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comparison build/tools/CreateMetaNetwork/CreateMetaNetwork.xml @ 10:6a112eaf8f38 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 71071300dd662ad01bd064abcf6866a192eeea95
author metexplore
date Mon, 03 Feb 2025 15:59:46 +0000
parents 0976a6257300
children 40c15b7467f1
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9:0976a6257300 10:6a112eaf8f38
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="develop"> 2 <tool id="met4j_CreateMetaNetwork" name="CreateMetaNetwork" version="2.0.0">
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:develop</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</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>
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73 <param name="sbml1FilePath" value="Human-GEM_pathways.xml"/> 63 <param name="sbml1FilePath" value="Human-GEM_pathways.xml"/>
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84 <param name="sbml2FilePath" value="ECOL.xml"/> 64 <param name="sbml2FilePath" value="ECOL.xml"/>
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95 <param name="external1" value="s"/> 65 <param name="external1" value="s"/>
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106 <param name="external2" value="e"/> 66 <param name="external2" value="e"/>
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117 <param name="n1prefix" value="hsa"/> 67 <param name="n1prefix" value="hsa"/>
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128 <param name="n2prefix" value="eco"/> 68 <param name="n2prefix" value="eco"/>
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139 <param name="mergingCriterion" value="by_metanetx"/> 69 <param name="mergingCriterion" value="by_metanetx"/>
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150 <output ftype="sbml" name="outputPath"> 70 <output ftype="sbml" name="outputPath">
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161 <assert_contents> 71 <assert_contents>
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172 <has_text text="&lt;/sbml&gt;"/> 72 <has_text text="&lt;/sbml&gt;"/>
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183 </assert_contents> 73 </assert_contents>
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194 </output> 74 </output>
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205 </test> 75 </test>
206 </tests> 76 </tests>
207 <help><![CDATA[Create a Meta-Network from two sub-networks in SBML format. 77 <help><![CDATA[Create a Meta-Network from two sub-networks in SBML format.
208 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> 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>
209 <citations/> 79 <citations/>