Mercurial > repos > public-health-bioinformatics > tbprofiler_json_to_tabular

diff 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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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tbprofiler_json_to_tabular.xml	Tue Sep 19 18:03:41 2023 +0000
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+<tool id="tbprofiler_json_to_tabular" name="Convert tbprofiler json report to tabular" version="0.1.0+galaxy2">
+    <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>