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comparison build/tools/CreateMetaNetwork/CreateMetaNetwork.xml @ 11:40c15b7467f1 draft default tip

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 61dbdbae896d18b519a470e056cb8b4f98394518
author metexplore
date Thu, 13 Feb 2025 15:08:22 +0000
parents 6a112eaf8f38
children
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10:6a112eaf8f38 11:40c15b7467f1
1 <?xml version="1.0" encoding="UTF-8" standalone="no"?> 1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <tool id="met4j_CreateMetaNetwork" name="CreateMetaNetwork" version="2.0.0"> 2 <tool id="met4j_CreateMetaNetwork" name="CreateMetaNetwork" version="2.0.1">
3 <description>Create a Meta-Network from two sub-networks in SBML format.</description> 3 <description>Create a Meta-Network from two sub-networks in SBML format.</description>
4 <xrefs> 4 <xrefs>
5 <xref type="bio.tools">met4j</xref> 5 <xref type="bio.tools">met4j</xref>
6 </xrefs> 6 </xrefs>
7 <requirements> 7 <requirements>
8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh reconstruction.CreateMetaNetwork -n1 "$sbml1FilePath" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh reconstruction.CreateMetaNetwork -n1 "$sbml1FilePath"
11 -n2 "$sbml2FilePath" 11 -n2 "$sbml2FilePath"
12 -n1ex "$external1" 12 -n1ex "$external1"
13 -n2ex "$external2" 13 -n2ex "$external2"
58 <outputs> 58 <outputs>
59 <data format="sbml" name="outputPath"/> 59 <data format="sbml" name="outputPath"/>
60 </outputs> 60 </outputs>
61 <tests> 61 <tests>
62 <test> 62 <test>
63
63 <param name="sbml1FilePath" value="Human-GEM_pathways.xml"/> 64 <param name="sbml1FilePath" value="Human-GEM_pathways.xml"/>
65
64 <param name="sbml2FilePath" value="ECOL.xml"/> 66 <param name="sbml2FilePath" value="ECOL.xml"/>
67
65 <param name="external1" value="s"/> 68 <param name="external1" value="s"/>
69
66 <param name="external2" value="e"/> 70 <param name="external2" value="e"/>
71
67 <param name="n1prefix" value="hsa"/> 72 <param name="n1prefix" value="hsa"/>
73
68 <param name="n2prefix" value="eco"/> 74 <param name="n2prefix" value="eco"/>
75
69 <param name="mergingCriterion" value="by_metanetx"/> 76 <param name="mergingCriterion" value="by_metanetx"/>
77
70 <output ftype="sbml" name="outputPath"> 78 <output ftype="sbml" name="outputPath">
79
71 <assert_contents> 80 <assert_contents>
81
72 <has_text text="&lt;/sbml&gt;"/> 82 <has_text text="&lt;/sbml&gt;"/>
83
73 </assert_contents> 84 </assert_contents>
85
74 </output> 86 </output>
87
75 </test> 88 </test>
76 </tests> 89 </tests>
77 <help><![CDATA[Create a Meta-Network from two sub-networks in SBML format. 90 <help><![CDATA[Create a Meta-Network from two sub-networks in SBML format.
78 A meta-network is a single model which contains several sub-networks that remains individualized within the meta-network (as opposed to model fusion), but which can share some of their components with other sub-networks through a shared "medium" compartment.]]></help> 91 A meta-network is a single model which contains several sub-networks that remains individualized within the meta-network (as opposed to model fusion), but which can share some of their components with other sub-networks through a shared "medium" compartment.]]></help>
79 <citations/> 92 <citations/>