<tool id="preMloc" name="pgma_graphclust" version="0.4" >
	<requirements>
		<requirement type="package" version="0.6.0">graphclust-wrappers</requirement>
		<requirement type="package" version='0.1'>pgma-simple</requirement>
	</requirements>
	<stdio>
		<exit_code range="1:" />
	</stdio>
	<command>
		<![CDATA[

		    'newpreMlocarna.pl'  $CI '$fast_cluster' '$fasta_data' '$fast_cluster_sim' '$data_map' $knn ''

]]>
	</command>
	<inputs>
		<param type="data" name="fast_cluster" label="fast_cluster" format="txt" help="stokholm format" />
		<param type="data" name="fasta_data" label="fasta_data" format="fasta" help="fasta format" />
		<param type="data" name="fast_cluster_sim" label="fast_cluster_sim" format="txt" help="similarity sclores" />
		<param type="data" name="data_map" label="data_map" format="txt" help="data map" />
		<param name="CI" type="integer" value="1" size="5" label="Number of current iteration "/>
		<param name="knn" type="integer" value="20" size="5" label="Number of nearest neighbors" help="must be the same as for previous step"/>
	</inputs>
	<outputs>
		<collection name="centers" type="list"  label="centers">
			<discover_datasets pattern="(?P&lt;name&gt;^[0-9]*\.[0-9]*\.center.fa$)" ext="txt" directory="CLUSTER"  />
		</collection>
		<collection name="trees" type="list" label="trees">
			<discover_datasets pattern="(?P&lt;name&gt;^[0-9]*\.[0-9]*\.tree$)"  ext="txt" directory="CLUSTER" />
		</collection>
		<collection name="cmFa" type="list"  label="cmfinder_fa" >
			<discover_datasets pattern="(?P&lt;name&gt;^[0-9]*\.[0-9]*\.cmfinder.fa$)" ext="txt"  directory="CLUSTER" />
		</collection>
		<collection name="model_tree_fa" type="list"  label="model_tree_fa" >
			<discover_datasets pattern="(?P&lt;name&gt;^[0-9]*\.[0-9]*\.model.tree.fa$)" ext="txt"  directory="CLUSTER" />
		</collection>
		<collection name="tree_matrix" type="list"  label="tree_matrix" >
			<discover_datasets pattern="(?P&lt;name&gt;^[0-9]*\.[0-9]*\.matrix.tree$)" ext="txt"  directory="CLUSTER" />
		</collection>
	</outputs>
	<tests>
		<test>
			<param name="fast_cluster" value="data.svector.1.fast_cluster"/>
			<param name="fasta_data" value="data.fasta"/>
			<param name="fast_cluster_sim" value="data.svector.1.fast_cluster_sim"/>
			<param name="data_map" value="data.map"/>
			<param name="knn" value="20"/>
			<param name="CI" value="1"/>
			<output_collection name="centers">
				<element name="1.1.center.fa" file="CLUSTER/1.1.center.fa"/>
				<element name="1.1.center.fa" file="CLUSTER/1.2.center.fa"/>
			</output_collection>
			<output_collection name="trees" >
				<element name="1.1.tree" file="CLUSTER/1.1.tree"/>
				<element name="1.2.tree" file="CLUSTER/1.2.tree"/>
			</output_collection>
			<output_collection name="cmFa">
				<element name="1.1.cmfinder.fa" file="CLUSTER/1.1.cmfinder.fa"/>
				<element name="1.2.cmfinder.fa" file="CLUSTER/1.2.cmfinder.fa"/>
			</output_collection>
			<output_collection name="tree_matrix">
				<element name="1.1.matrix.tree" file="CLUSTER/1.1.matrix.tree"/>
				<element name="1.2.matrix.tree" file="CLUSTER/1.2.matrix.tree"/>
			</output_collection>
		</test>
	</tests>
	<help>
		<![CDATA[

**What it does**

This tool prepares files for locarna step.

.. class:: warningmark

The number of nearest neighbors must be the same as in the previous step (NSPDK step)

]]>
	</help>
	<citations>
  </citations>
</tool>