<tool id="tb_profiler_profile" name="TB-Profiler Profile" version="2.1.0">
    <description>Infer strain types and drug resistance markers from sequences</description>	
    <requirements>
        <requirement type="package" version="2.1.0">tb-profiler</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        tb-profiler profile
            
            --platform '${platform.value}'

            #if $fastq_or_bam.input_select.value == "fastq":
                --read1 '${read1}'

                #if $read2:
                    --read2 '${read2}'
                #end if

            #else if $fastq_or_bam.input_select.value == "bam":
                --bam '${bam_input}'
            #end if 

            --call_method '${call_method}'
            --min_depth '${min_depth}'
            --threads "\${GALAXY_SLOTS:-1}"
            --mapper '${mapper}'
            --min_gene_frac '${min_gene_frac}'

            #if $txt:
                --txt
            #end if

    ]]></command>
    <inputs>
        <param name="platform" type="select" label="Platform">
            <option value="Illumina" selected="true">Illumina</option>
            <option value="minION">minION</option>
        </param>
        <conditional name="fastq_or_bam">
            <param name="input_select" type="select" label="Input File Type">
                <option value="fastq">fastq</option>
                <option value="bam">bam</option>
            </param>
            <when value="fastq">
                <param name="read1" type="data" format="fastq" label="Read1" help="First read file (default: None)"/>
                <param name="read2" type="data" format="fastq" optional="true" label="Read2" help="Second read file (default: None)"/>
                </when>
            <when value="bam">
                <param name="bam_input" type="data" format="bam" label="Bam" help="Warning!!!: The BAM files must have been created using the ensembl version of the genome."/>
            </when>
        </conditional>
        <param name="call_method" type="select" label="Call Method" help="Level of quality stringency required. (default: low)">
            <option value="low" selected="true">low</option>
            <option value="high">high</option>
            <option value="optimise">optimise</option>
        </param>
        <param name="min_depth" label="Min Depth" type="integer" value="10" help="Minimum depth required to call variant. Bases with depth below this cutoff will be marked as missing (default: 10)"/>
        <param name="mapper" label="Mapper" type="select" help="Mapping tools to use (default: bwa)">
            <option value="bwa" selected="true">bwa</option>
            <option value="minimap2">minimap2</option>
            <option value="bowtie2">bowtie2</option>
        </param>
        <param name="min_gene_frac" label="Minimum Gene Fraction" type="float" value="0.9" help="Used to infer a deletion if the fraction of a gene covered falls below this value. Also used to see if sample is high quality to continue by checking the fraction for rpoB (where deletion should not occur). (default: 0.9)"/>
        <param name="txt" label="Generate text file ouput" type="boolean" value="false" help="Create reader-friendly text output in addition to standard JSON output (default: False)"/>
    </inputs>
    <outputs>
        <data name="results_json" format="json" from_work_dir="results/tbprofiler.results.json" label="${tool.name} on ${on_string}: Results.json"/>
        <data name="results_txt" format="txt" from_work_dir="results/tbprofiler.results.txt" label="${tool.name} on ${on_string}: Results.txt">
            <filter>txt</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="read1" value="rif_resistant.fastq.gz"/>
            <output name="results_json" value="results_1.json"/>
        </test>
        <test expect_num_outputs="2">
            <param name="read1" value="rif_resistant.fastq.gz"/>
            <param name="txt" value="true"/>
            <param name="call_method" value="high"/>
            <param name="min_depth" value="11"/>
            <output name="results_json" value="results_2.json"/>
            <output name="results_txt" value="results_2.txt"/>
        </test>
    </tests>
    <help><![CDATA[    
Summary
=======

The pipeline aligns reads to the H37Rv reference using bowtie2, BWA or minimap2 and then calls variants using SAMtools. These variants are then compared to a drug-resistance database. We also predict the number of reads supporting drug resistance variants as an insight into hetero-resistance (not applicable for minION data).

Produces a JSON output file by default.

    ]]></help>
    <citations>
        <citation type="bibtex">
@UNPUBLISHED{Phelan2016,
    author = {Phelan, Jody},
    title = {TBProfiler},
    year = {2016},
    url = {https://github.com/jodyphelan/TBProfiler},
}
        </citation>
    </citations>
</tool>