diff build/tools/ChokePoint/ChokePoint.xml @ 9:0976a6257300 draft

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

--- a/build/tools/ChokePoint/ChokePoint.xml	Wed Jul 26 15:33:45 2023 +0000
+++ b/build/tools/ChokePoint/ChokePoint.xml	Fri Jan 31 18:28:53 2025 +0000
@@ -1,11 +1,11 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_ChokePoint" name="ChokePoint" version="1.5.0">
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<tool id="met4j_ChokePoint" name="ChokePoint" version="develop">
   <description>Compute the Choke points of a metabolic network.</description>
   <xrefs>
     <xref type="bio.tools">met4j</xref>
   </xrefs>
   <requirements>
-    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.5.0</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 networkAnalysis.ChokePoint -i "$inputPath"
  -o "$outputPath"
@@ -18,19 +18,130 @@
   </outputs>
   <tests>
     <test>
-			<param name="inputPath" value="XF_network.sbml"/>
-			<output ftype="tsv" name="outputPath">
-				<assert_contents>
-					<has_n_lines n="695"/>
-					<has_n_columns n="3"/>
-					<has_line_matching expression="R_ADEtex.*adenine_transport_via_diffusion__extracellular_to_periplasm_.*M_ade_e &lt;==&gt; M_ade_p" n="1"/>
-					<has_line_matching expression="R_AGDC_r.*R_AGDC_r.*M_acgam6p_c \+ M_h2o_c --&gt; M_ac_c \+ M_gam6p_c" n="1"/>
-				</assert_contents>
-			</output>
-		</test>
+                                                                  			
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      <param name="inputPath" value="XF_network.sbml"/>
+                                                                  			
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      <output ftype="tsv" name="outputPath">
+                                                                                        				
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        <assert_contents>
+                                                                                                              					
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          <has_n_lines n="695"/>
+                                                                                                              					
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          <has_n_columns n="3"/>
+                                                                                                              					
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          <has_line_matching expression="R_ADEtex.*adenine_transport_via_diffusion__extracellular_to_periplasm_.*M_ade_e &lt;==&gt; M_ade_p" n="1"/>
+                                                                                                              					
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          <has_line_matching expression="R_AGDC_r.*R_AGDC_r.*M_acgam6p_c \+ M_h2o_c --&gt; M_ac_c \+ M_gam6p_c" n="1"/>
+                                                                                                              				
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        </assert_contents>
+                                                                                        			
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      </output>
+                                                                  		
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    </test>
   </tests>
   <help><![CDATA[Compute the Choke points of a metabolic network.
-Choke points constitute an indicator of lethality and can help identifying drug target Choke points are reactions that are required to consume or produce one compound. Targeting of choke point can lead to the accumulation or the loss of some metabolites, thus choke points constitute an indicator of lethality and can help identifying drug target 
-See : Syed Asad Rahman, Dietmar Schomburg; Observing local and global properties of metabolic pathways: ‘load points’ and ‘choke points’ in the metabolic networks. Bioinformatics 2006; 22 (14): 1767-1774. doi: 10.1093/bioinformatics/btl181]]></help>
-  <citations/>
+Choke points are reactions that are required to consume or produce one compound. Targeting of choke point can lead to the accumulation or the loss of some metabolites, thus choke points constitute an indicator of lethality and can help identifying drug target.]]></help>
+  <citations>
+    <citation type="doi">10.1093/bioinformatics/btl181</citation>
+  </citations>
 </tool>