Mercurial > repos > metexplore > met4j

annotate tools/reconstruction/SbmlCheckBalance/SbmlCheckBalance.xml @ 11:40c15b7467f1 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 61dbdbae896d18b519a470e056cb8b4f98394518
author metexplore
date Thu, 13 Feb 2025 15:08:22 +0000
parents 6a112eaf8f38
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
9
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
metexplore
parents: 6
diff changeset
1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
11
40c15b7467f1 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 61dbdbae896d18b519a470e056cb8b4f98394518
metexplore
parents: 10
diff changeset
2 <tool id="met4j_SbmlCheckBalance" name="SbmlCheckBalance" version="2.0.1">
5
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
3 <description>Check balance of all the reactions in a SBML.</description>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
4 <xrefs>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
5 <xref type="bio.tools">met4j</xref>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
6 </xrefs>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
7 <requirements>
11
40c15b7467f1 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 61dbdbae896d18b519a470e056cb8b4f98394518
metexplore
parents: 10
diff changeset
8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container>
5
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
9 </requirements>
9
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
metexplore
parents: 6
diff changeset
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh reconstruction.SbmlCheckBalance -i "$sbml"
5
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
11 -out "$out"
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
12 ]]></command>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
13 <inputs>
9
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
metexplore
parents: 6
diff changeset
14 <param argument="-i" format="sbml" label="Input Sbml file" name="sbml" optional="false" type="data" value=""/>
5
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
15 </inputs>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
16 <outputs>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
17 <data format="tsv" name="out"/>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
18 </outputs>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
19 <tests/>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
20 <help><![CDATA[Check balance of all the reactions in a SBML.
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
21 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.
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
22 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>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
23 <citations/>
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents:
diff changeset
24 </tool>