<tool id="evolmap_output" name="EvolMAP Output Tool">
	<description>Modifies EvolMAP output</description>
	<command interpreter="perl">output.pl $file $numDiffGenes '$speciesList'  
#for $file in $fileList
	${file.treeFile}
#end for</command>
	
	<inputs>
		<repeat name="fileList" title="Species fasta files - must be same order as original tree">
			<param name="treeFile" type="data" format="fasta" label="fasta file"/>
		</repeat>
		<param name="file" type="data" label="EvolMAP output file"/>
		<param name="numDiffGenes" type="integer" value="1" label="Number of different species" />
		<param name="speciesList" type="text" area="true" size="3x25" label="Species tree - Must be same format as original EvolMAP run." />
	</inputs>

	<outputs>
		<data from_work_dir="result.dat" format="txt"/>
	</outputs>

	<help>
	
	http://labs.eemb.ucsb.edu/oakley/todd/
	
	Modifies EvolMAP output. Must provide the original EvolMAP output and files used.
	
	Input preconditions:
		Species fasta files - must be inputted in the same order as the original tree from the EvolMAP run
		EvolMAP output file - must be from an EvolMAP run
		Number of different species - the number of different species you want searched and pulled to the output file
		Species tree - must be the same tree you used to get the EvolMAP output file in the original EvolMAP run
	
	Input file format:
		FASTA (.fasta/.fa)
	
	Output format:
		Text (txt)
	</help>

</tool>