<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>
     		<when value="No">
     		</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>
     		<when value="No">
     		</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>