<?xml version="1.0"?>
<tool id="kma_build_index" name="KMA Index Builder" tool_type="manage_data" version="1.2.21+galaxy0" profile="19.01">
    <description>kma index builder</description>
    <requirements>
        <requirement type="package" version="1.2.21">kma</requirement>
        <requirement type="package" version="3.7">python</requirement>
    </requirements>
    <version_command>kma -v</version_command>
    <command detect_errors="exit_code">
    <![CDATA[
        python '${__tool_directory__}/kma_build_index.py'
          '${out_file}'
          --k ${k}
          --k_t ${k_t}
          --k_i ${k_i}
	  --ML ${ML}
	  --ht ${ht}
	  --hq ${hq}
          --name '${name}'
	  '${fasta}'
    ]]>
    </command>
    <inputs>
        <param name="k" type="integer" value="16" min="8" max="32" label="kmer size used for indexing the database." />
        <param name="k_t" type="integer" value="16" min="8" max="32" label="kmer size used to identify template candidates when running KMA." />
        <param name="k_i" type="integer" value="16" min="8" max="32" label="kmer size used when performing alignments between two sequences." />
        <param name="ML" type="integer" value="16" label="Minimum length of templates" />
        <param name="ht" type="float" value="1.0" min="0.0" max="1.0" label="Homology template" />
        <param name="hq" type="float" value="1.0" min="0.0" max="1.0" label="Homology query" />
	<param name="name" type="text" label="Name for index" />
	<param name="fasta" type="data" format="fasta" label="Sequence to index (fasta)" />
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json" />
    </outputs>
    <tests>
        <test>
            <param name="fasta" value="phiX174.fasta"/>
            <param name="name" value="index"/>
            <output name="out_file" value="kma_data_manager.json" compare="sim_size" />
        </test>
    </tests>
    <help>
    </help>
    <citations>
        <citation type="doi">10.1186/s12859-018-2336-6</citation>
    </citations>
</tool>