<tool id="tbprofiler_json_to_tabular" name="Convert tbprofiler json report to tabular" version="0.1.0+galaxy0">
    <description>Convert tbprofiler json report to tabular</description>
    <requirements>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        '$__tool_directory__/tbprofiler_json_to_tabular.py'
          ${report} \
          --qc ${qc} \
          --gene-coverage ${gene_coverage} \
          --missing-positions ${missing_positions \ 
          --resistance-variants ${resistance_variants} 
          --other-variants ${other_variants} \
          --analysis-metadata ${analysis_metadata}
    ]]></command>
    <inputs>
      <param name="report" type="data" format="json" />
    </inputs>
    <outputs>
      <data name="qc" label="QC" format="tabular"/>
      <data name="gene_coverage" label="Gene Coverage" format="tabular"/>
      <data name="missing_positions" label="Missing positions" format="tabular"/>
      <data name="resistance_variants" label="Resistance variants" format="tabular"/>
      <data name="other_variants" label="Other variants" format="tabular"/>
      <data name="analysis_metadata" label="Analysis metadata" format="tabular"/>
    </outputs>
    <tests>
      <test>
        <param name="report" value="test-01_tbprofiler.json" />
        <output name="qc" file="test-01_qc.tsv" ftype="tabular" />
        <output name="gene_coverage" file="test-01_gene_coverage.tsv" ftype="tabular" />
        <output name="missing_positions" file="test-01_missing_positions.tsv" ftype="tabular" />
        <output name="resistance_variants" file="test-01_resistance_variants.tsv" ftype="tabular" />
        <output name="other_variants" file="test-01_other_variants.tsv" ftype="tabular" />
        <output name="analysis_metadata" file="test-01_analysis_metadata.tsv" ftype="tabular" />
      </test>
    </tests>
    <help><![CDATA[
    ]]></help>
    <citations>
    </citations>
</tool>