<tool id="kmerfinder" name="Kmerfinder" version="@VERSION@+galaxy0">
    <description> Species identification using kmer</description>
    <macros>
        <token name="@VERSION@">3.0.2</token>
    </macros>
    <requirements>
        <requirement type="package" version="@VERSION@">kmerfinder</requirement>
        <!-- <container type="singularity">kmerfinder.sif</container> -->
    </requirements>
    <version_command>echo "3.0.2"</version_command>
    <command detect_errors="exit_code"><![CDATA[
        #import re
        #if $input.is_of_type('fastqsanger', 'fastq'):
            #set $ext = 'fastq'
        #elif $input.is_of_type('fastqsanger.gz'):
            #set $ext = 'fastq.gz'
        #elif $input.is_of_type('fastq'):
            #set $ext = 'fastq'
        #elif $input.is_of_type('fastq.gz'):
            #set $ext = 'fastq.gz'
        #elif $input.is_of_type('fasta.gz'):
            #set $ext = 'fasta.gz'
        #elif $input.is_of_type('fasta'):
            #set $ext = 'fasta'
        #end if
        #set $safename = re.sub('[^\w\-_\.]', '_', $input.element_identifier)
        ln -fs '$input' $safename.$ext &&

        kmerfinder.py 
        -i '$safename.$ext'
        -db '${kmerfinder_databases.fields.path}.ATG'
        -tax '${kmerfinder_databases.fields.path}.tax'
        -o output
    ]]>    </command>
    <inputs>
        <param name="input" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" multiple="false" label="Sequence files" help="Fasta for Fastq"/>
        <!-- DATABASE INPUT-->
        <param label="Select a database" name="kmerfinder_databases" type="select">
            <options from_data_table="kmerfinder_databases">
                <validator message="No database is available" type="no_options" />
            </options>
        </param>
    </inputs>
    <outputs>
        <data name="results" format="tabular" label="${tool.name} on ${on_string} Results" from_work_dir="output/results.txt"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="test.fastq.gz" ftype="fastqsanger.gz"/>
            <param name="kmerfinder_databases" value="pseudomonas"/>
            <output name="results">
                <assert_contents>
                    <has_text text="Pseudomonas aeruginosa genome assembly PAO1OR" />
                    <has_text text="NZ_LN871187.1" />
                </assert_contents>
            </output>
        </test>
     </tests>
    <help><![CDATA[
        Kmerfinder finds the best match (species identification) to the reads in one or more fastq files or one fasta file in a (kmer) database produced using the KMA program. The method outputs the best matches, along with additional taxonomic information, if that option is selected.

        _`Document`:  https://bitbucket.org/genomicepidemiology/kmerfinder

    ]]></help>
    <citations>
        <citation type="doi">10.1128/JCM.02981-13</citation>
        <citation type="doi">10.1128/JCM.02452-13</citation>
        <citation type="doi">10.1186/s12859-018-2336-6</citation>
    </citations>

</tool>