# HG changeset patch
# User pieter.lukasse@wur.nl
# Date 1391166694 -3600
# Node ID d1edc7971d489cd8e185ea79d1289a0c0c1586df
# Parent  5d99c9d0615d76b4db1a29f28c58423ffc66efc1
fixes in tool forms (<when> tags)

diff -r 5d99c9d0615d -r d1edc7971d48 Csv2Apml.jar
Binary file Csv2Apml.jar has changed
diff -r 5d99c9d0615d -r d1edc7971d48 MsFilt.jar
Binary file MsFilt.jar has changed
diff -r 5d99c9d0615d -r d1edc7971d48 NapQ.jar
Binary file NapQ.jar has changed
diff -r 5d99c9d0615d -r d1edc7971d48 PRIMS.jar
Binary file PRIMS.jar has changed
diff -r 5d99c9d0615d -r d1edc7971d48 ProgenesisConv.jar
Binary file ProgenesisConv.jar has changed
diff -r 5d99c9d0615d -r d1edc7971d48 Quantifere.jar
Binary file Quantifere.jar has changed
diff -r 5d99c9d0615d -r d1edc7971d48 Quantiline.jar
Binary file Quantiline.jar has changed
diff -r 5d99c9d0615d -r d1edc7971d48 SedMat_cli.jar
Binary file SedMat_cli.jar has changed
diff -r 5d99c9d0615d -r d1edc7971d48 isofix.xml
--- a/isofix.xml	Mon Jan 27 12:11:29 2014 +0100
+++ b/isofix.xml	Fri Jan 31 12:11:34 2014 +0100
@@ -33,6 +33,8 @@
      		<when value="Yes">
      			<param name="fastaFile" type="data" format="fasta" label="Protein sequences (fasta file)"/>
      		</when>
+     		<when value="No">
+     		</when>
      	</conditional>	 
      	
 	</inputs>
diff -r 5d99c9d0615d -r d1edc7971d48 napq.xml
--- a/napq.xml	Mon Jan 27 12:11:29 2014 +0100
+++ b/napq.xml	Fri Jan 31 12:11:34 2014 +0100
@@ -8,9 +8,9 @@
 	<command interpreter="java -jar ">
 	    NapQ.jar 
 	    -identificationsConfigFile $identificationsConfigFile
-	    -namingConventionCodesForSamples $namingConventionCodesForSamples
+	    -namingConventionCodesForSamples "$namingConventionCodesForSamples"
 	    #if $is2D_LC_MS.fractions == True
-        	-namingConventionCodesForFractions $is2D_LC_MS.namingConventionCodesForFractions
+        	-namingConventionCodesForFractions "$is2D_LC_MS.namingConventionCodesForFractions"
         #end if
 	    -outputApml $outputApml
 	    -outputTsv $outputTsv
@@ -43,6 +43,8 @@
      				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>
+     		<when value="No">
+     		</when>
      	</conditional>     	
      	
 	</inputs>
diff -r 5d99c9d0615d -r d1edc7971d48 progenesisconverter.xml
--- a/progenesisconverter.xml	Mon Jan 27 12:11:29 2014 +0100
+++ b/progenesisconverter.xml	Fri Jan 31 12:11:34 2014 +0100
@@ -30,6 +30,8 @@
 				       label="Column name" 
 				       help="Name of the column containing the scoring scheme name" />
      		</when>
+     		<when value="No">
+     		</when>
      	</conditional>
      	
      	<conditional name="statisticalMeasure">
@@ -41,6 +43,8 @@
 				       label="Column name" 
 				       help="Name of the column containing the statistical measure" />     			
      		</when>
+     		<when value="No">
+     		</when>
      	</conditional>
      	
 	</inputs>
diff -r 5d99c9d0615d -r d1edc7971d48 quantifere.xml
--- a/quantifere.xml	Mon Jan 27 12:11:29 2014 +0100
+++ b/quantifere.xml	Fri Jan 31 12:11:34 2014 +0100
@@ -57,6 +57,8 @@
      				in different fractions can be merged together. Otherwise each (fraction) file
      				is seen as a separate sample."/> <!-- could do regular expressions as well but this would be hard for biologists, e.g. _F\d\b -->
      		</when>
+     		<when value="No">
+     		</when>
      	</conditional>
    		
    		<param name="statisticalMeasuresConfig" type="text" area="true" size="6x70" label="Statistical measures configuration" 
diff -r 5d99c9d0615d -r d1edc7971d48 sedmat.xml
--- a/sedmat.xml	Mon Jan 27 12:11:29 2014 +0100
+++ b/sedmat.xml	Fri Jan 31 12:11:34 2014 +0100
@@ -89,6 +89,8 @@
      		<when value="Yes">
      			<param name="namingConventionCodesForMatching" type="text" size="100" value="" label="List of codes in naming convention" help="Add the CSV list of codes that occur in the file names and that link them together. E.g. '_F1,_F2,_F3,etc.'"/>
      		</when>
+     		<when value="No">
+     		</when>
      	</conditional>	 
 
  		<param name="chargeStatesToGenerate" type="select" display="checkboxes" multiple="true" label="Generate extra charge states" help="The selected charge states will be generated for each MS2 feature ">
@@ -110,6 +112,8 @@
 				<param name="rtEnd" optional="false" type="integer" size="10" value="20" label="Set rention time end (minutes) " />
 				<param name="filterSourceName" type="text" size="100" value="" label="Restrict matching to a specific subset of the files " help="Part of a file name that occurs in both a ms1 and ms2 file (e.g. 'RibO_1_msE1')"/>
      		</when>
+     		<when value="No">
+     		</when>
      	</conditional>
      	
 	</inputs>