annotate interpro/paso4.xml @ 0:c342ebb50f0b draft default tip

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<tool id="DLaGiFer_3" name="Common attributes selection" version="1.0.0">
    <description>Extraction of common sequences attributes</description>
    <command interpreter="perl">
    paso4.pl "$infile" "$outfile"
    </command>

         <inputs>
            <param name="infile" type="data" format="gff" label="Sequence in Fasta File"/>

          
           </inputs>
	<outputs><data format="txt" name="outfile"/>
	</outputs>

<stdio><exit_code range="1:" level="fatal" description="Error" /></stdio>
    <help>


**What it does**

This tool obtains certain common attributes of the sequences contained in a gff3 format file.  


**Dependencies**

Perl is required for running this tool.



#####
Input
#####

A gff3 file with protein attributes is required.  

Generic Feature Format Version 3 (GFF3)

The GFF3 format is a flat tab-delimited file, which is much richer then the TSV output format. It allows you to trace back from matches to predicted proteins and to nucleic acid sequences. It also contains a FASTA format representation of the predicted protein sequences and their matches. You will find a documentation of all the columns and attributes used on [http://www.sequenceontology.org/gff3.shtml].


######
Output
######


A text file is generated by this tool.

Example Output
--------------

The common atributes of the sequences Q0KIY3 P02185 P02178 Q0KIY5 Q0KIY1 are:

For Name atribute: SSF46458 PF00042 PR00613 G3DSA:1.10.490.10 PS01033

For Ontology_term atribute: "GO:0005506" "GO:0020037" "GO:0015671" "GO:0019825"

For Dbxref atribute: "InterPro:IPR009050" "InterPro:IPR000971" "InterPro:IPR002335" "InterPro:IPR012292"  



**Galaxy Wrapper Authors**::

    * Laura Entrambasaguas
    * Ginés Almagro
    * Fernando Pérez

    </help>
</tool>