<tool id="tn93_readreduce" name="Merge matching reads" version="@VERSION@">
    <description>into clusters with TN-93</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="@VERSION@">tn93</requirement>
    </requirements>
    <version_command><![CDATA[tn93 --version]]></version_command>
    <command detect_errors="exit_code"><![CDATA[
    readreduce
    -q
    -o '$output'
    #if str($options.advanced) == 'advanced':
        -a $options.ambigs
        -l $options.overlap
        #if $options.counts_in_name:
            -d '$options.counts_in_name'
        #end if
        -s '$size'
    #end if
    '$input'
    ]]></command>
    <inputs>
        <param name="input" type="data" format="fasta" label="Input in FASTA format" />
        <conditional name="options">
            <param label="Additional options" name="advanced" type="select">
                <option value="defaults">Use defaults</option>
                <option value="advanced">Specify additional parameters</option>
            </param>
            <when value="defaults" />
            <when value="advanced">
                <param name="size" argument="-s" type="integer" min="0" value="18" label="Mimimum cluster size to report in output" />
                <param name="ambigs" argument="-a" type="select" label="Strategy for ambiguous nucleotides">
                    <option value="handle">handle</option>
                    <option value="resolve">resolve</option>
                    <option value="average">average</option>
                    <option value="skip">skip</option>
                    <option value="gapmm">gapmm</option>
                </param>
                <param name="overlap" argument="-l" type="integer" value="100"
                    label="Only count pairs that overlap by at least N bases" />
                <param name="counts_in_name" argument="-d" type="text"
                    optional="true" label="Sequence name component immediately preceding a copy number" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="fasta" name="output" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="readreduce-in1.fa" />
            <output file="readreduce-out1.fa" ftype="fasta" name="output" sort="True" />
        </test>
        <test>
            <param name="input" value="readreduce-in2.fa" />
            <output file="readreduce-out2.fa" ftype="fasta" name="output" sort="True" />
        </test>
    </tests>
    <help><![CDATA[
readreduce
----------

Merge matching reads into clusters using the
[Tamura Nei 93 distance](http://www.ncbi.nlm.nih.gov/pubmed/8336541) algorithm.
]]></help>
    <expand macro="citations" />
</tool>