<tool id="rnaz_select_seqs" name="RNAz Select Seqs" version="2.1">
    <requirements>
        <requirement type="package" version="2.1">rnaz</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
    rnazSelectSeqs.pl
        --num-seqs $numseqs
        --num-samples $numsamples
        --opt-id $optid
        --max-id $maxid
        #if $noref:
            --no-ref $noref
        #end if
        '$input'
    > '$output'
    ]]></command>
    <inputs>
        <param format="txt" name="input" type="data" label="Input Alignment File" />
        <param argument="--num-seqs" name="numseqs" type="integer" value="6" label="Number of sequences in the output alignment(s). (Default:6)" />
        <param argument="--num-samples" name="numsamples" type="integer" value="1" label="Number of output alignments (Default: 1)" />
        <param argument="--opt-id" name="optid" type="integer" value="80"
            label="The resulting alignment(s) is (are) optimized for this value of mean pairwise identity (in percent, default: 80)" />
        <param argument="--max-id" name="maxid" type="integer" value="99"
            label="Sequences from pairs with pairwise identity higher than X% are removed (default: 99, i.e. only almost identical sequences areremoved)" />
        <param argument="--no-reference" name="noref" type="boolean" checked="false" truevalue="--no-reference" falsevalue=""
            label="By default the first sequence (=reference sequence) is always present in the output alignment(s). If you do not care having it removed, set this flag." />
    </inputs>
    <outputs>
        <data name="output" format="txt" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="tRNA.aln"/>
            <param name="numseqs" value="1"/>
            <output name="output" file="tRNA_selected.aln"/>
        </test>
    </tests>
    <help><![CDATA[ RNAz up to version 1.0 was limited to alignments
    of at most 6 sequences.  As of version 2.0, there is no limit on
    the maximum number of sequences.  However, under some cirumstances
    (e.g. for very large alignments) it is still useful to reduce the
    number of sequences prior to running RNAz.  You can select an
    optimal subset of sequences using rnazSelectSeqs.pl before you
    put it into RNAz:

    Usage:
    rnazSelectSeqs.pl [options] [file]

    Options:
    -n N, --num-seqs=N
    Number of sequences in the output alignment(s). (Default:6)

    -a N, --num-samples=N
    Number of output alignments (Default: 1)

    -i X, --opt-id=X
    The resulting alignment(s) is (are) optimized for this value of
    mean pairwise identity (in percent, default: 80)

    --max-id=X
    Sequences from pairs with pairwise identity higher than X% are
    removed (default: 99, i.e. only almost identical sequences are
    removed)

    -x, --no-reference
    By default the first sequence (=reference sequence) is always
    present in the output alignment(s). If you do not care having it
    removed, set this flag.

    -v, --version
    Prints version information and exits.

    -h, --help
    Prints a short help message and exits.

    --man   Prints a detailed manual page and exits.


    ]]></help>

    <citations>
        <citation type="doi">10.1142/9789814295291_0009</citation>
    </citations>    

</tool>