e93153c07be0 xcms.r
--- a/xcms.r	Thu Oct 26 11:14:49 2017 -0400
+++ b/xcms.r	Tue Feb 13 04:42:24 2018 -0500
@@ -13,7 +13,7 @@
 # ----- PACKAGE -----
 cat("\tPACKAGE INFO\n")
 #pkgs=c("xcms","batch")
-pkgs=c("tools","parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","snow","batch")
+pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","snow","batch")
 for(pkg in pkgs) {
     suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
     cat(pkg,"\t",as.character(packageVersion(pkg)),"\n",sep="")
@@ -65,6 +65,10 @@
 }
 
 #saving the specific parameters
+rplotspdf = "Rplots.pdf"
+if (!is.null(listArguments[["rplotspdf"]])){
+    rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL
+}
 sampleMetadataOutput = "sampleMetadata.tsv"
 if (!is.null(listArguments[["sampleMetadataOutput"]])){
     sampleMetadataOutput = listArguments[["sampleMetadataOutput"]]; listArguments[["sampleMetadataOutput"]]=NULL
@@ -90,6 +94,11 @@
     intval = listArguments[["intval"]]; listArguments[["intval"]]=NULL
 }
 
+if (thefunction %in% c("xcmsSet","retcor")) {
+    ticspdf = listArguments[["ticspdf"]]; listArguments[["ticspdf"]]=NULL
+    bicspdf = listArguments[["bicspdf"]]; listArguments[["bicspdf"]]=NULL
+}
+
 
 if (thefunction %in% c("xcmsSet","retcor","fillPeaks"))  {
     if (!exists("singlefile")) singlefile=NULL
@@ -138,7 +147,7 @@
 
 #change the default display settings
 #dev.new(file="Rplots.pdf", width=16, height=12)
-pdf(file="Rplots.pdf", width=16, height=12)
+pdf(file=rplotspdf, width=16, height=12)
 if (thefunction == "group") {
     par(mfrow=c(2,2))
 }
@@ -188,12 +197,12 @@
 if (thefunction == "xcmsSet") {
     cat("\t\tGET TIC GRAPH\n")
     sampleNamesList = getSampleMetadata(xcmsSet=xset, sampleMetadataOutput=sampleMetadataOutput)
-    getTICs(xcmsSet=xset, rt="raw")
-    getBPCs(xcmsSet=xset, rt="raw")
+    getTICs(xcmsSet=xset, pdfname=ticspdf,rt="raw")
+    getBPCs(xcmsSet=xset,rt="raw",pdfname=bicspdf)
 } else if (thefunction == "retcor") {
     cat("\t\tGET TIC GRAPH\n")
-    getTICs(xcmsSet=xset, rt="corrected")
-    getBPCs(xcmsSet=xset, rt="corrected")
+    getTICs(xcmsSet=xset, pdfname=ticspdf,rt="corrected")
+    getBPCs(xcmsSet=xset,rt="corrected",pdfname=bicspdf)
 }
 
 if ((thefunction == "group" || thefunction == "fillPeaks") && exists("intval")) {