<tool id="profilemafft" name="profilemafft" version="1.0" force_history_refresh='True'>
    <description> Add Sequence(s) to existing Multiple Sequence Alignment </description>
    <requirements>
        <requirement type="package">mafft</requirement>
    </requirements>
    <command interpreter="perl">
        profilemafft.pl $new_sequences $existing_alignment
    </command>
    <inputs>
        <param format="fasta" name="new_sequences" type="data" label="Sequence(s) in fasta format" help=""/>
        <param format="fasta" name="existing_alignment" type="data" label="Aligned sequences in fasta format" help=""/>
    </inputs>
    <outputs>
        <data from_work_dir="log.txt" format="txt" name="screen" label="${tool.name} on ${on_string}: Screen Output" />
        <data from_work_dir="seqs_aligned.fasta" format="fasta" name="seqs_aligned" label="${tool.name} on ${on_string}: Full Alignment" />
    </outputs>
    <tests>
    </tests>
    <help>
**What it does**

This tool runs MAFFT profile alignment to add new sequences to an existing alignment

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**Inputs**

FASTA -- aligned sequences
FASTA -- new sequences to add to alignment

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**Outputs**

aligns new sequences into existing alignment outputting fasta

------

**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

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**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

Additional Citations for this tool

MAFFT: MAFFT: Katoh, Toh 2008 (Briefings in Bioinformatics 9:286-298)
Recent developments in the MAFFT multiple sequence alignment program.

MAFFT website: http://mafft.cbrc.jp/alignment/server/index.html

    </help>
</tool>