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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/de_prokka/de_prokka.xml	Thu Dec 22 04:45:31 2016 -0500
@@ -0,0 +1,15 @@
+<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>