diff tools/convert/Tab2Sbml/Tab2Sbml.xml @ 9:0976a6257300 draft

planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273

--- a/tools/convert/Tab2Sbml/Tab2Sbml.xml	Wed Jul 26 15:33:45 2023 +0000
+++ b/tools/convert/Tab2Sbml/Tab2Sbml.xml	Fri Jan 31 18:28:53 2025 +0000
@@ -1,11 +1,11 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_Tab2Sbml" name="Tab2Sbml" version="MET4J_VERSION_TEST">
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<tool id="met4j_Tab2Sbml" name="Tab2Sbml" version="develop">
   <description>Create a Sbml File from a tabulated file that contains the reaction ids and the formulas</description>
   <xrefs>
     <xref type="bio.tools">met4j</xref>
   </xrefs>
   <requirements>
-    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:MET4J_VERSION_TEST</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Tab2Sbml#if str($colid) != 'nan':
  -ci "$colid"
@@ -19,12 +19,12 @@
  -e "$e"
 #end if
 #if str($i):
- -i "$i"
+ -irr "$i"
 #end if
 #if str($r):
- -r "$r"
+ -rev "$r"
 #end if
- -in "$in"
+ -i "$in"
 #if str($id):
  -id "$id"
 #end if
@@ -35,7 +35,7 @@
 #if str($nSkip) != 'nan':
  -n "$nSkip"
 #end if
- -sbml "$sbml"
+ -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"/>
@@ -47,17 +47,17 @@
         <valid initial="string.printable"/>
       </sanitizer>
     </param>
-    <param argument="-i" label="[--&gt;] String for irreversible reaction" name="i" optional="true" type="text" value="--&gt;">
+    <param argument="-irr" label="[--&gt;] String for irreversible reaction" name="i" optional="true" type="text" value="--&gt;">
       <sanitizer invalid_char="_">
         <valid initial="string.printable"/>
       </sanitizer>
     </param>
-    <param argument="-r" label="[&lt;==&gt;] String for reversible reaction" name="r" optional="true" type="text" value="&lt;==&gt;">
+    <param argument="-rev" label="[&lt;==&gt;] String for reversible reaction" name="r" optional="true" type="text" value="&lt;==&gt;">
       <sanitizer invalid_char="_">
         <valid initial="string.printable"/>
       </sanitizer>
     </param>
-    <param argument="-in" format="tsv" label="Tabulated file" name="in" optional="false" type="data" value=""/>
+    <param argument="-i" format="tsv" label="Tabulated file" name="in" optional="false" type="data" value=""/>
     <param argument="-id" label="[NA] Model id written in the SBML file" name="id" optional="true" type="text" value="NA">
       <sanitizer invalid_char="_">
         <valid initial="string.printable"/>
@@ -76,63 +76,657 @@
   </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>
   <help><![CDATA[Create a Sbml File from a tabulated file that contains the reaction ids and the formulas]]></help>