<tool id="uvp" name="Unified Variant analysis Pipeline for M. tuberculosis complex" version="@TOOL_VERSION@+galaxy0">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">uvp</requirement>
    </requirements>
    <version_command>uvp --version</version_command>
    <command detect_errors="exit_code">
        <![CDATA[
        #if $single_paired.single_paired_selector == 'yes'
            ln -s '${single_paired.forward_input}' 'R1.fastq.gz' &&
            ln -s '${single_paired.reverse_input}' 'R2.fastq.gz' &&
        #elif $single_paired.single_paired_selector == "collection":
            ln -s '${single_paired.input_pair.forward}' 'R1.fastq.gz' &&
            ln -s '${single_paired.input_pair.reverse}' 'R2.fastq.gz' &&
        #else:
            ln -s '${single_paired.input_sequences}' 'R1.fastq.gz' &&
        #end if
        uvp
            --threads \${GALAXY_SLOTS:-1}
            --verbose
            #if $single_paired.single_paired_selector == 'yes'
                -n 'sample'
                -q 'R1.fastq.gz'
                -q2 'R2.fastq.gz'
            #elif $single_paired.single_paired_selector == "collection":
                -n 'sample'
                -q 'R1.fastq.gz'
                -q2 'R2.fastq.gz'
            #else:
                -n 'sample'
                -q 'R1.fastq.gz'
            #end if
            --krakendb '${kraken_database.fields.path}'
            -r '${reference}'
            ${annotate}
	]]>
    </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" />
            </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"/>
            </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="kraken_database" type="select">
	    <options from_data_table="kraken_databases">
	        <validator type="no_options" message="No Kraken databases are available" />
            </options>
        </param>
	<param name="reference" type="data" format="fasta" label="Reference Sequence" />
	<param name="annotate" type="boolean" truevalue="--annotate" falsevalue="" />
    </inputs>
    <outputs>
        <data name="lineage_report" label="Lineage Report" format="tabular" from_work_dir="Results/sample/sample.lineage_report.txt"/>
        <data name="validation_report" label="Validation Report" format="tabular" from_work_dir="Results/sample/validation/Validation_report.txt"/>
	<data name="kraken_report" label="Kraken Report" format="tabular" from_work_dir="Results/sample/kraken/final_report.txt"/>
        <data name="low_quals" label="Low-quality" format="tabular" from_work_dir="QC/low_quals.txt"/>
    </outputs>
    <tests>
    </tests>
    <help>
      <![CDATA[
      ]]>
    </help>
    <expand macro="citations" />
</tool>