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+++ b/profia_config.xml	Sun Mar 26 17:37:12 2017 -0400
@@ -0,0 +1,283 @@
+<tool id="profia" name="proFIA" version="3.0.0">
+  <description>Preprocessing of FIA-HRMS data</description>
+  
+  <requirements>
+    <requirement type="package">r-batch</requirement>
+    <requirement type="package">r-FNN</requirement>
+    <requirement type="package">r-maxLik</requirement>
+    <requirement type="package">r-minpack.lm</requirement>
+    <requirement type="package">r-pracma</requirement>
+    <requirement type="package">bioconductor-proFIA</requirement>
+  </requirements>
+  
+  <stdio>
+    <exit_code range="1:" level="fatal" />
+  </stdio>
+  
+  <command><![CDATA[
+  Rscript $__tool_directory__/profia_wrapper.R
+
+  #if $inputs.input == "lib":
+  library $__app__.config.user_library_import_dir/$__user_email__/$inputs.library
+  #elif $inputs.input == "zip_file":
+  zipfile $inputs.zip_file
+  #end if
+  
+  ppmN "$ppmN"
+  ppmGroupN "$ppmGroupN"
+  fracGroupN "$fracGroupN"
+  kI "$kI"
+
+  dataMatrix_out "$dataMatrix_out"
+  sampleMetadata_out "$sampleMetadata_out"
+  variableMetadata_out "$variableMetadata_out"
+  figure "$figure"
+  information "$information"
+  ]]></command>
+  
+  <inputs>
+    <conditional name="inputs">
+      <param name="input" type="select" label="Choose your input method" >
+        <option value="zip_file" selected="true">Zip file from your history containing your raw files</option>
+        <option value="lib" >Library directory name</option>
+      </param>
+      <when value="zip_file">
+        <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" />
+      </when>
+      <when value="lib">
+        <param name="library" type="text" size="40" label="Library directory name" help="The name of your directory containing all your data" >
+          <validator type="empty_field"/>
+        </param>
+      </when>     
+    </conditional>
+    
+    <param name="ppmN" label="Maximum deviation between centroids during band detection (in ppm)" type="text" value = "5" help="[ppm]" />	  
+    <param name="ppmGroupN" label="Accuracy of the mass spectrometer to be used during feature alignment (in ppm)" type="text" value = "5" help="[ppmGroup] Should be inferior or equal to the deviation parameter above." />
+    <param name="fracGroupN" label=" Minimum fraction of samples in which a peak should be detected in at least one class to be kept during feature alignment" type="text" value = "0.5" help="[fracGroup]" />
+    <param name="kI" label="Number of neighbour features to be used for imputation (select 0 to skip the imputation step)" type="text" value = "5" help="[k]" />
+  </inputs>
+  
+  <outputs>
+    <data name="dataMatrix_out" label="${tool.name}_dataMatrix.tsv" format="tabular" ></data>
+    <data name="sampleMetadata_out" label="${tool.name}_sampleMetadata.tsv" format="tabular" ></data>
+    <data name="variableMetadata_out" label="${tool.name}_variableMetadata.tsv" format="tabular" ></data>
+    <data name="figure" label="${tool.name}_figure.pdf" format="pdf"/>
+    <data name="information" label="${tool.name}_information.txt" format="txt"/>
+  </outputs>
+  
+  <tests>
+    <test>
+      <param name="inputs|input" value="zip_file" />
+      <param name="inputs|zip_file" value="input-plasFIA.zip" ftype="zip" />
+      <param name="ppmN" value="2"/>
+      <param name="ppmGroupN" value="1"/>
+      <param name="fracGroupN" value="0.1"/>
+      <param name="kI" value="2"/>
+      <output name="dataMatrix_out" file="output-dataMatrix.tsv"/>
+    </test>
+  </tests>
+  
+  <help>	
+
+.. class:: infomark
+
+**Author**	Alexis Delabriere and Etienne Thevenot (CEA, LIST, MetaboHUB Paris, etienne.thevenot@cea.fr)
+
+---------------------------------------------------
+
+.. class:: infomark
+
+**Please cite**
+
+Delabriere A., Hohenester U., Junot C. and Thevenot E.A. *proFIA*: A data preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry. *submitted*.
