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1 <tool id="tbprofiler_json_to_tabular" name="Convert tbprofiler json report to tabular" version="0.1.0+galaxy0">
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2 <description>Convert tbprofiler json report to tabular</description>
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3 <requirements>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 '$__tool_directory__/tbprofiler_json_to_tabular.py'
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7 ${report} \
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8 --qc ${qc} \
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9 --gene-coverage ${gene_coverage} \
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10 --missing-positions ${missing_positions \
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11 --resistance-variants ${resistance_variants}
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12 --other-variants ${other_variants} \
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13 --analysis-metadata ${analysis_metadata}
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14 ]]></command>
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15 <inputs>
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16 <param name="report" type="data" format="json" />
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17 </inputs>
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18 <outputs>
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19 <data name="qc" label="QC" format="tabular"/>
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20 <data name="gene_coverage" label="Gene Coverage" format="tabular"/>
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21 <data name="missing_positions" label="Missing positions" format="tabular"/>
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22 <data name="resistance_variants" label="Resistance variants" format="tabular"/>
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23 <data name="other_variants" label="Other variants" format="tabular"/>
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24 <data name="analysis_metadata" label="Analysis metadata" format="tabular"/>
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25 </outputs>
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26 <tests>
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27 <test>
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28 <param name="report" value="test-01_tbprofiler.json" />
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29 <output name="qc" file="test-01_qc.tsv" ftype="tabular" />
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30 <output name="gene_coverage" file="test-01_gene_coverage.tsv" ftype="tabular" />
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31 <output name="missing_positions" file="test-01_missing_positions.tsv" ftype="tabular" />
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32 <output name="resistance_variants" file="test-01_resistance_variants.tsv" ftype="tabular" />
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33 <output name="other_variants" file="test-01_other_variants.tsv" ftype="tabular" />
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34 <output name="analysis_metadata" file="test-01_analysis_metadata.tsv" ftype="tabular" />
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35 </test>
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36 </tests>
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37 <help><![CDATA[
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38 ]]></help>
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39 <citations>
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40 </citations>
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41 </tool>
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