Mercurial > repos > lecorguille > xcms_xcmsset

--- a/README.rst	Mon Apr 03 07:50:18 2017 -0400
+++ b/README.rst	Tue Oct 24 11:46:21 2017 -0400
@@ -13,15 +13,19 @@

 **How**

- - The file `destinations_input_type.py` (shiped with this tool) must be place in `lib/galaxy/jobs/rules/`
- - The `job_conf.xml` must be inspired by the `job_conf.xml.sample` shiped with this tool
- - The final destination names must match between the `job_conf.xml` and the `destinations_input_type.py`
- - Restart Galaxy
+1. The file [`destinations_input_type.py`](https://raw.githubusercontent.com/workflow4metabolomics/xcms/master/galaxy/xcms_xcmsset/destinations_input_type.py) (shiped with this tool) must be place in `lib/galaxy/jobs/rules/`
+2. The `job_conf.xml` must be inspired by the [`job_conf.xml.sample`](https://github.com/workflow4metabolomics/xcms/blob/master/galaxy/xcms_xcmsset/job_conf.xml.sample) shiped with this tool
+3. The final destination names must match between the `job_conf.xml` and the `destinations_input_type.py`
+4. Restart Galaxy


 Changelog/News
 --------------

+**Version 2.2.0 - 19/10/2017**
+
+- NEW: The TIC and BPC is new exported as tabular files to be visualized using MultiQC.
+
 **Version 2.1.0 - 22/02/2017**

 - NEW: The W4M tools will be able now to take as input a single file. It will allow to submit in parallel several files and merge them afterward using "xcms.xcmsSet Merger" before "xcms.group".
--- a/abims_xcms_xcmsSet.xml	Mon Apr 03 07:50:18 2017 -0400
+++ b/abims_xcms_xcmsSet.xml	Tue Oct 24 11:46:21 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.1.0">
+<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.2.0">
     <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>
@@ -21,9 +21,6 @@

         xsetRdataOutput '$xsetRData'
         sampleMetadataOutput '$sampleMetadata'
-        ticspdf '$ticsRawPdf'
-        bicspdf '$bpcsRawPdf'
-

         #if $options_scanrange.option == "show":
             scanrange "c($options_scanrange.scanrange)"
@@ -59,7 +56,13 @@
             scales "c($methods.scales)"
             SNR.method "$methods.SNR_method"
         #end if
-        @COMMAND_LOG_EXIT@
+
+        #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>

     <inputs>
@@ -155,39 +158,47 @@
                 <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="${input.name.rsplit('.',1)[0]}.sampleMetadata.tsv">
             <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter>
         </data>
-        <data name="ticsRawPdf"   format="pdf" label="${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" />
+        <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" visible="true" />
+        </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" visible="true" />
+        </collection>
     </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" />
@@ -219,56 +230,21 @@
                     <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" />
@@ -301,6 +277,8 @@
                     <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" />
@@ -317,6 +295,8 @@
                     <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>

@@ -328,7 +308,6 @@
 Xcms.xcmsSet
 ============

------------
 Description
 -----------

@@ -338,18 +317,16 @@
 .. _here: http://web11.sb-roscoff.fr/download/w4m/howto/w4m_HowToPerformXcmsPreprocessing_v02.pdf


------------------
 Workflow position
 -----------------

 **Upstream tools**

-========================= ================= ======= =========
-Name                      output file       format  parameter
-========================= ================= ======= =========
-NA                        NA                zip     NA
-========================= ================= ======= =========
-
++------------------------+--------------------+-----------------------------+-----------+
+| Name                   | output file        | format                      | parameter |
++------------------------+--------------------+-----------------------------+-----------+
+| Upload File            | Dataset Collection | mzXML, mzML, mzData, netCDF | NA        |
++------------------------+--------------------+-----------------------------+-----------+

 **Downstream tools**

@@ -358,90 +335,89 @@
 +===========================+====================+=================+
 |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 : num + label   |   Format                         |
+| Parameter                 |   Format                         |
 +===========================+==================================+
+| OR : Single file          |   mzXML, mzML, mzData, netCDF    |
++---------------------------+----------------------------------+
 | OR : Zip file             |   zip                            |
 +---------------------------+----------------------------------+
-| OR : Single file          |   mzXML, mzML, mzData, netCDF    |
-+---------------------------+----------------------------------+
-
-**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 (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.

