comparison tools/networkAnalysis/ChokePoint/ChokePoint.xml @ 9:0976a6257300 draft

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

8:1274e2a62479

<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_ChokePoint" name="ChokePoint" version="MET4J_VERSION_TEST">
  <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:MET4J_VERSION_TEST</container>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ChokePoint -i "$inputPath"
 -o "$outputPath"
]]></command>
  <inputs>

  <outputs>
    <data format="tsv" name="outputPath"/>
  </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>
  </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/>
</tool>

9:0976a6257300

<?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:develop</container>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ChokePoint -i "$inputPath"
 -o "$outputPath"
]]></command>
  <inputs>

  <outputs>
    <data format="tsv" name="outputPath"/>
  </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>
  </tests>
  <help><![CDATA[Compute the Choke points of a metabolic network.
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>