view pfamScan/pfamScan.xml @ 0:68a3648c7d91 draft default tip

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<tool id="pfamScam" name="PFAM Annotator">
	<description>Annotate PFAM domains. </description>
	<command> /home/inmare/galaxy/tools/pfamScan/pfam_scan.pl -fasta $input -cpu 2 -dir /home/inmare/galaxy/tools/pfamScan/hmm > $output</command>
	
	<inputs>
		<param format="fasta" name="input" type="data" label="Source file"/>
	</inputs>
	
	<outputs>
		<data format="tabular" name="output" />
	</outputs>

	<tests>
		<test>
			<param name="input" value="htt.fas"/>
			<output name="out_file1" file="htt.dom.txt"/>
		</test>
	</tests>
	<citations>
		Predicting active site residue annotations in the Pfam database.
		(2007) BMC bioinformatics 8 :298
		PMID: 17688688

		The EMBL-EBI bioinformatics web and programmatic tools framework.
		(2015 July 01) Nucleic acids research 43 (W1) :W580-4
		PMID: 25845596

	</citations>	
	<help>
		The pfam_scan.pl script is used to annotate PFAM domains on the input file sequences. Only PFAM A class domains are predicted. See http://www.ebi.ac.uk/Tools/pfa/pfamscan/help/ for instructions on how to obtain pfamSCAN and for a brief description of the output format.
	</help>
</tool>