--- a/mascot.xml	Tue Mar 05 00:18:41 2013 -0500
+++ b/mascot.xml	Sun Jun 09 08:17:38 2013 -0500
@@ -2,13 +2,28 @@
 
 
 	<requirements>
-	    <requirement type="package" version="1.2.0">galaxy_protk</requirement>
+	    <requirement type="package" version="1.2.2">galaxy_protk</requirement>
    </requirements>
 
 	<description>Mascot MS/MS Search</description>
 
 
-	<command>rvm 1.9.3@protk-1.2.0 do mascot_search.rb -d $database -f $fragment_ion_tol -S $server $input_file -o $output -r
+	<command>rvm 1.9.3@protk-1.2.2 do mascot_search.rb 
+
+		#if $database.source_select=="built_in":
+		-d $database.dbkey
+		#else 
+		-d $database.custom_db
+		#end if
+
+		-f $fragment_ion_tol 
+
+		-S $server $input_file 
+
+		-o $output 
+
+		-r
+		
 		## Variable Mods
 
 		--var-mods='
@@ -18,34 +33,61 @@
 		--fix-mods='
 		$fixed_mods
 		'		
-		--allowed-charges=$allowed_charges	--enzyme=$enzyme --instrument=$instrument --precursor-ion-tol-units=$precursor_tolu --email=$email --username=$username -v $missed_cleavages
-		
+		--allowed-charges=$allowed_charges	
+
+		--enzyme=$enzyme 
+
+		--instrument=$instrument 
+
+		--precursor-ion-tol-units=$precursor_tolu 
+
+		--email=$email 
+
+		-v $missed_cleavages
+
+		#if $security.security_use
+		--use-security
+		--username $security.username
+		--password $security.password
+		#end if
+
+		#if $proxy
+		--proxy $proxy
+		#end if
+
 	</command>
 
 	<inputs>
 	
     <param name="input_file" type="data" format="mgf" multiple="false" label="MSMS File" help="A Mascot Generic Format file containing MSMS Spectra"/>
 
-	<param name="database" type="select" format="text" >
-	    <label>Database</label>
-		<options from_file="mascot_databases.loc">
-			<column name="name" index="0" />
-			<column name="value" index="2" />
-		</options>
-	</param>
+	<conditional name="database">
+		<param name="source_select" type="select" label="Database Type">
+			<option value="built_in">Built-In</option>
+			<option value="custom_defined">Custom</option>
+		</param>
+		<when value="built_in">
+			<param name="dbkey" type="select" format="text" >
+				<label>Database</label>
+				<options from_file="mascot_databases.loc">
+					<column name="name" index="0" />
+					<column name="value" index="2" />
+				</options>
+			</param>
+		</when>
+		<when value="custom_defined">
+			<param name="custom_db" type="text" size="80" value="SwissProt" label="Database Name" help="Exact name of a database defined on the Mascot server (case-sensitive)"/>
+		</when>
+	</conditional>
 
-
-
-	<param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while
-		clicking to select multiple items">
+	<param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Multiple values allowed">
 		<options from_file="mascot_mods.loc">
 			<column name="name" index="0" />
 			<column name="value" index="2" />
 		</options>
 	</param>		
 
-	<param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while
-	clicking to select multiple items">
+	<param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Multiple values allowed">
 		<options from_file="mascot_mods.loc">
 			<column name="name" index="0" />
 			<column name="value" index="2" />
@@ -108,24 +150,33 @@
 		<option value="CID+ETD">CID+ETD</option>
 	</param>
 	
-	<param name="fragment_ion_tol" label="Fragment Ion Tolerance in Daltons" type="float" value="0.65" min="0" max="10000" help="Fragment ion tolerance in Daltons"/>
+	<param name="fragment_ion_tol" label="Fragment Ion Tolerance" type="float" value="0.65" min="0" max="10000" help="Fragment ion tolerance in Daltons"/>
 
-	<param name="precursor_ion_tol" label="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" help="Precursor ion tolerance"/>
+	<param name="precursor_ion_tol" label="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" help="Enter a value in Daltons or ppm depending on the units chosen below"/>
 	<param name="precursor_tolu" type="select" format="text">
 	    <label>Precursor Ion Tolerance Units</label>
 	    <option value="ppm">ppm</option>		
 		<option value="Da">Da</option>
 	</param>
 
-	<param name="server" type="text" label="URL to Mascot Server cgi " size="60" value="http://www.exampleserver.com/mascot/cgi/"/>
+	<param name="server" type="text" label="URL to the cgi directory on the Mascot Server " size="60" value="http://www.exampleserver.com/mascot/cgi/"/>
+	<param name="proxy" type="text" label="Proxy Server URL including proxy port" size="60" value="" help="eg http://proxy.latrobe.edu.au:8080"/>
+
+	<conditional name="security">
+		<param name="security_use" type="boolean" label="Use Mascot Security?" help="Select this if you need to enter a username and password" truevalue="true" falsevalue="false" />
+		<when value="false" />
+		<when value="true">
+			<param name="username" type="text" label="Username" size="60" value="" help="Username on Mascot Server"/>
+			<param name="password" type="text" label="Password" size="60" value="" help="Mascot Password. Password is encrypted when over the internet but is stored in clear-text on the Galaxy server"/>
+		</when>
+	</conditional>
+	<param name="email" type="text" label="Email " size="60" value="" help=""/>
 	
-	<param name="email" type="text" label="Email " size="60" value="" help="Not Supported Yet."/>
 	
-	<param name="username" type="text" label="Username" size="60" value="" help="Not Supported Yet."/>	
 
   </inputs>
   <outputs>
-    <data format="mascotdat" name="output" metadata_source="input_file" label="mascot_vs_${database}.${input_file.display_name}.mascotdat"/>
+    <data format="mascotdat" name="output" metadata_source="input_file" label="mascot_vs_${database.dbkey if $database.has_key('dbkey') else $database.custom_db}.${input_file.display_name}.mascotdat"/>
   </outputs>
 
   <help>