--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NmrNormalization_xml.xml	Tue Oct 02 12:14:47 2018 -0400
@@ -0,0 +1,262 @@
+<tool id="normalization" name="Normalization" version="1.0.6">
+
+    <description> Normalization of (preprocessed) spectra </description>
+
+    <requirements>
+          <requirement type="package" version="1.1_4">r-batch</requirement>
+    </requirements>
+
+      <stdio>
+        <exit_code range="1:" level="fatal" />
+    </stdio>
+
+    <command><![CDATA[
+        Rscript $__tool_directory__/NmrNormalization_wrapper.R
+
+            ## Data matrix of bucketed and integrated spectra
+            dataMatrix $dataMatrix
+
+            ## Normalization method
+            scalingMethod $scalingMethod.method
+            #if $scalingMethod.method == "PQN":
+                ## Sample metadata matrix
+                sampleMetadata $scalingMethod.sampleMetadata
+
+                ## Biological factor of interest (column number in samplemetadata)
+                factor $scalingMethod.factor
+
+                ## Reference class
+                controlGroup $scalingMethod.controlGroup
+            #end if
+            #if $scalingMethod.method == "QuantitativeVariable":
+                ## Sample metadata matrix
+                sampleMetadata $scalingMethod.sampleMetadata
+
+                ## Biological factor of interest (column number in samplemetadata)
+                factor $scalingMethod.factor
+            #end if
+
+            ## Spectra representation
+            graphType $graphType
+
+            ## Outputs
+            logOut $logOut
+            dataMatrixOut $dataMatrixOut
+            graphOut $graphOut
+    ]]></command>
+
+    <inputs>
+        <param name="dataMatrix" type="data" label="Data matrix of preprocessed data" help="" format="tabular" />
+
+        <conditional name="scalingMethod" >
+            <param name="method" label="Normalization method" type="select" help="Default method is total intensity" >
+                <option value="None">None normalization</option>
+                <option value="Total">Total intensity</option>
+                <option value="PQN">Probabilistic Quotient Normalization</option>
+                <option value="QuantitativeVariable">Quantitative variable</option>
+            </param>
+            <when value="None" />
+            <when value="Total" />
+            <when value="PQN">
+                <param name="sampleMetadata" type="data" label="Sample metadata matrix" help="" format="tabular" />
+                <param name="factor" label="Name of the column of the biological factor of interest (for PQN method)" type="text" />
+                <param name="controlGroup" label="Name of reference level for PQN normalization" type="text" help=""/>
+            </when>
+            <when value="QuantitativeVariable">
+                <param name="sampleMetadata" type="data" label="Sample metadata matrix" help="" format="tabular" />
+                <param name="factor" label="Name of the column of the numerical variable for normalization (weight, osmolality, ...)" type="text" />
+            </when>
+        </conditional>
+
+        <param name="graphType" label="Spectra representation" type="select" help="Select 'None' for no representation,'Overlay' to overlay all spectra on a unique chart and 'One per individual' to generate an individual chart for each observation">
+            <option value="None"> none </option>
+            <option value="Overlay"> Overlay </option>
+            <option value="One_per_individual"> One_per_individual </option>
+        </param>
+    </inputs>
+
+
+    <outputs>
+        <data format="txt" name="logOut" label="${tool.name}_log" />
+        <data format="tabular" name="dataMatrixOut" label="${tool.name}_dataMatrix" />
+        <data format="pdf" name="graphOut" label="${tool.name}_spectra" >
+            <filter> graphType != "None" </filter>
+        </data>
+    </outputs>
+
+  <tests>
+        <test>
+            <param name="dataMatrix" value="MTBLS1_bucketedData.tabular" ftype="tabular" />
+            <conditional name="scalingMethod" >
+                <param name="method" value="Total" />
+            </conditional>
+            <param name="graphType" value="Overlay" />
+            <output name="dataMatrixOut" file="MTBLS1_bucketedData_normalized.tabular" />
+        </test>
+    </tests>
+
+    <help>
+
+.. class:: infomark
+
+**Authors** Marie Tremblay-Franco (marie.tremblay-franco@toulouse.inra.fr) and Marion Landi (marion.landi@clermont.inra.fr)
+  MetaboHUB: The French National Infrastructure for Metabolomics and Fluxomics (http://www.metabohub.fr/en)
+
+---------------------------------------------------
+
+.. class:: infomark
+
+**Please cite**
+
+F. Dieterle, A. Ross, G. Schlotterbeck, and H. Senn (2006). Probabilistic Quotient Normalization as Robust Method to Account for Dilution of Complex Biological Mixtures. Application in 1H NMR Metabonomics.
