# HG changeset patch
# User pieter.lukasse@wur.nl
# Date 1394123359 -3600
# Node ID 72d4a37869ee8382d6a4211effe0c438f4c84029
# Parent  cb5d1a3b9aae47a69a0db044fab97dc2e07bfec3
updated msfilt/napq interfaces

diff -r cb5d1a3b9aae -r 72d4a37869ee msfilt.xml
--- a/msfilt.xml	Thu Mar 06 16:54:09 2014 +0100
+++ b/msfilt.xml	Thu Mar 06 17:29:19 2014 +0100
@@ -1,4 +1,4 @@
-<tool name="MsFilt" id="msfilt" version="1.0.2">
+<tool name="MsFilt" id="msfilt" version="1.0.3">
 	<description>Filters annotations based MS/MS peptide identification and annotation quality measures</description>
 	<!-- 
 	   For remote debugging start you listener on port 8000 and use the following as command interpreter:
@@ -38,8 +38,6 @@
    		
    		<repeat name="annotationSourceFiles" title="(Optional) 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>
    		
      	<!-- 
@@ -117,7 +115,7 @@
 		<configfile name="annotationSourceConfigFile">## start comment
 		## iterate over the selected files and store their names in the config file
 		#for $i, $s in enumerate( $annotationSourceFiles )
-			${s.identificationsFile}|${s.spectraFile}
+			${s.identificationsFile}
 			## 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
diff -r cb5d1a3b9aae -r 72d4a37869ee napq.xml
--- a/napq.xml	Thu Mar 06 16:54:09 2014 +0100
+++ b/napq.xml	Thu Mar 06 17:29:19 2014 +0100
@@ -22,8 +22,6 @@
 
    		<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=""