# HG changeset patch
# User pieter.lukasse@wur.nl
# Date 1388411821 -3600
# Node ID bc9300d88f1ab75550ecfb6d596aa2b2b37400b8
# Parent  2479eff53fc88f3e86661f610ec1f6170c115647# Parent  d3569edd995cc1a167f27bc5bdbd1a1b36f70016
Merge

diff -r d3569edd995c -r bc9300d88f1a csv2apml.xml
--- a/csv2apml.xml	Mon Dec 30 08:50:30 2013 -0500
+++ b/csv2apml.xml	Mon Dec 30 14:57:01 2013 +0100
@@ -1,4 +1,4 @@
-<tool name="Csv2Apml" id="csv2apml" version="1.0.1">
+<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:
diff -r d3569edd995c -r bc9300d88f1a msfilt.xml
--- a/msfilt.xml	Mon Dec 30 08:50:30 2013 -0500
+++ b/msfilt.xml	Mon Dec 30 14:57:01 2013 +0100
@@ -1,4 +1,4 @@
-<tool name="MsFilt" id="msfilt" version="1.0.1">
+<tool name="MsFilt" id="msfilt" version="1.0.2">
 	<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:
diff -r d3569edd995c -r bc9300d88f1a napq.xml
--- a/napq.xml	Mon Dec 30 08:50:30 2013 -0500
+++ b/napq.xml	Mon Dec 30 14:57:01 2013 +0100
@@ -1,5 +1,5 @@
-<tool name="NapQ" id="napq" version="1.0.2">
-	<description>[[experimental]]'no alignment'(alignment-free) peptide quantification</description>
+<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 
diff -r d3569edd995c -r bc9300d88f1a progenesisconverter.xml
--- a/progenesisconverter.xml	Mon Dec 30 08:50:30 2013 -0500
+++ b/progenesisconverter.xml	Mon Dec 30 14:57:01 2013 +0100
@@ -1,4 +1,4 @@
-<tool name="ProgenesisConverter" id="progenesisconv1" version="1.0.1">
+<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:
diff -r d3569edd995c -r bc9300d88f1a quantifere.xml
--- a/quantifere.xml	Mon Dec 30 08:50:30 2013 -0500
+++ b/quantifere.xml	Mon Dec 30 14:57:01 2013 +0100
@@ -1,4 +1,4 @@
-<tool name="Quantifere" id="quantifere1" version="1.0.1">
+<tool name="Quantifere" id="quantifere1" version="1.0.2">
 	<description>Protein Inference by Peptide Quantification patterns</description>
 	<!-- 
 	   For remote debugging start you listener on port 8000 and use the following as command interpreter:
@@ -6,7 +6,7 @@
 	                    //////////////////////////
 	    -->
 	<command interpreter="java -jar ">
-	    Quantifere.jar   
+	    Quantifere.jar 
 	    -annotatedQuantificationFilesList $annotatedQuantificationFilesList
 	    -identificationFilesList $identificationFilesList
     	-statisticalMeasuresConfigFile $statisticalMeasuresConfigFile
diff -r d3569edd995c -r bc9300d88f1a quantiline.xml
--- a/quantiline.xml	Mon Dec 30 08:50:30 2013 -0500
+++ b/quantiline.xml	Mon Dec 30 14:57:01 2013 +0100
@@ -1,4 +1,4 @@
-<tool name="Quantiline" id="quantiline1" version="1.0.1">
+<tool name="Quantiline" id="quantiline1" version="1.0.2">
 	<description>Labeled ms/ms data pre-processing for Protein Quantification (and Inference) pipelines</description>
 	<!-- 
 	   For remote debugging start you listener on port 8000 and use the following as command interpreter:
diff -r d3569edd995c -r bc9300d88f1a repository_dependencies.xml
--- a/repository_dependencies.xml	Mon Dec 30 08:50:30 2013 -0500
+++ b/repository_dependencies.xml	Mon Dec 30 14:57:01 2013 +0100
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
 <repositories description="Required proteomics dependencies.">
   <repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="09b89b345de2" />
-  <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="7101f7e4b00b" />
+  <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="7101f7e4b00b" /> 
 </repositories>
diff -r d3569edd995c -r bc9300d88f1a sedmat.xml
--- a/sedmat.xml	Mon Dec 30 08:50:30 2013 -0500
+++ b/sedmat.xml	Mon Dec 30 14:57:01 2013 +0100
@@ -1,4 +1,4 @@
-<tool name="SedMat" id="sedmat1" version="1.0.1">
+<tool name="SedMat" id="sedmat1" version="1.0.2">
 	<description>Matches MS and MS/MS results</description>
 	<!-- 
 	   For remote debugging start you listener on port 8000 and use the following as command interpreter: