<design>
	<formatversion>1.1</formatversion>

	<startPosition>0</startPosition>
	<oligolength>60</oligolength>


	<genomefile>trichoderma.fasta</genomefile>
	<genomemaskedfile>trichoderma.allmasked</genomemaskedfile>
	<outputdir></outputdir>

	<!-- A example of constant -->
	<constants>
		<constant>
			<name>myconstant</name>
			<value>myvalue</value>
		</constant>
        </constants>

	<!-- Sequences creation phase -->
	<sequencecreation skip="false" />

	<!-- Sequences filtering phase -->
	<sequencefilters skip="false">
		<sequencefilter>
			<name>redundancy</name>
		</sequencefilter>
		<sequencefilter>
			<name>Sequencexn</name>
		</sequencefilter>
	</sequencefilters>

	<!-- Computation measurements phase -->
	<measurements skip="false">
		<measurement>
			<name>oligosequence</name>
		</measurement>
		<measurement>
			<name>tm</name>
		</measurement>
		<measurement>
			<name>%gc</name>
		</measurement>
		<measurement>
			<name>complexity</name>
		</measurement>
		<measurement>
			<name>unicity</name>
			<parameters>
				<parameter>
					<name>maxprefixlength</name>
					<value>30</value>
				</parameter>
			</parameters>

		</measurement>
	</measurements>

	<!-- Filtering measurements phase -->
	<measurementfilters skip="false">
		<measurementfilter>
			<name>floatrange</name>
			<parameters>
				<parameter>
					<name>measurement</name>
					<value>%gc</value>
				</parameter>
				<parameter>
					<name>min</name>
					<value>0</value>
				</parameter>
				<parameter>
					<name>max</name>
					<value>1</value>
				</parameter>
			</parameters>
		</measurementfilter>
		<measurementfilter>
			<name>floatrange</name>
			<parameters>
				<parameter>
					<name>measurement</name>
					<value>tm</value>
				</parameter>
				<parameter>
					<name>min</name>
					<value>0</value>
				</parameter>
				<parameter>
					<name>max</name>
					<value>100</value>
				</parameter>
			</parameters>
		</measurementfilter>
		<measurementfilter>
			<name>floatrange</name>
			<parameters>
				<parameter>
					<name>measurement</name>
					<value>complexity</value>
				</parameter>
				<parameter>
					<name>min</name>
					<value>0</value>
				</parameter>
				<parameter>
					<name>max</name>
					<value>1</value>
				</parameter>
			</parameters>
		</measurementfilter>
		<measurementfilter>
			<name>floatrange</name>
			<parameters>
				<parameter>
					<name>measurement</name>
					<value>Unicity</value>
				</parameter>
				<parameter>
					<name>min</name>
					<value>0</value>
				</parameter>
				<parameter>
					<name>max</name>
					<value>${oligolength}</value>
				</parameter>
			</parameters>
		</measurementfilter>
	</measurementfilters>

	<!-- Select phase -->
	<selector skip="false">
		<name>tiling</name>
		<parameters>
			<parameter>
				<name>windowlength</name>
				<value>140</value>
			</parameter>
			<parameter>
				<name>windowstep</name>
				<value>140</value>
			</parameter>
		</parameters>
		<measurement>
			<name>tm</name>
			<weight>0.300</weight>
			<parameters>
				<parameter>
					<name>reference</name>
					<value>74.32</value>
				</parameter>
				<parameter>
					<name>deviation</name>
					<value>24.4</value>
				</parameter>
			</parameters>
		</measurement>
		<measurement>
			<name>%gc</name>
			<weight>0.150</weight>
			<parameters>
				<parameter>
					<name>reference</name>
					<value>0.5333</value>
				</parameter>
				<parameter>
					<name>deviation</name>
					<value>0.3333</value>
				</parameter>
			</parameters>
		</measurement>
		<measurement>
			<name>complexity</name>
			<weight>0.075</weight>
		</measurement>
		<measurement>
			<name>unicity</name>
			<weight>0.225</weight>
			<parameters>
				<parameter>
					<name>max</name>
					<value>42</value>
				</parameter>
			</parameters>
		</measurement>
		<measurement>
			<name>position</name>
			<weight>0.25</weight>
		</measurement>
	</selector>

	<!-- Output parameters -->
        <outputs>
		<output>
			<name>fasta</name>
		</output>
		<output>
			<name>default</name>
		</output>
	</outputs>

</design>
