# HG changeset patch
# User pieter.lukasse@wur.nl
# Date 1391166417 -3600
# Node ID 153e9eb5f2ff2da726e6bea2449a2ce326e55ab3
# Parent  33899d82fbc1dcf22b7ba94e96c0408a1460c127
new option in file splitter; small fix in xtandem form

diff -r 33899d82fbc1 -r 153e9eb5f2ff MassComb.jar
Binary file MassComb.jar has changed
diff -r 33899d82fbc1 -r 153e9eb5f2ff masscomb_dbsearch_xtandem.xml
--- a/masscomb_dbsearch_xtandem.xml	Mon Jan 27 09:47:22 2014 +0100
+++ b/masscomb_dbsearch_xtandem.xml	Fri Jan 31 12:06:57 2014 +0100
@@ -197,6 +197,9 @@
       		help="Max E-Value of a 'refine based' hit to be reported. Notice that the default value here is stricter than
       		the same parameter for 'non-refine based' identifications above. "/>
 	      </when>
+	  		
+	  	  <when value="no">
+		  </when>	
 	  </conditional>
       <param name="reverse_scoring" type="select" label="Scoring, include reverse" help=" Use the X! Tandem protein sequence reverse method (sequences are reversed in memory and searched again, the tag ':reversed' is added to the protein description).">
       	<option value="yes">Yes</option>
diff -r 33899d82fbc1 -r 153e9eb5f2ff masscomb_file_splitter.xml
--- a/masscomb_file_splitter.xml	Mon Jan 27 09:47:22 2014 +0100
+++ b/masscomb_file_splitter.xml	Fri Jan 31 12:06:57 2014 +0100
@@ -18,9 +18,11 @@
     
 	<param name="splitExpression" type="select"   label="(regular)Expression to split on" help="">
       	<option value="^>.+">line start with &gt;alphanumeric (^&gt;.+)</option>
+      	<option value=".*&lt;peak_listSLASHW+.*">APML peak_list tag (.*&lt;peak_list\W+.*)</option>
     </param>
     <param name="nameExpression" type="select" label="(regular)Expression for file name" help="">
       	<option value="SLASHw+">alphanumeric part (\w)</option>
+      	<option value="SLASHw+SLASH.raw">APML peak_list raw source file name (\w+\.raw)</option>
     </param>
     
     <param name="extension" type="text" size="30" label="File extension for the 'sub-files'" value=".txt" help=""/>
@@ -34,6 +36,13 @@
 	</test>
 </tests>
 <help>
-
+This tool splits files of mainly custom formats. The lists of "Expression to split on" and 
+"Expression for file name" are populated based on feedback from users. Users don't need
+to learn the regular expressions but can select options based on descriptions. 
+A free input text box for the expressions is not supported for a number of reasons, 
+one of them being the performance impact small errors could have. 
+<!-- furthermore galaxy is not escaping all special characters correctly, so 
+     having a text input box where advanced users can type in their expressions is 
+     not supported. -->
 </help>
 </tool>