Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

<tool id="uniprotfasta2phytab" name="UNIPROTPHYTAB2FASTA" version="1.0">
    <description>Converts FASTA file downloaded from uniprot with sequences from same species and gene family to PHYTAB
format</description>
    <command interpreter="perl">
		uniprotfasta2phytab.pl $infile $gene > $outfile
    </command>
    <inputs>
	    <param name="infile" type="data" format="fasta" label="Input File" help="fasta file to convert" />
	    <param name="gene" type="text" format="tabular" label="Name of gene family" help="" />
    </inputs>
    <outputs>
	<data format="tabular" name="outfile" label="${tool.name} on ${on_string}: Out file" />
    </outputs>
    <help>
**What it does**

FASTA2PHYTAB takes an input FASTA file with sequences from the gene family, and extracts species name and
partition (gene family) name that will apply for all sequences. The output is a PHYTAB tabular format file.

------

**Inputs**

A FASTA file downloaded from uniprot. This should have a header something like
    >tr|B9UM22|B9UM22_MOUSE G protein-coupled receptor 81 OS=Mus musculus GN=Gpr81 PE=2 SV=1

------

**Outputs**

PHYTAB file format: http://osiris-phylogenetics.blogspot.com/2012/09/introduction-to-phytab-format.html

------

**Additional Information**

Please direct questions or comments to ucsb_phylogenetics@lifesci.ucsb.edu or, if you can, enter them on the
osiris_phylogenetics site at bitbucket.org

------

**Citations**

This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use of this tool in a
publication, please consider citing the following.

Current Osiris Citation is here

http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
    </help>
</tool>
author	osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date	Tue, 11 Mar 2014 12:19:13 -0700
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