# HG changeset patch
# User metexplore
# Date 1763720646 0
# Node ID cb9942e68c8c54d1e16b1ea63e23c99c6bd0abc9
# Parent  97e6505bf8dae37deef01638924cdd9a674443c5
planemo upload for repository https://forge.inrae.fr/metexplore/met4j-galaxy commit 71335d4a636672d264cc4f443c07856907571928

diff -r 97e6505bf8da -r cb9942e68c8c SideCompoundsScan.xml
--- a/SideCompoundsScan.xml	Mon Aug 25 16:09:42 2025 +0000
+++ b/SideCompoundsScan.xml	Fri Nov 21 10:24:06 2025 +0000
@@ -29,15 +29,15 @@
     <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
     <param argument="-s" checked="false" falsevalue="" label="output compounds flagged as side compounds only" name="sideOnly" truevalue="-s" type="boolean" value="false"/>
     <param argument="-id" checked="false" falsevalue="" label="do not report values in output, export ids of compounds flagged as side compounds, allowing piping results" name="noReportValue" truevalue="-id" type="boolean" value="false"/>
-    <param argument="-d" label="flag as side compounds any compound with degree above threshold" name="degree" optional="true" type="text" value="400">
+    <param argument="-d" label="flag as side compounds any compound with degree above threshold. Ignored if negative" name="degree" optional="true" type="text" value="-1">
       <sanitizer invalid_char="_">
         <valid initial="string.printable"/>
       </sanitizer>
     </param>
-    <param argument="-dp" label="flag as side compounds the top x% of compounds according to their degree" name="degreePrecentile" optional="true" type="float" value="NaN"/>
+    <param argument="-dp" label="flag as side compounds the top x% of compounds according to their degree. Ignored if negative" name="degreePrecentile" optional="true" type="float" value="2.0"/>
     <param argument="-cc" checked="false" falsevalue="" label="flag as side compound any compound with less than 2 carbons in formula" name="flagInorganic" truevalue="-cc" type="boolean" value="false"/>
     <param argument="-uf" checked="false" falsevalue="" label="flag as side compound any compound with no valid chemical formula" name="flagNoFormula" truevalue="-uf" type="boolean" value="false"/>
-    <param argument="-nc" label="flag as side compound any compound with a number of parallel edges shared with a neighbor above the given threshold" name="parallelEdge" optional="true" type="float" value="NaN"/>
+    <param argument="-nc" label="flag as side compound any compound with a number of parallel edges shared with a neighbor above the given threshold. Ignored if negative" name="parallelEdge" optional="true" type="float" value="-1.0"/>
     <param argument="-m" label="degree is shared between compounds in different compartments. Use names if consistent and unambiguous across compartments, or identifiers if compartment suffix is present (id in form &quot;xxx_y&quot; with xxx as base identifier and y as compartment label)." name="mergingStrat" optional="true" type="select" value="no">
       <option selected="true" value="no">no</option>
       <option value="by_name">by_name</option>
@@ -52,7 +52,7 @@
       <param name="inputPath" value="XF_network.sbml"/>
       <output ftype="tsv" name="outputPath">
         <assert_contents>
-          <has_n_lines n="1108"/>
+          <has_n_lines min="1000"/>
           <has_n_columns n="4"/>
         </assert_contents>
       </output>
@@ -62,7 +62,7 @@
       <param name="noReportValue" value="true"/>
       <output ftype="tsv" name="outputPath">
         <assert_contents>
-          <has_n_lines n="6"/>
+          <has_n_lines min="30"/>
           <has_n_columns n="1"/>
         </assert_contents>
       </output>
diff -r 97e6505bf8da -r cb9942e68c8c macros.xml
--- a/macros.xml	Mon Aug 25 16:09:42 2025 +0000
+++ b/macros.xml	Fri Nov 21 10:24:06 2025 +0000
@@ -3,7 +3,7 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="2.1.0">met4j</requirement>
+            <requirement type="package" version="2.2.0">met4j</requirement>
             <yield/>
         </requirements>
     </xml>
@@ -12,10 +12,10 @@
             <xref type="bio.tools">met4j</xref>
         </xrefs>
     </xml>
-    <token name="@TOOL_VERSION@">2.1.0</token>
+    <token name="@TOOL_VERSION@">2.2.0</token>
     <token name="@ATTRIBUTION@"><![CDATA[
 **Attribution**
 
-This Galaxy tool relies on the met4j toolkit which is dedicated to the structural analysis of metabolic networks (https://forge.inrae.fr/metexplore/met4j)
+This Galaxy tool relies on the met4j toolkit which is dedicated to the structural analysis of metabolic networks (https://forgemia.inra.fr/metexplore/met4j)
     ]]></token>
 </macros>
\ No newline at end of file