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

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author matteoc
date Thu, 22 Dec 2016 04:45:31 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pfamScan/pfamScan.xml	Thu Dec 22 04:45:31 2016 -0500
@@ -0,0 +1,32 @@
+<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>