Mercurial > repos > metexplore > met4j
diff tools/attributes/ExtractAnnotations/ExtractAnnotations.xml @ 10:6a112eaf8f38 draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 71071300dd662ad01bd064abcf6866a192eeea95
| author | metexplore |
|---|---|
| date | Mon, 03 Feb 2025 15:59:46 +0000 |
| parents | 0976a6257300 |
| children | 40c15b7467f1 |
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--- a/tools/attributes/ExtractAnnotations/ExtractAnnotations.xml Fri Jan 31 18:28:53 2025 +0000 +++ b/tools/attributes/ExtractAnnotations/ExtractAnnotations.xml Mon Feb 03 15:59:46 2025 +0000 @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_ExtractAnnotations" name="ExtractAnnotations" version="develop"> +<tool id="met4j_ExtractAnnotations" name="ExtractAnnotations" version="2.0.0"> <description>Extract databases' references from SBML annotations or notes.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.ExtractAnnotations -i "$inputPath" -export "$export" @@ -34,238 +34,40 @@ </outputs> <tests> <test> - - - - - - <param name="inputPath" value="Human-GEM_pathways.xml"/> - - - - - - <param name="export" value="METABOLITE"/> - - - - - - <param name="db" value="metanetx.chemical"/> - - - - - - <output ftype="tsv" name="outputPath"> - - - - - - <assert_contents> - - - - - - <has_n_lines n="146"/> - - - - - - <has_n_columns n="2"/> - - - - - - </assert_contents> - - - - - - </output> - - - - - - </test> <test> - - - - - - <param name="inputPath" value="Human-GEM_pathways.xml"/> - - - - - - <param name="export" value="METABOLITE"/> - - - - - - <param name="db" value="metanetx.chemical"/> - - - - - - <param name="skip" value="true"/> - - - - - - <output ftype="tsv" name="outputPath"> - - - - - - <assert_contents> - - - - - - <has_n_lines n="145"/> - - - - - - <has_n_columns n="2"/> - - - - - - </assert_contents> - - - - - - </output> - - - - - - </test> <test> - - - - - - <param name="inputPath" value="Human-GEM_pathways.xml"/> - - - - - - <param name="export" value="METABOLITE"/> - - - - - - <param name="db" value="metanetx.chemical"/> - - - - - - <param name="skip" value="true"/> - - - - - - <param name="uniq" value="true"/> - - - - - - <output ftype="tsv" name="outputPath"> - - - - - - <assert_contents> - - - - - - <has_n_lines n="111"/> - - - - - - <has_n_columns n="2"/> - - - - - - </assert_contents> - - - - - - </output> - - - - - - </test> </tests> <help><![CDATA[Extract databases' references from SBML annotations or notes. The references are exported as a tabulated file with one column with the SBML compound, reaction or gene identifiers, and one column with the corresponding database identifier.The name of the targeted database need to be provided under the same form than the one used in the notes field or the identifiers.org uri.]]></help>