+
+---------------------------------------------------
+
+.. class:: infomark
+
+**R package**
+
+The **proFIA** package is available from the bioconductor repository `http://bioconductor.org/packages/proFIA &lt;http://bioconductor.org/packages/proFIA&gt;`_
+
+---------------------------------------------------
+
+.. class:: infomark
+
+**Tool updates**
+
+See the **NEWS** section at the bottom of this page
+  
+---------------------------------------------------
+
+==========================================================
+*proFIA*: Preprocessing workflow for FIA-HRMS data
+==========================================================
+
+-----------
+Description
+-----------
+
+**Flow Injection Analysis coupled to High-Resolution Mass Spectrometry (FIA-HRMS)** is a promising approach for **high-throughput metabolomics** (Madalinski *et al.*, 2008; Fuhrer *et al.*, 2011; Draper *et al.*, 2013). FIA- HRMS data, however, cannot be preprocessed with current software tools which rely on liquid chromatography separation, or handle low resolution data only.
+
+The **proFIA module is a workflow** allowing to preprocess FIA-HRMS raw data in **centroid** mode and open format (netCDF, mzData, mzXML, and mzML), and generates the table of peak intensities (**peak table**). The workflow consists in **peak detection and quantification** within individual sample files, followed by **alignment** between files in the m/z dimension, and **imputation** of the missing values in the final peak table (Delabriere *et al.*, submitted). For each ion, the graph representing the intensity as a function of time is called a **flowgram**. A flowgram can be modeled as I = kP + ME(P) + B + e, where k is the response factor (corresponding to the ionization properties of the analyte), P is the **sample peak** (normalized profile which is common for all analytes from a sample and depends on the flow injection conditions only), ME is the **matrix effect**, B is the **solvent baseline**, and e is the heteroscedastic noise.
+
+The generated peak table is available in the '3 table' W4M tabular format (**dataMatrix**, **sampleMetadata**, and **variableMetadata**) for downstream statistical analysis and annotation with W4M modules.
+
+A figure provides **diagnostics** and visualization of the preprocessed data set.
+
+---------------------------------------------------
+
+.. class:: infomark
+
+**References**
+
+| Delabriere A., Hohenester U., Junot C. and Thevenot E.A. proFIA: A data preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry. *submitted*.
+| Draper J., Lloyd A., Goodacre R. and Beckmann M. (2013). Flow infusion electrospray ionisation mass spectrometry for high throughput, non-targeted metabolite fingerprinting: a review. *Metabolomics* 9, 4-29.
+| Fuhrer T., Dominik H., Boris B. and Zamboni N. (2011). High-throughput, accurate mass metabolome profiling of cellular extracts by flow injection-time-of-flight mass spectrometry. *Analytical Chemistry* 83, 7074-7080.
+| Madalinski G., Godat E., Alves S., Lesage D., Genin E., Levi P., Labarre J., Tabet J., Ezan E. and Junot, C. (2008). Direct introduction of biological samples into a LTQ-orbitrap hybrid mass spectrometer as a tool for fast metabolome analysis. *Analytical Chemistry* 80, 3291-3303.
+
+---------------------------------------------------
+
+-----------------
+Workflow position
+-----------------
+
+.. image:: profia_workflowPositionImage.png
+        :width: 600
+
+-----------
+Input files
+-----------
+
++---------------------------+------------+
+| Parameter : num + label   |   Format   |
++===========================+============+
+| 1 : Choose your inputs    |   zip      |
++---------------------------+------------+
+
+
+You have two methods for your inputs:
+    | Zip file (recommended): You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).
+    | library folder: You must specify the name of your "library" (folder) created within your space project (for example: /projet/externe/institut/login/galaxylibrary/yourlibrary). Your library must contain all your conditions as sub-directories.