+Analytical Chemistry 78(13): 4281-4290.
+
+---------------------------------------------------
+
+===============
+ Normalization
+===============
+
+-----------
+Description
+-----------
+
+Normalization (operation applied on each (preprocessed) individual spectrum) of preprocessed data
+
+-----------------
+Workflow position
+-----------------
+
+**Upstream tools**
+
++----------------------+------------------------------------+---------+-------------+
+| Name                 | output file                        | format  | parameter   |
++======================+====================================+=========+=============+
+| NMR_Bucketing        | Normalization_bucketedData.tsv     | tabular | Ions Matrix |
++----------------------+------------------------------------+---------+-------------+
+
+
+
+
+**Downstream tools**
+
++---------------------------+----------------------+--------+
+| Name                      | Output file          | Format |
++===========================+======================+========+
+|Univariate                 | variableMetadata.tsv | Tabular|
++---------------------------+----------------------+--------+
+|Multivariate               | sampleMetadata.tsv   | Tabular|
++---------------------------+----------------------+--------+
+|                           | variableMetadata.tsv | Tabular|
++---------------------------+----------------------+--------+
+
+
+-----------
+Input files
+-----------
+
++---------------------------+------------+
+| Parameter : num + label   |   Format   |
++===========================+============+
+| DataMatrix                |   Tabular  |
++---------------------------+------------+
+
+**DataMAtrix**
+
+    | variable x sample dataMatrix tabular separated file containing (preprocessed) spectra, with . as decimal, and NA for missing values
+
+
+----------
+Parameters
+----------
+
+DataMatrix
+    | see "Input files" section above
+    |
+
+Normalization method
+    | normalization to apply on each spectrum:
+
++---------------------------+--------------------------------------+
+| Name                      | Normalization                        |
++===========================+======================================+
+|None                       | No                                   |
++---------------------------+--------------------------------------+
+|Total                      | Total intensity                      |
++---------------------------+--------------------------------------+
+|PQN                        | Probabilistic Quotient Normalization |
++---------------------------+--------------------------------------+
+|QuantitativeVariable       | Weight, osmolality, ...              |
++---------------------------+--------------------------------------+
+
+
+sampleMetadata
+    | sample x metadata **sample** tabular separated file of the numeric and/or character sample metadata, with . as decimal and NA for missing values
+    | Mandatory for "PQN" or "Quantitative" normalization method
+    | The row names must be identical to the column names of the dataMatrix file
+    |
+
+
+Spectra representation:
+    | Graphical chart of bucketed and integrated raw files
+    | If "Overlay": the n (sample number) spectra are overlaid on the same figure
+    | If "One_per_individual": pdf file includes n pages (1 per sample)
+    |
+
+
+------------
+Output files
+------------
+
+
+dataMatrix.tsv
+    | tabular output
+    | Data matrix with p rows (variable) and n columns (samples) containing the intensities
+    |
+
+spectra.pdf
+    | pdf output
+    | Graphical chart of bucketed and integrated data
+    |
+
+
+---------------------------------------------------
+
+---------------
+Working example
+---------------
+
+
+.. class:: warningmark
+
+Under construction
+
+.. image:: ./static/images/Mth_Travaux.png
+        :width: 100
+
+
+---------------------------------------------------
+
+--------------
+Changelog/News
+--------------
+
+**Version 1.0.3 - 30/01/2017**
+
+- BUGFIX: Fix a bug: stack overflow for integers
+        
+**Version 1.0.2 - 22/10/2016**
+
+- NEW: this tool was previously named NMR Normalization. It had been generalize to deal with all kind of preprocessed data
+
+**Version 1.0.1 - 14/04/2016**
+
+- TEST: refactoring to pass planemo test using conda dependencies
+
+**Version 2015-01-28 - 28/01/2015**
+
+   </help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btu813</citation>
+    </citations>
+</tool>