--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/progenesisconverter.xml	Wed Jan 08 11:39:16 2014 +0100
@@ -0,0 +1,68 @@
+<tool name="ProgenesisConverter" id="progenesisconv1" version="1.0.2">
+	<description>Converts Progenesis aligned feature lists in CSV format to APML</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 ">
+	    ProgenesisConv.jar 
+	    -progenesisFile $progenesisFile
+	    -apmlFile $apmlFile 
+	    #if $multipleScoringSchemes.containsMultipleScoringSchemes == True
+	    	-scoringSchemeNameColumn $multipleScoringSchemes.scoringSchemeNameColumn
+	    #end if
+	    #if $statisticalMeasure.containsStatisticalMeasure == True
+	    	-statisticalMeasureColumn $statisticalMeasure.statisticalMeasureColumn
+	    #end if
+	</command>
+	
+	<inputs>
+	 	
+   		<param name="progenesisFile" type="data" format="csv" label="Progenesis aligned feature lists CSV file" />
+     	
+     	<conditional name="multipleScoringSchemes">
+     		<param name="containsMultipleScoringSchemes" type="boolean" truevalue="Yes" falsevalue="No" checked="false" 
+     		       label="Progenesis scores contain multiple scoring schemes"
+     		       help="Set this if the scores in the 'Score' column come from two or more different schemes (e.g. MSE and DDA)"/>
+     		<when value="Yes">
+     			<param name="scoringSchemeNameColumn" type="text" optional="true" size="30" 
+				       label="Column name" 
+				       help="Name of the column containing the scoring scheme name" />
+     		</when>
+     	</conditional>
+     	
+     	<conditional name="statisticalMeasure">
+     		<param name="containsStatisticalMeasure" type="boolean" truevalue="Yes" falsevalue="No" checked="false" 
+     		       label="Input sheet contains a statistical measure column"
+     		       help="Set this if the the input sheet also contains a column with a statistical measure (e.g. p-value, e-value, etc)"/>
+     		<when value="Yes">
+				<param name="statisticalMeasureColumn" type="text" optional="true" size="30" 
+				       label="Column name" 
+				       help="Name of the column containing the statistical measure" />     			
+     		</when>
+     	</conditional>
+     	
+	</inputs>
+	<outputs>
+	  <data name="apmlFile" format="apml" label="${progenesisFile.metadata.base_name} - ${tool.name} on ${on_string}: APML" metadata_source="progenesisFile">
+	  </data>
+	</outputs>
+	<tests>
+	</tests>
+  <help>
+  
+.. class:: infomark
+  
+This tool converts a Progenesis CSV file to the APML xml format. 
+This format can be used to submit the data for annotation by SEDMAT. SEDMAT can use MS2 identification data
+and couple it to this MS1 data, thereby annotating the MS1 feature list with identifications.
+
+-----
+
+**Output example**
+
+This tools returns APML output that can be used as input for the SEDMAT tool. 
+
+  </help>
+</tool>