annotate pfam_annot/pfam_annot.xml @ 0:68a3648c7d91 draft default tip

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<tool id="pfam_Annot" name="PFAM output annotator" version="0.">
 <description>Generate synthetic reports</description>
 <command> /home/inmare/galaxy/tools/pfam_annot/annota.pl $prot $pfam $out</command>
 <inputs>
 	<param name="prot" type="data" format="fasta" label="protein file used as input with pfamScan" help="fasta only"/>
 	<param name="pfam" type="data" format="tabular" label="pfamScan output" help="this file should match the protein file"/>
 </inputs>
 <outputs>
 	<data name="out" ftype="tabular" format="html" label="annotated pfam file"/>
 </outputs>
 <test/>
 <help> This tools produce a synthetic report, in fasta format, containing a description of PFAM domains annotated to each protein. A separate report is generated for each fosmid. Fosmid names are inferred from the heades of the input fasta file, using the naming convention described in the "Sanger Fosmid End" annotator tool.  Therefore contigs should be assigned to fosmids prior to perform this step and ideally prior to the annotation of functional domains. The output file contains links to the PFAM wiki, where a more comprehensive description of the domains can be found. A pfamScan output table is required as input.  The output of this tool is compatible with the PFAM search utility, which might be used in order to perform keyword searches on the annotation  </help>
</tool>