<tool id="rbc_mafft" name="MAFFT" version="7.221.3">
    <description>Add sequence to a alignment already done.</description>
    <requirements>
        <requirement type="package" version="7.221">mafft</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
        <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
    </stdio>
    <version_command>
    <![CDATA[
        mafft --version
    ]]>
    </version_command>
    <command>
    <![CDATA[
        mafft --thread \${GALAXY_SLOTS:-1} --add $seqtoadd --reorder $existingalignment $outputFormat > $outputAlignment
    ]]>
    </command>
    <inputs>
        <param name="seqtoadd" type="data" format="fasta" label="Sequences to add" help="Sequences to add in FASTA format."/>
        <param name="existingalignment" type="data" format="fasta" label="Alignment already done" help="Multi-alignment in FASTA format."/>
        <param name="outputFormat" type="select" label="Output format" help="Either FASTA or ClustalW or Phylip">
            <option value="" selected="true">FASTA</option>
            <option value="--clustalout">ClustalW</option>
            <option value="--phylipout">Phylip</option>
        </param>
    </inputs>
    <outputs>
        <data format="fasta" name="outputAlignment" label="${tool.name} on ${on_string}">
            <change_format>
                <when input="outputFormat" value="--clustalout" format="clustal"/>
                <when input="outputFormat" value="--phylipout" format="phylip"/>
            </change_format>
        </data>
    </outputs>
    <help>
    <![CDATA[
**What it does**

MAFFT is a multiple sequence alignment program for unix-like operating systems.  
It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), 
FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.

Using only to add new sequence in alignment already done.

    ]]>
    </help>
    <citations>
        <citation type="doi">10.1093/molbev/mst010</citation>
    </citations>
</tool>