Mercurial > repos > metexplore > met4j
diff tools/convert/Sbml2Tab/Sbml2Tab.xml @ 0:dcd16521b969 draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
author | metexplore |
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date | Fri, 10 Jun 2022 10:31:34 +0000 |
parents | |
children | 9b162ee6ff8e |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/convert/Sbml2Tab/Sbml2Tab.xml Fri Jun 10 10:31:34 2022 +0000 @@ -0,0 +1,62 @@ +<?xml version="1.0" encoding="UTF-8"?> +<tool id="met4j_Sbml2Tab" name="Sbml2Tab" version="0.11.0"> + <description>Create a tabulated file from a SBML file</description> + <xrefs> + <xref type="bio.tools">met4j</xref> + </xrefs> + <requirements> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container> + </requirements> + <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Tab#if str($i): + -i "$i" +#end if +#if str($r): + -r "$r" +#end if + -in "$in" + -out "$out" +]]></command> + <inputs> + <param argument="-i" label="[-->] String for irreversible reaction" name="i" optional="true" type="text" value="-->"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + <param argument="-r" label="[<==>] String for reversible reaction" name="r" optional="true" type="text" value="<==>"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + <param argument="-in" format="sbml" label="Sbml file" name="in" optional="false" type="data" value=""/> + </inputs> + <outputs> + <data format="tsv" name="out"/> + </outputs> + <tests> + <test> + <param name="in" value="toy_model.xml"/> + <output ftype="tsv" name="out"> + <assert_contents> + <has_n_lines n="8"/> + <has_n_columns n="9"/> + <has_text text="2.0 E[c] --> D[c]"/> + <has_text text="A[c] <==> B[c]"/> + </assert_contents> + </output> + </test> + <test> + <param name="in" value="toy_model.xml"/> + <param name="i" value="->"/> + <param name="r" value="="/> + <output ftype="tsv" name="out"> + <assert_contents> + <has_n_lines n="8"/> + <has_n_columns n="9"/> + <has_text text="2.0 E[c] -> D[c]"/> + <has_text text="A[c] = B[c]"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[Create a tabulated file from a SBML file]]></help> +</tool>