--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/isofix.xml	Wed Jan 08 11:39:16 2014 +0100
@@ -0,0 +1,66 @@
+<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 $useOriginalProteinSequences.fastaFile
+        #end if
+	</command>
+	
+	<inputs>
+	 	
+   		<param name="identificationsFile" type="data" format="apml" label="MS/MS identifications file" />
+     	
+     	<param name="rtTol" type="integer" size="10" value="15" label="Retention time tolerance (seconds) " />
+     	
+     	<param name="createLogFile" type="boolean" checked="true" label="Generate log file" help="Lists the in-source decay peptides found"/>
+     	
+     	<conditional name="useOriginalProteinSequences">
+     		<param name="useOriginalProteinSequencesFile" type="boolean" 
+     		truevalue="Yes" falsevalue="No" checked="true" 
+     		label="Use original protein sequences for detecting peptide source relations" 
+     		help="This can reduce redundancy in final set by correctly identifying which peptides derive from bigger peptides that are also identified"/>
+     		<when value="Yes">
+     			<param name="fastaFile" type="data" format="fasta" label="Protein sequences (fasta file)"/>
+     		</when>
+     	</conditional>	 
+     	
+	</inputs>
+	<outputs>
+	  <data name="outputFile" format="apml" label="${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>