--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/quantiline.xml	Wed Jan 08 11:39:16 2014 +0100
@@ -0,0 +1,62 @@
+<tool name="Quantiline" id="quantiline1" version="1.0.2">
+	<description>Labeled ms/ms data pre-processing for Protein Quantification (and Inference) pipelines</description>
+	<!-- 
+	   For remote debugging start you listener on port 8000 and use the following as command interpreter:
+	       java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000 
+	                    //////////////////////////
+	    -->
+	<command interpreter="java -jar ">
+	    Quantiline.jar 
+	    -ppidsFileName $ppidsFileName
+	    -spectraDataFile $spectraDataFile
+	    -ppidsInputFormat MZID 
+	    -labelMzValues "$labelMzValues"
+	    -labelmTol $labelmTol
+	    -outputFile $outputFile
+	    -outReport $outReport
+	</command>
+	<inputs>
+	 	
+	 	<param name="ppidsFileName" type="data" format="prims.fileset.zip" label="MS/MS peptide identifications fileSet (N mzidentml files)"/>
+	 	<param name="spectraDataFile" type="data" format="prims.fileset.zip" label="MS/MS spectra fileSet (N mzml files)"/>
+		      		
+	 	<param name="labelMzValues" type="text" size="20" label="Label m/z values" 
+	 	help="e.g. for 4plexed iTRAQ : 114.0,115.0,116.0,117.0"/>
+	 	
+		<param name="labelmTol" type="float" size="10" value="0.5" label="Label detection tolerance (Da)" 
+		help="Tolerance in daltons for label detection."/>
+	 	
+	</inputs>
+	<outputs>
+	  <data name="outputFile" format="apml" label="${tool.name} on ${on_string}: Peptides quantification (APML)" />
+	  <data name="outReport" format="html" label="${tool.name} on ${on_string}: Peptides quantification report (HTML)"/>
+	</outputs>
+	<tests>
+	</tests>
+  <help>
+  
+.. class:: infomark
+  
+This tool can read spectra files (mzML) and their respective identification files (mzIdentML) and based
+on the configured label masses produce a file that contains the merged information:
+peptides and their quantification based on label fragment intensity values read from the spectrum in which they 
+were identified. 
+
+In other words, it produces the peptide (relative) quantification file. This file can subsequently be used 
+by other tools for protein inference and protein quantification (e.g. Quantifere).
+
+
+-----
+
+**Output details**
+
+*Peptide quantification file (APML)*
+
+This is the list of peptides with their (relative) quantification based on the labels and their 
+intensities found in the label peaks of the corresponding spectrum. 
+
+
+
+
+  </help>
+</tool>