# HG changeset patch
# User metexplore
# Date 1769009613 0
# Node ID fb6f80555393d5ddf6d98dbcec8f18bc3692ac25
# Parent  1c1ec9e0ea14344632f162dfe0353fa461c6a2f4
planemo upload for repository https://forge.inrae.fr/metexplore/met4j-galaxy commit e757d0398a8407d983f1ef3f900b31cafc26e170

diff -r 1c1ec9e0ea14 -r fb6f80555393 Tab2Sbml.xml
--- a/Tab2Sbml.xml	Fri Nov 21 10:24:12 2025 +0000
+++ b/Tab2Sbml.xml	Wed Jan 21 15:33:33 2026 +0000
@@ -12,11 +12,6 @@
 #if str($colformula) != 'nan':
  -cf "$colformula"
 #end if
- $rp
- $mp
-#if str($e):
- -e "$e"
-#end if
 #if str($i):
  -irr "$i"
 #end if
@@ -27,25 +22,22 @@
 #if str($id):
  -id "$id"
 #end if
- $createCompartment
 #if str($defaultCompartment):
  -dcpt "$defaultCompartment"
 #end if
+ $usePalssonConvention
+#if str($boundaryCompartment):
+ -b "$boundaryCompartment"
+#end if
 #if str($nSkip) != 'nan':
  -n "$nSkip"
 #end if
+ $keepGoing
  -o "$sbml"
 ]]></command>
   <inputs>
     <param argument="-ci" label="[1] number of the column where are the reaction ids" name="colid" optional="true" type="integer" value="1"/>
     <param argument="-cf" label="[2] number of the column where are the reaction formulas" name="colformula" optional="true" type="integer" value="2"/>
-    <param argument="-rp" checked="false" falsevalue="" label="[deactivated] format the reaction ids in a Palsson way (R_***)" name="rp" truevalue="-rp" type="boolean" value="false"/>
-    <param argument="-mp" checked="false" falsevalue="" label="[deactivated] format the metabolite ids in a Palsson way (M_***_c)" name="mp" truevalue="-mp" type="boolean" value="false"/>
-    <param argument="-e" label="[_b] flag to assign metabolite as external" name="e" optional="true" type="text" value="_b">
-      <sanitizer invalid_char="_">
-        <valid initial="string.printable"/>
-      </sanitizer>
-    </param>
     <param argument="-irr" label="[--&gt;] String for irreversible reaction" name="i" optional="true" type="text" value="--&gt;">
       <sanitizer invalid_char="_">
         <valid initial="string.printable"/>
@@ -62,78 +54,24 @@
         <valid initial="string.printable"/>
       </sanitizer>
     </param>
-    <param argument="-cpt" checked="false" falsevalue="" label="[deactivated] Create compartment from metabolite suffixes. If this option is deactivated, only one compartment (the default compartment) will be created" name="createCompartment" truevalue="-cpt" type="boolean" value="false"/>
     <param argument="-dcpt" label="[c] Default compartment" name="defaultCompartment" optional="true" type="text" value="c">
       <sanitizer invalid_char="_">
         <valid initial="string.printable"/>
       </sanitizer>
     </param>
+    <param argument="-M_c" checked="false" falsevalue="" label="[false] Use Palsson et al. convention: compartment suffix in metabolite ids with _ separator" name="usePalssonConvention" truevalue="-M_c" type="boolean" value="false"/>
+    <param argument="-b" label="set a compartment as the system boundary. All metabolites in this compartment will have the attribute `boundaryCondition` set to true in the sbml." name="boundaryCompartment" optional="true" type="text" value="">
+      <sanitizer invalid_char="_">
+        <valid initial="string.printable"/>
+      </sanitizer>
+    </param>
     <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="integer" value="0"/>
+    <param argument="-ign" checked="false" falsevalue="" label="skip lines with parsing errors instead of stopping the process" name="keepGoing" truevalue="-ign" type="boolean" value="false"/>
   </inputs>
   <outputs>
     <data format="sbml" name="sbml"/>
   </outputs>
-  <tests>
-    <test>
-      <param name="in" value="toy_model.tsv"/>
-      <output ftype="sbml" name="sbml">
-        <assert_contents>
-          <is_valid_xml/>
-          <has_line_matching expression=".*reaction .*" n="7"/>
-          <has_line_matching expression=".*species .*" n="8"/>
-        </assert_contents>
-      </output>
-    </test>
-    <test>
-      <param name="in" value="toy_model_otherColumns.tsv"/>
-      <param name="colid" value="2"/>
-      <param name="colformula" value="3"/>
-      <output ftype="sbml" name="sbml">
-        <assert_contents>
-          <is_valid_xml/>
-          <has_line_matching expression=".*reaction .*" n="7"/>
-          <has_line_matching expression=".*species .*" n="8"/>
-        </assert_contents>
-      </output>
-    </test>
-    <test>
-      <param name="in" value="toy_model_otherSigns.tsv"/>
-      <param name="i" value="-&gt;"/>
-      <param name="r" value="="/>
-      <output ftype="sbml" name="sbml">
-        <assert_contents>
-          <is_valid_xml/>
-          <has_line_matching expression=".*reaction .*" n="7"/>
-          <has_line_matching expression=".*species .*" n="8"/>
-        </assert_contents>
-      </output>
-    </test>
-    <test>
-      <param name="in" value="toy_model.tsv"/>
-      <param name="rp" value="true"/>
-      <param name="mp" value="true"/>
-      <param name="e" value="_e"/>
-      <param name="createCompartment" value="true"/>
-      <output ftype="sbml" name="sbml">
-        <assert_contents>
-          <is_valid_xml/>
-          <has_line_matching expression=".*boundaryCondition=.true.*" n="3"/>
-          <has_line_matching expression=".*id=.M_A_ext_e.*" n="1"/>
-          <has_line_matching expression=".*id=.R_reac2.*" n="1"/>
-        </assert_contents>
-      </output>
-    </test>
-    <test>
-      <param name="in" value="toy_model.tsv"/>
-      <param name="id" value="myModel"/>
-      <output ftype="sbml" name="sbml">
-        <assert_contents>
-          <is_valid_xml/>
-          <has_line_matching expression=".*myModel.*" n="1"/>
-        </assert_contents>
-      </output>
-    </test>
-  </tests>
+  <tests/>
   <help><![CDATA[Create a Sbml File from a tabulated file that contains the reaction ids and the formulas
 @ATTRIBUTION@]]></help>
   <citations/>
diff -r 1c1ec9e0ea14 -r fb6f80555393 macros.xml
--- a/macros.xml	Fri Nov 21 10:24:12 2025 +0000
+++ b/macros.xml	Wed Jan 21 15:33:33 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**