<tool name="File Splitter" id="masscomb_filesplitter" version="0.0.1">
	<description>Basic file splitting</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 
	-->    
	<command interpreter="java -jar">
	    MassComb.jar 
	    -action FILESPLITTER 
	    -inputFile $inputFile 
	    -outputFile $outputFile 
	    -splitExpression $splitExpression
	    -nameExpression $nameExpression
	    -extension $extension
	    </command>
<inputs>
	<param name="inputFile" type="data" format="" label="Input file to split"/>
    
	<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=""/>

</inputs>
<outputs>
	<data format="prims.fileset.zip" name="outputFile" />
</outputs>
<tests>
	<test>
	</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>