<?xml version="1.0" encoding="UTF-8"?>
<tool name="TestApp" version="0.1.0" docurl="http://www.seqan.de" category="SeqAn/Testing" >
	<executableName>test_app</executableName>
	<description>This is a test-app.</description>
	<manual>This is the first line of our test description.
The second one contains formating &lt;bla&gt;.
</manual>
	<cli>
		<clielement optionIdentifier="--write-ctd-file-ext" isList="false">
			<mapping referenceName="test_app.write-ctd-file-ext" />
		</clielement>
		<clielement optionIdentifier="--double" isList="false">
			<mapping referenceName="test_app.double" />
		</clielement>
		<clielement optionIdentifier="--integer" isList="false">
			<mapping referenceName="test_app.integer" />
		</clielement>
		<clielement optionIdentifier="--int64" isList="false">
			<mapping referenceName="test_app.int64" />
		</clielement>
		<clielement optionIdentifier="--string" isList="true">
			<mapping referenceName="test_app.string" />
		</clielement>
		<clielement optionIdentifier="--in" isList="false">
			<mapping referenceName="test_app.in" />
		</clielement>
		<clielement optionIdentifier="--in-file-ext" isList="false">
			<mapping referenceName="test_app.in-file-ext" />
		</clielement>
		<clielement optionIdentifier="--out" isList="false">
			<mapping referenceName="test_app.out" />
		</clielement>
		<clielement optionIdentifier="--out-file-ext" isList="false">
			<mapping referenceName="test_app.out-file-ext" />
		</clielement>
		<clielement optionIdentifier="--input-prefix-option" isList="false">
			<mapping referenceName="test_app.input-prefix-option" />
		</clielement>
		<clielement optionIdentifier="--output-prefix-option" isList="false">
			<mapping referenceName="test_app.output-prefix-option" />
		</clielement>
		<clielement optionIdentifier="--hidden" isList="false">
			<mapping referenceName="test_app.hidden" />
		</clielement>
		<clielement optionIdentifier="--arg-4-file-ext" isList="false">
			<mapping referenceName="test_app.arg-4-file-ext" />
		</clielement>
		<!-- Following clielements are arguments. You should consider providing a help text to ease understanding. -->
		<clielement optionIdentifier="" isList="false">
			<mapping referenceName="test_app.argument-0" />
		</clielement>
		<clielement optionIdentifier="" isList="false">
			<mapping referenceName="test_app.argument-1" />
		</clielement>
		<clielement optionIdentifier="" isList="false">
			<mapping referenceName="test_app.argument-2" />
		</clielement>
		<clielement optionIdentifier="" isList="false">
			<mapping referenceName="test_app.argument-3" />
		</clielement>
	</cli>
	<PARAMETERS version="1.6.2" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_6_2.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
		<NODE name="test_app" description="This is a test-app.">
			<ITEM name="write-ctd-file-ext" value="" type="string" description="Override file extension for --write-ctd" required="false" advanced="true" tags="file-ext-override,gkn-ignore" />
			<ITEM name="double" value="" type="double" description="set a double option" required="false" advanced="false" />
			<ITEM name="integer" value="" type="int" description="set an integer option" restrictions="1:10" required="false" advanced="false" />
			<ITEM name="int64" value="" type="int" description="set a 64 bit integer option" required="false" advanced="false" />
			<ITEMLIST name="string" type="string" description="set a string option" restrictions="a,b,c" required="false" advanced="false" >
			</ITEMLIST>
			<ITEM name="in" value="" type="input-file" description="set an input file" supported_formats="*.fasta" required="false" advanced="false" />
			<ITEM name="in-file-ext" value="" type="string" description="Override file extension for --in" restrictions="fasta" required="false" advanced="true" tags="file-ext-override,gkn-ignore" />
			<ITEM name="out" value="" type="output-file" description="set an output file" supported_formats="*.sam" required="false" advanced="false" />
			<ITEM name="out-file-ext" value="" type="string" description="Override file extension for --out" restrictions="sam" required="false" advanced="true" tags="file-ext-override,gkn-ignore" />
			<ITEM name="input-prefix-option" value="" type="input-prefix" description="set an input prefix" supported_formats="*.btx" required="false" advanced="false" />
			<ITEM name="output-prefix-option" value="" type="output-prefix" description="set an output prefix" supported_formats="*.blub" required="false" advanced="false" />
			<ITEM name="hidden" value="" type="string" description="a hidden option - will be advanced in the ctd" required="false" advanced="true" />
			<ITEM name="arg-4-file-ext" value="" type="string" description="Override file extension for argument 4" required="false" advanced="true" tags="file-ext-override,gkn-ignore" />
			<ITEM name="argument-0" value="" type="double" description="Double Argument" required="true" advanced="false" />
			<ITEM name="argument-1" value="" type="string" description="String Argument" required="true" advanced="false" />
			<ITEM name="argument-2" value="" type="string" description="Documentated Argument with formating" required="true" advanced="false" />
			<ITEM name="argument-3" value="" type="output-file" description="Testing output file arguments" required="true" advanced="false" />
		</NODE>
	</PARAMETERS>
</tool>
