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comparison tbprofiler_json_to_tabular.xml @ 0:3e0d5ceeeb0f draft default tip

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planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
author public-health-bioinformatics
date Tue, 19 Sep 2023 18:03:41 +0000
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1 <tool id="tbprofiler_json_to_tabular" name="Convert tbprofiler json report to tabular" version="0.1.0+galaxy2">
2 <description>Convert tbprofiler json report to tabular</description>
3 <requirements>
4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[
6 '$__tool_directory__/tbprofiler_json_to_tabular.py'
7 ${report}
8 --qc ${qc}
9 --gene-coverage ${gene_coverage}
10 --missing-positions ${missing_positions}
11 --resistance-variants ${resistance_variants}
12 --other-variants ${other_variants}
13 --analysis-metadata ${analysis_metadata}
14 ]]></command>
15 <inputs>
16 <param name="report" type="data" format="json" />
17 </inputs>
18 <outputs>
19 <data name="qc" label="QC" format="tabular"/>
20 <data name="gene_coverage" label="Gene Coverage" format="tabular"/>
21 <data name="missing_positions" label="Missing positions" format="tabular"/>
22 <data name="resistance_variants" label="Resistance variants" format="tabular"/>
23 <data name="other_variants" label="Other variants" format="tabular"/>
24 <data name="analysis_metadata" label="Analysis metadata" format="tabular"/>
25 </outputs>
26 <tests>
27 <test>
28 <param name="report" value="test-01_tbprofiler.json" />
29 <output name="qc" file="test-01_qc.tsv" ftype="tabular" />
30 <output name="gene_coverage" file="test-01_gene_coverage.tsv" ftype="tabular" />
31 <output name="missing_positions" file="test-01_missing_positions.tsv" ftype="tabular" />
32 <output name="resistance_variants" file="test-01_resistance_variants.tsv" ftype="tabular" />
33 <output name="other_variants" file="test-01_other_variants.tsv" ftype="tabular" />
34 <output name="analysis_metadata" file="test-01_analysis_metadata.tsv" ftype="tabular" />
35 </test>
36 </tests>
37 <help><![CDATA[
38 ]]></help>
39 <citations>
40 </citations>
41 </tool>