--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/napq.xml	Wed Jan 08 11:39:16 2014 +0100
@@ -0,0 +1,93 @@
+<tool name="NapQ" id="napq" version="0.0.1">
+	<description>'no alignment'(alignment-free) peptide quantification</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 ">
+	    NapQ.jar 
+	    -identificationsConfigFile $identificationsConfigFile
+	    -namingConventionCodesForSamples $namingConventionCodesForSamples
+	    #if $is2D_LC_MS.fractions == True
+        	-namingConventionCodesForFractions $is2D_LC_MS.namingConventionCodesForFractions
+        #end if
+	    -outputApml $outputApml
+	    -outputTsv $outputTsv
+	    -outReport $htmlReportFile
+	    -outReportPicturesPath $htmlReportFile.files_path
+	</command>
+	
+	<inputs>
+
+   		<repeat name="identificationFileList" title="Peptide identification files" help="Full set of MS/MS peptide identification files, including peptides that could not be quantified.">
+   			<param name="identificationsFile" type="data" format="apml,mzidentml,prims.fileset.zip" label="Identifications file (APML or MZIDENTML or MZIDENTML fileSet)" />
+   			<param name="spectraFile" type="data" format="mzidentml,prims.fileset.zip" optional="true" label="(Optional) Spectra fileSet (mzml file or fileSet)"
+   				   help="Select this in case your Identifications file is MZIDENTML or MZIDENTML fileSet" />
+   		</repeat>
+
+		<param name="namingConventionCodesForSamples" type="text" size="100" value="" 
+		label="Part of run/file name that identifies the sample" 
+		help="Add the CSV list of codes that occur in the file names 
+			and that stand for a sample code. E.g. '_S1,_S2,_S3,etc.' "/> <!-- could do regular expressions as well but this would be hard for biologists, e.g. _F\d\b -->
+
+   		
+   		<conditional name="is2D_LC_MS">
+     		<param name="fractions" type="boolean" truevalue="Yes" falsevalue="No" checked="false" 
+     		label="Data is from 2D LC-MS"
+     		help="Data acquisition was done in multiple fractions."/>
+     		<when value="Yes"> 
+     			<param name="namingConventionCodesForFractions" type="text" size="100" value="" 
+     			label="Part of run/file name that identifies the 2D LC-MS fraction" 
+     			help="Add the CSV list of codes that occur in the file names 
+     				and that stand for a fraction code. E.g. '_F1,_F2,_F3,etc.' Use this to avoid
+     				that each (fraction) file is seen as a separate run."/> <!-- could do regular expressions as well but this would be hard for biologists, e.g. _F\d\b -->
+     		</when>
+     	</conditional>     	
+     	
+	</inputs>
+	<configfiles>
+		<configfile name="identificationsConfigFile">## start comment
+		## iterate over the selected files and store their names in the config file
+		#for $i, $s in enumerate( $identificationFileList )
+			${s.identificationsFile}|${s.spectraFile}
+			## also print out the datatype in the next line, based on previously configured datatype
+			#if isinstance( $s.identificationsFile.datatype, $__app__.datatypes_registry.get_datatype_by_extension('apml').__class__):
+				apml
+			#else:
+        		mzid
+      		#end if
+		#end for
+		## end comment</configfile>
+	</configfiles>
+	<outputs>
+	  <data name="outputApml" format="apml" label="${tool.name} on ${on_string}: peptide quantifications (APML)"/>
+	  <data name="outputTsv" format="tabular" label="${tool.name} on ${on_string}: peptide quantifications (TSV)"/>
+	  <!-- in tsv we can have cols like: pep, avg_m/z, avg rt, m/z window, rt window, i_s1, i_s2, ...-->
+	  <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - HTML report"/>
+	  <!-- here we show the samples extracted and the files used to 'build up' each sample -->
+	</outputs>
+	<tests>
+	</tests>
+  <help>
+  
+.. class:: infomark
+  
+This tool takes in multiple peptide identification result files that have peptide identifications 
+coupled to some quantification (e.g. precursor intensity information or for example data coming 
+from MS^E acquisition where peptide identification and quantification are done in the same run and reported together). 
+Then, based on the given experiment design parameters (i.e. how the result files related back to 
+replicate runs and samples), it produces a new file in which the peptides are reported with 
+their calculated quantifications at the sample level. 
+
+The figure below explains this: 
+
+.. image:: $PATH_TO_IMAGES/napq_overview.png 
+
+
+
+
+
+
+  </help>
+</tool>