diff tools/reconstruction/SbmlCheckBalance/SbmlCheckBalance.xml @ 5:35c9abcd8934 draft

planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
author metexplore
date Thu, 12 Jan 2023 13:45:13 +0000
parents
children 7a6f2380fc1d
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/reconstruction/SbmlCheckBalance/SbmlCheckBalance.xml	Thu Jan 12 13:45:13 2023 +0000
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+<?xml version="1.0" encoding="UTF-8"?>
+<tool id="met4j_SbmlCheckBalance" name="SbmlCheckBalance" version="1.2.1">
+  <description>Check balance of all the reactions in a SBML.</description>
+  <xrefs>
+    <xref type="bio.tools">met4j</xref>
+  </xrefs>
+  <requirements>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.1</container>
+  </requirements>
+  <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh reconstruction.SbmlCheckBalance -sbml "$sbml"
+ -out "$out"
+]]></command>
+  <inputs>
+    <param argument="-sbml" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/>
+  </inputs>
+  <outputs>
+    <data format="tsv" name="out"/>
+  </outputs>
+  <tests/>
+  <help><![CDATA[Check balance of all the reactions in a SBML.
+A reaction is balanced if all its reactants have a chemical formula with a good syntax and if the quantity of each atom is the same in both sides of the reaction.
+For each reaction, indicates if the reaction is balanced, the list of the atoms and the sum of their quantity, and the list of the metabolites that don't have a correct chemical formula.]]></help>
+  <citations/>
+</tool>