diff build/tools/Kegg2Sbml/Kegg2Sbml.xml @ 6:7a6f2380fc1d draft

planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
author metexplore
date Wed, 17 May 2023 13:26:37 +0000
parents
children 1436e9cde9c9
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/build/tools/Kegg2Sbml/Kegg2Sbml.xml	Wed May 17 13:26:37 2023 +0000
@@ -0,0 +1,29 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<tool id="met4j_Kegg2Sbml" name="Kegg2Sbml" version="1.3.0">
+  <description>Build a SBML file from KEGG organism-specific pathways. Uses Kegg API.</description>
+  <xrefs>
+    <xref type="bio.tools">met4j</xref>
+  </xrefs>
+  <requirements>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.3.0</container>
+  </requirements>
+  <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Kegg2Sbml#if str($org):
+ -org "$org"
+#end if
+ -sbml "$sbml"
+]]></command>
+  <inputs>
+    <param argument="-org" label="[] Kegg org id. Must be 3 letters (" name="org" optional="true" type="text" value="">
+      <sanitizer invalid_char="_">
+        <valid initial="string.printable"/>
+      </sanitizer>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="sbml" name="sbml"/>
+  </outputs>
+  <tests/>
+  <help><![CDATA[Build a SBML file from KEGG organism-specific pathways. Uses Kegg API.
+Errors returned by this program could be due to Kegg API dysfunctions or limitations. Try later if this problem occurs.]]></help>
+  <citations/>
+</tool>