# HG changeset patch
# User pieter.lukasse@wur.nl
# Date 1418985022 -3600
# Node ID 35f506f30ae4ebac6781d122409a9b4e538036f3
# Parent  458e05d1d1723b6b598646f6a9abfc2c0773c240
fixed small rule in pdfread, and other small enhancements

diff -r 458e05d1d172 -r 35f506f30ae4 rankfilter_GCMS/pdfread.py
--- a/rankfilter_GCMS/pdfread.py	Fri Dec 12 12:28:08 2014 +0100
+++ b/rankfilter_GCMS/pdfread.py	Fri Dec 19 11:30:22 2014 +0100
@@ -75,7 +75,7 @@
                         # replaces of known cases by the same with a white space:    
                         name_tmp = name_tmp.replace('lC', 'l C').replace(']C', '] C').replace('sC', 's C').replace('9C', '9 C').replace('.C', '. C')
                         name_tmp = name_tmp.replace(')C', ') C').replace('eC', 'e C').replace('yC', 'y C').replace('oC', 'o C').replace('-C', '- C').replace('dC', 'd C').replace('rC', 'r C')
-                        name_tmp = name_tmp.replace('-, LC', '-, L C').replace('-, DC', '-, D C')
+                        name_tmp = name_tmp.replace(', LC', ', L C').replace(', DC', ', D C')
                         
                         name.append((' '.join(name_tmp.split(' ')[0:len(name_tmp) - 1])).replace("  ", " "))
                         if name_tmp:
diff -r 458e05d1d172 -r 35f506f30ae4 xcms_get_alignment_eic.r
--- a/xcms_get_alignment_eic.r	Fri Dec 12 12:28:08 2014 +0100
+++ b/xcms_get_alignment_eic.r	Fri Dec 19 11:30:22 2014 +0100
@@ -124,7 +124,7 @@
 						write(paste("<img src='", "figure", i,".png' />", sep="") ,
 			      				file=args.htmlReportFile, append=TRUE)
 			
-						png( figureName, type="cairo" ) 
+						png( figureName, type="cairo", width=800 ) 
 						plot(eiccor, xsetData, groupidx = i)
 						devname = dev.off()
 						
diff -r 458e05d1d172 -r 35f506f30ae4 xcms_get_alignment_eic.xml
--- a/xcms_get_alignment_eic.xml	Fri Dec 12 12:28:08 2014 +0100
+++ b/xcms_get_alignment_eic.xml	Fri Dec 19 11:30:22 2014 +0100
@@ -30,11 +30,12 @@
 	help="Comma or line-separated list of sample names. Optional field where you can specify the subset of samples
 	to use for the EIC plots. NB: if your dataset has many samples, specifying a subset here can significantly speed up the processing time." >
 		<sanitizer>
-			<!-- this translates from line-separated to comma separated list -->
+			<!-- this translates from line-separated to comma separated list, removes quotes  -->
 			<valid/>
 			<mapping initial="none">
 		    	<add source="&#10;" target=","/>
 		    	<add source="&#13;" target=""/>
+		    	<add source="&quot;" target=""/>
  			</mapping>
 		</sanitizer>	
 	</param>
diff -r 458e05d1d172 -r 35f506f30ae4 xcms_get_mass_eic.xml
--- a/xcms_get_mass_eic.xml	Fri Dec 12 12:28:08 2014 +0100
+++ b/xcms_get_mass_eic.xml	Fri Dec 19 11:30:22 2014 +0100
@@ -16,7 +16,7 @@
 		#else
 			-1
 			-1
-			$massParameters.mzList
+			"$massParameters.mzList" 
 			$massParameters.mzTolPpm
 		#end if  
 		"$sampleNames" 
@@ -43,11 +43,12 @@
 			<param name="mzList" type="text" area="true" size="7x70" label="m/z list" 
 				help="Comma or line-separated list of m/z values for which to plot an EIC. One EIC will be plotted for each m/z given here.">
 				<sanitizer>
-					<!-- this translates from line-separated to comma separated list -->
+					<!-- this translates from line-separated to comma separated list, removes quotes -->
 					<valid/>
 					<mapping initial="none">
 				    	<add source="&#10;" target=","/>
 				    	<add source="&#13;" target=""/>
+				    	<add source="&quot;" target=""/>
 		 			</mapping>
 				</sanitizer>
 			</param>
@@ -65,10 +66,12 @@
 		help="Comma or line-separated list of sample names. Here you can specify the subset of samples
 		to use for the EIC plots. NB: if your dataset has many samples, specifying a subset here can significantly speed up the processing time." >
 		<sanitizer>
+			<!-- this translates from line-separated to comma separated list, removes quotes  -->
 			<valid/>
 			<mapping initial="none">
 		    	<add source="&#10;" target=","/>
 		    	<add source="&#13;" target=""/>
+		    	<add source="&quot;" target=""/>
  			</mapping>
 		</sanitizer>	
 	</param>