-Zip file: Steps for creating the zip file
------------------------------------------
+* 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

 **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).
+    | 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

-For more informations, don't hesitate to send us an email at supportATworkflow4metabolomics.org).
+Raw file format
+---------------

-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 to convert your raw files to **mzXML** in centroid mode (smaller files) and the files will be compatible with the xcms 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


 ----------
@@ -475,28 +451,16 @@
 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@

-.. class:: infomark
+sampleMetadata.tsv [if using zip]

-The output file is an xset.RData file. You can continue your analysis using it in **xcms.group** tool.
+    | 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.

 ---------------------------------------------------

@@ -507,49 +471,20 @@
 Input files
 -----------

-    | zip_file -> **sacuri.zip**
+    | Dataset Collection -> build using this dataset_
+
+.. _dataset: http://download.workflow4metabolomics.org/datasets/sacurine-neg-subset_mzXML.zip

 Parameters
 ----------

-    | 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
+    | **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


 ---------------------------------------------------
@@ -557,6 +492,10 @@
 Changelog/News
 --------------

+**Version 2.2.0 - 19/10/2017**
+
+- NEW: The TIC and BPC is new exported as tabular files to be visualized using MultiQC.
+
 **Version 2.1.0 - 22/02/2017**

 - NEW: The W4M tools will be able now to take as input a single file. It will allow to submit in parallel several files and merge them afterward using "xcms.xcmsSet Merger" before "xcms.group".
@@ -593,7 +532,7 @@
 - TEST: refactoring to feed the new report tool


-**Version 2.0.2 - 18/01/2016
+**Version 2.0.2 - 18/01/2016**

 - BUGFIX: Some zip files were tag as "corrupt" by R. We have changed the extraction mode to deal with thoses cases.
--- a/destinations_input_type.py	Mon Apr 03 07:50:18 2017 -0400
+++ b/destinations_input_type.py	Tue Oct 24 11:46:21 2017 -0400
@@ -18,6 +18,6 @@
     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-men_free10'
+        return 'thread1-mem_free10'
     else: # zip file
         return 'thread4-men_free10'
--- a/job_conf.xml.sample	Mon Apr 03 07:50:18 2017 -0400
+++ b/job_conf.xml.sample	Tue Oct 24 11:46:21 2017 -0400
@@ -2,7 +2,6 @@
 <!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). -->
 <job_conf>
     <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
         <plugin id="sge" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" type="runner"/>
         <plugin id="dynamic" type="runner" >
             <param id="rules_module">galaxy.jobs.rules</param>
@@ -12,11 +11,10 @@
         <handler id="main"/>
     </handlers>
     <destinations default="sge_default">
-        <destination id="local" runner="local"/>
         <destination id="sge_default" runner="sge">
              <param id="nativeSpecification">-V -w n -q galaxy.q</param>
         </destination>
-
+
         <destination id="thread1-men_free10" runner="sge">
              <param id="nativeSpecification">-V -w n -q galaxy.q -pe thread 1 -R y -l mem_free=10G </param>
         </destination>
@@ -31,6 +29,5 @@
     </destinations>
     <tools>
         <tool destination="python_destination_input_type" id="abims_xcms_xcmsSet" />
-        <tool destination="local" id="upload1"/>
     </tools>
 </job_conf>
--- a/lib.r	Mon Apr 03 07:50:18 2017 -0400
+++ b/lib.r	Tue Oct 24 11:46:21 2017 -0400
@@ -51,6 +51,42 @@
     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)
@@ -94,6 +130,9 @@
             rtcor <- NULL

         TIC[[j]] <- getBPC(files[j],rtcor=rtcor)
+
+        exportTicBpcTabular(TIC[[j]], files[j], "BPC", rt=rt)
+
         # TIC[[j]][,1]<-rtcor
     }

@@ -221,6 +260,8 @@
             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)
@@ -476,7 +517,7 @@


 # 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"]]
--- a/macros.xml	Mon Apr 03 07:50:18 2017 -0400
+++ b/macros.xml	Tue Oct 24 11:46:21 2017 -0400
@@ -12,6 +12,7 @@
             <requirement type="package" version="1.46.0">bioconductor-xcms</requirement>
         </requirements>
     </xml>
+
     <xml name="stdio">
         <stdio>
             <exit_code range="1" level="fatal" />
@@ -116,14 +117,55 @@
         </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.

