<tool id="kraken2" name="kraken2" version="@TOOL_VERSION@+galaxy0">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement>
    </requirements>
    <version_command>kraken2 --version</version_command>
    <command detect_errors="exit_code">
        <![CDATA[
        kraken2
            --threads \${GALAXY_SLOTS:-1}
            #if $single_paired.single_paired_selector == 'yes'
                #if $forward_input.is_of_type( 'fastq' ):
                    --fastq-input
                #else:
                    --fasta-input
                #end if
                '${single_paired.forward_input}' '${single_paired.reverse_input}'
                ${single_paired.check_names}
            #elif $single_paired.single_paired_selector == "collection":
                #if $single_paired.input_pair.forward.is_of_type( 'fastq' ):
                    --fastq-input
                #else:
                    --fasta-input
                #end if
                '${single_paired.input_pair.forward}' '${single_paired.input_pair.reverse}'
                ${single_paired.check_names}
            #else:
                #if $single_paired.input_sequences.is_of_type('fastq')
                    --fastq-input
                #else:
                    --fasta-input
                #end if
                '${single_paired.input_sequences}'
            #end if
            --db '$kraken2_database'
            > '$output'
	]]>
    </command>
    <inputs>
        <conditional name="single_paired">
            <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired">
                <option value="collection">Collection</option>
                <option value="yes">Paired</option>
                <option selected="True" value="no">Single</option>
            </param>
            <when value="collection">
                <param format="fasta,fastq" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTA or FASTQ datasets" />
                <param name="check_names" argument="--check-names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match"/>
            </when>
            <when value="yes">
                <param format="fasta,fastq" name="forward_input" type="data" label="Forward strand" help="FASTA or FASTQ dataset"/>
                <param format="fasta,fastq" name="reverse_input" type="data" label="Reverse strand" help="FASTA or FASTQ dataset"/>
                <param name="check_names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match" help="--check-names" />
            </when>
            <when value="no">
                <param format="fasta,fastq" label="Input sequences" name="input_sequences" type="data" help="FASTA or FASTQ datasets"/>
            </when>
        </conditional>
	<param name="kraken2_database" type="select">
	    <options from_data_table="kraken2_databases">
	        <validator type="no_options" message="No Kraken2 databases are available" />
            </options>
        </param>
    </inputs>
    <outputs>
        <data name="output" format="" />
    </outputs>
    <tests>
        <test>
            <param name="single_paired_selector" value="no"/>
            <param name="input_sequences" value="kraken_test1.fa" ftype="fasta"/>
            <param name="split_reads" value="false"/>
            <param name="quick" value="no"/>
            <param name="only-classified-output" value="false"/>
            <param name="kraken_database" value="new_style_test_entry"/>
            <output name="output" file="kraken_test1_output.tab" ftype="tabular"/>
        </test>
    </tests>
    <help>
      <![CDATA[
Kraken is a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm. 
      ]]>
    </help>
    <expand macro="citations" />
</tool>