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<tool id="de_prokka" name="Prokka parser" version="0.">
 <description>Parsing of Prokka output</description>
 <command> /home/inmare/galaxy/tools/de_prokka/de_prokka.pl $prot $pfam $out</command>
 <inputs>
 	<param name="prot" type="data" format="fasta" label="protein file by prokka" help="fasta only"/>
 	<param name="pfam" type="data" format="tabular" label="gff by prokka" help="this file should match the protein file"/>
 </inputs>
 <outputs>
 	<data name="out" ftype="data" format="fasta" label="annotated prokka file"/>
 </outputs>
 <test/>
 <help>
	This tool add information, derived from the gff file to the headers of a fasta files containing the sequences of proteins predicted by prokka. The operation is required in order to keep track of all the information related to the proteins and the scaffolds/contigs from which they are predicted, so that they are not lost in the functional annotation step. This tool is a simple parser based on regular expressions. Works only with Prokka version xxx. Any usage outside A-Game is discouraged
 </help>
</tool>