--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/csv2apml.xml	Wed Jan 08 11:39:16 2014 +0100
@@ -0,0 +1,127 @@
+<tool name="Csv2Apml" id="csv2apml" version="1.0.2">
+	<description>Converts MS/MS data in CSV format to APML format</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 ">
+	    Csv2Apml.jar 
+	    -peptideAndProteinMatchListCSV $peptideAndProteinMatchListCSV
+	    -attributesMappingCSV $attributesMappingCSV
+		-apmlFile $apmlFile
+	</command>
+	
+	<inputs>
+	 	
+   		<param name="peptideAndProteinMatchListCSV" type="data" 
+   		format="csv" label="MS/MS CSV file"
+   		help="MS/MS CSV file containing peptide identifications and protein matches" />
+     	
+		<param name="mz" type="text" optional="false" size="30" 
+		       label="Column name for precursor m/z" />     			
+
+		<param name="rt" type="text" optional="false" size="30" 
+		       label="Column name for precursor rt" />
+     	
+		<param name="charge" type="text" optional="false" size="30" 
+		       label="Column name for precursor charge (z)" />
+
+		<param name="pepSequence" type="text" optional="false" size="30" 
+		       label="Column name for peptide sequence" />
+		       
+		<param name="ppidScore" type="text" optional="false" size="30" 
+		       label="Column name for peptide identification score" />
+		       
+		<param name="scoringSchemeName" type="text" optional="true" size="30" 
+		       label="(Optional) Column name containing scoring scheme name" />
+
+		<param name="statisticalMeasure" type="text" optional="true" size="30" 
+			   label="(Optional) Column name for reported statistical measure values" 
+			   help="(e.g. column containing p-values or e-values)" /> 
+
+		<param name="ppidTheoreticalMz" type="text" optional="true" size="30" 
+		       label="(Optional) Column name for peptide theoretical m/z" />
+		       
+		<param name="modifications" type="text" optional="true" size="30" 
+		       label="(Optional) Column name for reported modifications" />
+		       
+		<param name="proteinAccession" type="text" optional="false" size="30" 
+		       label="Column name for protein accession code" />
+		       
+		<param name="protSequenceLength" type="text" optional="true" size="30" 
+		       label="(Optional) Column name for protein sequence length" />
+		       
+		<param name="pepProtStart" type="text" optional="true" size="30" 
+		       label="(Optional) Column name for protein match location start" 
+		       help="Where peptide sequence starts in protein"/>
+
+		<param name="pepProtEnd" type="text" optional="true" size="30" 
+		       label="(Optional) Column name for protein match location end" 
+		       help="Where peptide sequence ends in protein"/>
+		       
+		<param name="sourceName" type="text" optional="true" size="30" 
+		       label="(Optional) Column name for sample names" />
+		       
+	</inputs>
+	<configfiles>
+		<configfile name="attributesMappingCSV">Generic name,name in S1 table CSV
+mz,${mz}
+rt,${rt}
+charge,${charge}
+pepSequence,${pepSequence}
+ppidScore,${ppidScore}
+proteinAccession,${proteinAccession}
+#if $ppidTheoreticalMz != "None"
+ppidTheoreticalMz,${ppidTheoreticalMz}
+#end if
+#if $modifications != "None"
+modifications,${modifications}
+#end if
+#if $scoringSchemeName != "None"
+scoringSchemeName,${scoringSchemeName}
+#end if
+#if $statisticalMeasure != "None"
+statisticalMeasure,${statisticalMeasure}
+#end if
+#if $protSequenceLength != "None"
+protSequenceLength,${protSequenceLength}
+#end if
+#if $pepProtStart != "None"
+pepProtStart,${pepProtStart}
+#end if
+#if $pepProtEnd != "None"
+pepProtEnd,${pepProtEnd}
+#end if
+#if $sourceName != "None"
+sourceName,${sourceName}
+#end if</configfile>
+	</configfiles>
+	
+	<outputs>
+	  <data name="apmlFile" format="apml" label="${tool.name} on ${on_string}: APML" >
+	  </data>
+	</outputs>
+	<tests>
+	</tests>
+  <help>
+  
+.. class:: infomark
+  
+This tool converts a CSV file containing MS/MS peptide identifications and their respective protein matches
+to the APML xml format. 
+The identifications in APML format can be used for example to annotate unidentified MS features via SEDMAT(*).
+This format is also compatible with what is expected by other post-processing tools like Quantifere (for 
+protein inference). 
+
+(*)SEDMAT can use MS2 identification data
+and couple it to this MS1 data, thereby annotating the MS1 feature list with identifications.
+
+-----
+
+**Output**
+
+This tools returns the input data in APML xml format. 
+
+  </help>
+</tool>