+
+**Steps for creating the zip file**
+
+**Step1: Creating your directory and hierarchize the subdirectories**
+
+.. class:: warningmark
+
+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).
+
+**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**
+
+.. class:: warningmark
+
+VERY IMPORTANT: your data must be in **centroid** mode. In addition, we recommend you to convert your raw files to mzXML.
+
+We recommend 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**
+
+----------
+Parameters
+----------
+   
+Maximum deviation between centroids during band detection; in ppm (default = 5)
+	| m/z tolerance of centroids corresponding to the same ion from one scan to the other.
+	| 
+
+Accuracy of the mass spectrometer to be used during feature alignment; in ppm (default = 5)
+	| Should be inferior or equal to the deviation parameter above.
+	| 
+    
+Minimum fraction of samples in which a peak should be detected in at least one class to be kept during feature alignment (default = 0.5)
+	| Identical to the corresponding parameter in XCMS. 
+	|     
+
+Number of neighbour features to be used for imputation (default = 5)
+	| Select 0 to skip the imputation step. 
+	|     	
+
+
+------------
+Output files
+------------
+
+dataMatrix.tabular
+	| **dataMatrix** tabular separated file with the variables as rows and samples as columns. Missing values are indicated as 'NA' (i.e. when the signal was not significantly different from noise).
+	|
+	
+sampleMetadata.tabular
+	| **sampleMetadata** tabular separated file containing the sample metadata as columns.
+	| 
+	
+variableMetadata.tabular
+	| **variableMetadata** tabular separated file containing the variable metadata as columns. The **timeShifted** flag is set to 1 when the flowgram is time shifted compared to the sample peak (probably due to liquid retention in the FI tube). The **corSampPeakMean** metric is the correlation between the feature flowgram and the sample peak (values are in [-1, 1]). A value below 0.2 suggests that the feature signal is affected by a strong matrix effect. The **meanSolvent** is the mean baseline signal in the feature flowgrams. The **signalOverSolventPvalueMean** is the mean p-value of the tests discriminating between signal and baseline solvent.
+	| 
+
+figure.pdf
+	| Visualization and diagnostics about the preprocessed data set; **Feature quality**: Number of detected features per sample for each of the three categories: 'Well-behaved' features have a peak shape close to the sample peak (optimal FIA acquisition is achieved when the majority of the features fall into this category); 'Shifted' indicates a time shift compared to the sample peak, and probably results from retention in the FI tube; 'Significant Matrix Effect' corresponds to a correlation between the feature and the samples peaks of less than 0.2, which is usually caused by a strong matrix effect; **Sample peaks**: Visualization of the peak model for each sample; should have close shapes in case of similar FIA conditions; **m/z density**: may allow to detect a missing m/z value, and in turn, suggest that the *ppm* parameter should be modified; **PCA score plot** of the log10 intensities to detect sample outliers.
+	| 
+			
+information.txt
+	| Text file with all messages and warnings generated during the computation.
+	|
+
+---------------------------------------------------
+
+---------------
+Working example
+---------------
+
+Figure output
+=============
+
+.. image:: profia_workingExampleImage.png
+        :width: 600
+        
+---------------------------------------------------
+
+----
+NEWS
+----
+
+CHANGES IN VERSION 3.0.0
+========================
+
+NEW FEATURE
+
+Creation of the tool
+
+</help>
+
+<citations>
+  <citation type="bibtex">@Article{DelabriereSubmitted,
+  Title                    = {proFIA: A data preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry},
+  Author                   = {Delabriere, Alexis and Hohenester, Ulli and Junot, Christophe and Thevenot, Etienne A},
+  Journal                  = {submitted},
+  Year                     = {submitted},
+  Pages                    = {--},
+  Volume                   = {},
+  Doi                      = {}
+  }</citation>
+  <citation type="doi">10.1093/bioinformatics/btu813</citation>
+</citations>
+
+</tool>