<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>