<tool name="IsoFix" id="isofix1" version="0.0.1">
	<description>Identifies in-source decay peptides and corrects protein assignments</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 ">
	    IsoFix.jar 
	    -identificationsFile $identificationsFile
	    -outputFile $outputFile 
	    -format apml
	    -rtTol $rtTol
	    -logFile $logFile
	    #if $useOriginalProteinSequences.useOriginalProteinSequencesFile == True
        	-fastaFile $useOriginalProteinSequences.fastaFile
        #end if
	</command>
	
	<inputs>
	 	
   		<param name="identificationsFile" type="data" format="apml" label="MS/MS identifications file" />
     	
     	<param name="rtTol" type="integer" size="10" value="15" label="Retention time tolerance (seconds) " />
     	
     	<param name="createLogFile" type="boolean" checked="true" label="Generate log file" help="Lists the in-source decay peptides found"/>
     	
     	<conditional name="useOriginalProteinSequences">
     		<param name="useOriginalProteinSequencesFile" type="boolean" 
     		truevalue="Yes" falsevalue="No" checked="true" 
     		label="Use original protein sequences for detecting peptide source relations" 
     		help="This can reduce redundancy in final set by correctly identifying which peptides derive from bigger peptides that are also identified"/>
     		<when value="Yes">
     			<param name="fastaFile" type="data" format="fasta" label="Protein sequences (fasta file)"/>
     		</when>
     		<when value="No">
     		</when>
     	</conditional>	 
     	
	</inputs>
	<outputs>
	  <data name="outputFile" format="apml" label="${identificationsFile.metadata.base_name} - ${tool.name} on ${on_string}: APML" metadata_source="identificationsFile"></data>
	  <data name="logFile" format="txt" label="${tool.name} on ${on_string} - LOG file">
	 	<!-- If the expression is false, the file is not created -->
	  	<filter>( createLogFile == True )</filter>
	  </data>
	</outputs>
	<tests>
	</tests>
  <help>
  
.. class:: infomark
  
This tool identifies in-source decay peptides and corrects protein assignments.

-----

**Output example**

This tools returns the given input file but then with corrected protein assignments and 
in-source decay peptides identified (by a small modification in their sequence string). 
E.g. if peptide TYNSIMK is found to be an in-source decay of HETTYNSIMK, then
its sequence is changed to HET}TYNSIMK (so the decayed part + "}" + own sequence).
E.g. decay from both sides: YNSI, HETTYNSIMK = HET}TYNSI{MK 


  </help>
</tool>