--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nmr_preprocessing/ReadFids_xml.xml	Mon Jul 30 10:33:03 2018 -0400
@@ -0,0 +1,228 @@
+<tool id="NMR_Read" name="NMR_Read" version="1.2.0">
+	<description> Read Bruker NMR raw files</description>
+	
+    <stdio>
+        <exit_code range="1:" level="fatal" />
+    </stdio>
+	
+  	<command>
+  	    ## Wrapper
+        Rscript $__tool_directory__/ReadFids_wrapper.R
+
+		## File input
+        fidzipfile $fidzipfile
+		
+		## Title line
+		title_line $title_line
+		
+		## Subdirectories
+		subdirectories $subdirectories
+		
+		## Use subdirectories names as FID names?
+		dirs_names $dirs_names
+
+        ## Outputs
+        dataMatrix $dataMatrix
+        sampleMetadata $sampleMetadata
+        logOut $logOut
+        graphOut $graphOut
+		
+	</command>
+		
+  	<inputs>
+		<param name="fidzipfile" type="data" format="no_unzip.zip" label="Bruker FID file" />
+        
+		<param name="title_line" label="Specify the line in the title file to recover the FID names (usually in pdata/1/title)" type="integer" value="1" size="100" help="Default value is line 1"/>
+
+        <param name="subdirectories" label="Presence of subdirectories?" type="select" help="Select 'FALSE' when there is no subdirectories, 'TRUE' if there are subdirectories">
+            <option value="FALSE"> FALSE </option>
+            <option value="TRUE"> TRUE </option>
+        </param>
+        
+        <param name="dirs_names" label="Use (sub)directories names as FID names?" type="select" help="Select 'TRUE' to use the subdirectories names as the FID names (instead of looking in the title file)">
+            <option value="FALSE"> FALSE </option>
+            <option value="TRUE"> TRUE </option>
+        </param>
+	</inputs>	
+
+	
+	
+	<outputs>
+		<data format="tabular" name="dataMatrix" label="${tool.name}_dataMatrix" />
+		<data format="tabular" name="sampleMetadata" label="${tool.name}_sampleMetadata" />
+		<data format="txt" name="logOut" label="${tool.name}_log" />
+		<data format="pdf" name="graphOut" label="${tool.name}_graph" />
+	</outputs>
+
+
+	<tests>
+        <test>
+          <param name="fidzipfile" value="MTBLS1.zip" ftype="zip" />
+          <param name="title_line" value="1" />
+          <param name="subdirectories" value="TRUE" />
+          <param name="dirs_names" value="TRUE" />
+           
+          <output name="dataMatrix" value="NMR_ReadFids_dataMatrix.tabular" />
+  
+        </test>
+  </tests>
+
+  
+  
+	<help>
+
+.. class:: infomark
+
+**Authors** Manon Martin (manon.martin@uclouvain.be) and Marie Tremblay-Franco (marie.tremblay-franco@inra.fr; Galaxy integration)
+
+.. class:: infomark
+
+
+=============
+NMR Read
+=============
+
+-----------
+Description
+-----------
+
+Nuclear Magnetic Resonance Bruker files reading (from the PEPS-NMR R package (https://github.com/ManonMartin/PEPSNMR))
+
+-----------------
+Workflow position
+-----------------
+
+**Upstream tools**
+
+========================= ================= =======
+Name                      output file       format
+========================= ================= =======
+NA                        NA                NA
+========================= ================= =======
+
+
+**Downstream tools**
+
++-----------------------+--------------------------+--------+
+| Name                  | Output file              | Format |
++=======================+==========================+========+
+|NMR_Preprocessing      | dataMatrix               | Tabular|
++-----------------------+--------------------------+--------+
+|NMR_Preprocessing      |  sampleMetadata          | Tabular|
++-----------------------+--------------------------+--------+
+|NMR_Preprocessing      |     NMR_Read_log         | TXT    |
++-----------------------+--------------------------+--------+
+|NMR_Preprocessing      |     NMR_Read_graph       | PDF    |
++-----------------------+--------------------------+--------+
+|NMR_Alignement         |     dataMatrix           | Tabular|
++-----------------------+--------------------------+--------+
+|NMR_Bucketing          |     dataMatrix           | Tabular|
++-----------------------+--------------------------+--------+
+|Normalization          |     dataMatrix           | Tabular|
++-----------------------+--------------------------+--------+
+|Univariate             |     variableMetadata     | Tabular|
++-----------------------+--------------------------+--------+
+|Multivariate           |     sampleMetadata       | Tabular|
++-----------------------+--------------------------+--------+
+|                       |     variableMetadata     | Tabular|
++-----------------------+--------------------------+--------+
+
+
+-----------
+Input files
+-----------
+
++---------------------------+-----------------+
+| Parameter : num + label   |   Format        |
++===========================+=================+
+| 1 : Choose your inputs    |     zip         |
++---------------------------+-----------------+
+
+
+**Choose your inputs**
+
+    | Zip file (recommended) of FID Bruker files: you can put a zip file containing your FID Bruker files: myinputs.zip.
+
+
+----------
+Parameters
+----------
+
+FID Title line
+	| Line in the acqus file to find the FID title (name)
+	|
+
+subdirectories
+	| Organization of individual's files
+	| TRUE: will search inside subdirectories for FIDs and will merge them to have unique FID and info matrices.
+	|
+	
+dirs_names
+	| Use the (sub)directories names as FID names?
+	|
+	
+	
+------------
+Output files
+------------
+
+NMR_Read_dataMatrix
+	| tabular output
+	| Data matrix with n rows (samples) and p columns (time) containing the raw FIDs.
+	|
+
+NMR_Read_sampleMetadata
+	| tabular output
+	| Data matrix with n rows (samples) containing the acquisition parameters for each sample.
+	|
+	
+NMR_Read_log
+	| Text output
+	| Contains warnings
+	|
+
+	
+NMR_Read_graph
+	| pdf output
+	| line plots of FID
+	|
+
+
+Creating the zip file
+-----------------------
+
+.. class:: warningmark you must use the 7Zip software (http://www.7-zip.org/) to zip under Windows.
+
+Must contain at least the following files for every sample: fid, acqu and acqus
+
+.. image:: ./static/images/ReadFids.png 
+    :height: 400 
+
+
+
+**Possible structure and parameters values:**
+
+
+(1) use title file and presence of sub-directories: set the FID Title line, subdirectories = TRUE,  dirs_names = FALSE
+(2) use title file and no sub-directories: set the FID Title line, subdirectories = FALSE,  dirs_names = FALSE
+(3) don't use title file and presence of sub-directories: subdirectories = TRUE,  dirs_names = TRUE
+(4) don't use title file and no sub-directories: subdirectories = FALSE,  dirs_names = TRUE
+
+
+
+   </help>
+   
+   
+   <citations>
+     
+      <citation type="bibtex">@PhDThesis{Rousseau2011,
+      title = {Statistical contribution to the analysis of metabonomics data in $^1$H NMR spectroscopy},
+      author = {Rousseau, R.},
+      school = {Institut de Statistique, Biostatistique et Sciences Actuarielles, Universit{\'e} catholique de Louvain},
+      year = {2011}}
+      </citation>
+      
+   </citations> 
+   
+   
+</tool>