diff tools/convert/Kegg2Sbml/Kegg2Sbml.xml @ 0:3cdcfdae8bd2 draft default tip

"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/convert/Kegg2Sbml/Kegg2Sbml.xml	Tue May 31 07:45:16 2022 +0000
@@ -0,0 +1,38 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<tool id="met4j_Kegg2Sbml" name="Kegg2Sbml" version="0.11.0">
+  <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:0.11.0</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>
+    <test maxseconds="600">
+      <param name="org" value="buc"/>
+      <output ftype="sbml" name="sbml">
+        <assert_contents>
+          <is_valid_xml/>
+
+        </assert_contents>
+      </output>
+    </test>
+  </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>
+</tool>