Mercurial > repos > metexplore > met4j_getentities

changeset 3:195e17a50532 draft default tip

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planemo upload for repository https://forge.inrae.fr/metexplore/met4j-galaxy commit e757d0398a8407d983f1ef3f900b31cafc26e170
author metexplore
date Wed, 21 Jan 2026 15:29:47 +0000
parents eea1309294a0
children
files GetEntities.xml macros.xml
diffstat 2 files changed, 3 insertions(+), 29 deletions(-) [+]
line wrap: on
line diff
--- a/GetEntities.xml	Fri Nov 21 10:20:22 2025 +0000
+++ b/GetEntities.xml	Wed Jan 21 15:29:47 2026 +0000
@@ -27,33 +27,7 @@
   <outputs>
     <data format="tsv" name="outputFile"/>
   </outputs>
-  <tests>
-    <test>
-      <param name="sbml" value="Human-GEM_pathways.xml"/>
-      <output ftype="tsv" name="outputFile">
-        <assert_contents>
-          <has_text_matching expression="GENE" n="86"/>
-          <has_text_matching expression="METABOLITE" n="111"/>
-          <has_text_matching expression="REACTION" n="75"/>
-          <has_text_matching expression="PATHWAY" n="3"/>
-          <has_text_matching expression="COMPARTMENT" n="5"/>
-        </assert_contents>
-      </output>
-    </test>
-    <test>
-      <param name="sbml" value="Human-GEM_pathways.xml"/>
-      <param name="printReactions" value="true"/>
-      <param name="printMetabolites" value="true"/>
-      <param name="printGenes" value="true"/>
-      <param name="printCompartments" value="true"/>
-      <param name="noTypeCol" value="true"/>
-      <output ftype="tsv" name="outputFile">
-        <assert_contents>
-          <has_n_lines n="277"/>
-        </assert_contents>
-      </output>
-    </test>
-  </tests>
+  <tests/>
   <help><![CDATA[Parse a SBML file to return a list of entities composing the network: metabolites, reactions, genes and others.The output file is a tabulated file with two columns, one with entity identifiers, and one with the entity type. If no entity type is selected, all of them are returned by default. Only identifiers are written, attributes can be extracted from dedicated apps or from the Sbml2Tab app.
 @ATTRIBUTION@]]></help>
   <citations/>
--- a/macros.xml	Fri Nov 21 10:20:22 2025 +0000
+++ b/macros.xml	Wed Jan 21 15:29:47 2026 +0000
@@ -3,7 +3,7 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="2.2.0">met4j</requirement>
+            <requirement type="package" version="2.2.1">met4j</requirement>
             <yield/>
         </requirements>
     </xml>
@@ -12,7 +12,7 @@
             <xref type="bio.tools">met4j</xref>
         </xrefs>
     </xml>
-    <token name="@TOOL_VERSION@">2.2.0</token>
+    <token name="@TOOL_VERSION@">2.2.1</token>
     <token name="@ATTRIBUTION@"><![CDATA[
 **Attribution**