@@ -131,6 +173,57 @@

     </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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/HU_neg_017-BPC_mqc.out	Tue Oct 24 11:46:21 2017 -0400
@@ -0,0 +1,2042 @@
+# 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
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/HU_neg_017-TIC_mqc.out	Tue Oct 24 11:46:21 2017 -0400
@@ -0,0 +1,2042 @@
+# 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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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/MM14-BPC_mqc.out	Tue Oct 24 11:46:21 2017 -0400
@@ -0,0 +1,122 @@
+# 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
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/MM14-TIC_mqc.out	Tue Oct 24 11:46:21 2017 -0400
@@ -0,0 +1,122 @@
+# 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
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ko15-BPC_mqc.out	Tue Oct 24 11:46:21 2017 -0400
@@ -0,0 +1,1288 @@
+# 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
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ko15-TIC_mqc.out	Tue Oct 24 11:46:21 2017 -0400
@@ -0,0 +1,1288 @@
+# 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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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ko16-BPC_mqc.out	Tue Oct 24 11:46:21 2017 -0400
@@ -0,0 +1,1288 @@
+# 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
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ko16-TIC_mqc.out	Tue Oct 24 11:46:21 2017 -0400
@@ -0,0 +1,1288 @@
+# 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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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/wt15-BPC_mqc.out	Tue Oct 24 11:46:21 2017 -0400
@@ -0,0 +1,1288 @@
+# 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
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/wt15-TIC_mqc.out	Tue Oct 24 11:46:21 2017 -0400
@@ -0,0 +1,1288 @@
+# 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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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/wt16-BPC_mqc.out	Tue Oct 24 11:46:21 2017 -0400
@@ -0,0 +1,1288 @@
+# 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
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/wt16-TIC_mqc.out	Tue Oct 24 11:46:21 2017 -0400
@@ -0,0 +1,1288 @@
+# 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
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--- a/xcms.r	Mon Apr 03 07:50:18 2017 -0400
+++ b/xcms.r	Tue Oct 24 11:46:21 2017 -0400
@@ -13,7 +13,7 @@
 # ----- PACKAGE -----
 cat("\tPACKAGE INFO\n")
 #pkgs=c("xcms","batch")
-pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","snow","batch")
+pkgs=c("tools","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="")
@@ -65,10 +65,6 @@
 }

 #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
@@ -94,11 +90,6 @@
     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
@@ -147,7 +138,7 @@

 #change the default display settings
 #dev.new(file="Rplots.pdf", width=16, height=12)
-pdf(file=rplotspdf, width=16, height=12)
+pdf(file="Rplots.pdf", width=16, height=12)
 if (thefunction == "group") {
     par(mfrow=c(2,2))
 }
@@ -197,12 +188,12 @@
 if (thefunction == "xcmsSet") {
     cat("\t\tGET TIC GRAPH\n")
     sampleNamesList = getSampleMetadata(xcmsSet=xset, sampleMetadataOutput=sampleMetadataOutput)
-    getTICs(xcmsSet=xset, pdfname=ticspdf,rt="raw")
-    getBPCs(xcmsSet=xset,rt="raw",pdfname=bicspdf)
+    getTICs(xcmsSet=xset, rt="raw")
+    getBPCs(xcmsSet=xset, rt="raw")
 } else if (thefunction == "retcor") {
     cat("\t\tGET TIC GRAPH\n")
-    getTICs(xcmsSet=xset, pdfname=ticspdf,rt="corrected")
-    getBPCs(xcmsSet=xset,rt="corrected",pdfname=bicspdf)
+    getTICs(xcmsSet=xset, rt="corrected")
+    getBPCs(xcmsSet=xset, rt="corrected")
 }

 if ((thefunction == "group" || thefunction == "fillPeaks") && exists("intval")) {