--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SetNames.xml	Thu Mar 13 15:51:56 2025 +0000
@@ -0,0 +1,116 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<tool id="met4j_SetNames" name="SetNames" version="@TOOL_VERSION@">
+  <description>Set names to network objects in a SBML file from a tabulated file containing the object ids and the names</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="bio_tools"/>
+  <expand macro="requirements"/>
+  <command detect_errors="exit_code"><![CDATA[met4j fr.inrae.toulouse.metexplore.met4j_toolbox.attributes.SetNames#if str($colname) != 'nan':
+ -cname "$colname"
+#end if
+#if str($colid):
+ -ci "$colid"
+#end if
+ $p
+ $s
+#if str($o):
+ -t "$o"
+#end if
+#if str($nSkip):
+ -n "$nSkip"
+#end if
+ -i "$sbml"
+#if str($tab) != 'None':
+ -tab "$tab"
+#end if
+#if str($c):
+ -c "$c"
+#end if
+ -o "$out"
+]]></command>
+  <inputs>
+    <param argument="-cname" label="[2] number of the column where are the names" name="colname" optional="true" type="integer" value="2"/>
+    <param argument="-ci" label="[1] number of the column where are the object ids" name="colid" optional="true" type="text" value="1">
+      <sanitizer invalid_char="_">
+        <valid initial="string.printable"/>
+      </sanitizer>
+    </param>
+    <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix R_ to reactions and M_ to metabolites" name="p" truevalue="-p" type="boolean" value="false"/>
+    <param argument="-s" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the suffix _comparmentID to metabolites" name="s" truevalue="-s" type="boolean" value="false"/>
+    <param argument="-t" label="[REACTION] Object type in the column id : REACTION;METABOLITE;GENE;PATHWAY" name="o" optional="true" type="text" value="REACTION">
+      <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="text" value="0">
+      <sanitizer invalid_char="_">
+        <valid initial="string.printable"/>
+      </sanitizer>
+    </param>
+    <param argument="-i" format="sbml" label="Original SBML file" name="sbml" optional="false" type="data" value=""/>
+    <param argument="-tab" format="tsv" label="Input Tabulated file" name="tab" optional="true" type="data" value=""/>
+    <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won't be read" name="c" optional="true" type="text" value="#">
+      <sanitizer invalid_char="_">
+        <valid initial="string.printable"/>
+      </sanitizer>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="sbml" name="out"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="sbml" value="toy_model.xml"/>
+      <param name="tab" value="namesMetabolites.tsv"/>
+      <param name="o" value="METABOLITE"/>
+      <output ftype="sbml" name="out">
+        <assert_contents>
+          <is_valid_xml/>
+          <has_line_matching expression=".*metaboliteA.*" n="1"/>
+          <has_line_matching expression=".*metaboliteB.*" n="1"/>
+        </assert_contents>
+      </output>
+    </test>
+    <test>
+      <param name="sbml" value="toy_model.xml"/>
+      <param name="tab" value="namesReactions.tsv"/>
+      <output ftype="sbml" name="out">
+        <assert_contents>
+          <is_valid_xml/>
+          <has_line_matching expression=".*reaction1.*" n="1"/>
+          <has_line_matching expression=".*reaction2.*" n="1"/>
+        </assert_contents>
+      </output>
+    </test>
+    <test>
+      <param name="sbml" value="XF_network.sbml"/>
+      <param name="tab" value="namesPathways.tsv"/>
+      <param name="o" value="PATHWAY"/>
+      <output ftype="sbml" name="out">
+        <assert_contents>
+          <is_valid_xml/>
+          <has_line_matching expression=".*groups:name=.CEB.*" n="1"/>
+          <has_line_matching expression=".*groups:name=.NSP.*" n="1"/>
+        </assert_contents>
+      </output>
+    </test>
+    <test>
+      <param name="sbml" value="XF_network.sbml"/>
+      <param name="tab" value="namesGenes.tsv"/>
+      <param name="o" value="GENE"/>
+      <output ftype="sbml" name="out">
+        <assert_contents>
+          <is_valid_xml/>
+          <has_line_matching expression=".*fbc:name=.G1.*" n="1"/>
+          <has_line_matching expression=".*fbc:name=.G2.*" n="1"/>
+        </assert_contents>
+      </output>
+    </test>
+  </tests>
+  <help><![CDATA[Set names to network objects in a SBML file from a tabulated file containing the object ids and the names
+The ids must correspond between the tabulated file and the SBML file.
+If prefix or suffix is different in the SBML file, use the -p or the -s options.
+@ATTRIBUTION@]]></help>
+  <citations/>
+</tool>