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comparison build/tools/CreateMetaNetwork/CreateMetaNetwork.xml @ 9:0976a6257300 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
author metexplore
date Fri, 31 Jan 2025 18:28:53 +0000
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children 6a112eaf8f38
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8:1274e2a62479 9:0976a6257300
1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <tool id="met4j_CreateMetaNetwork" name="CreateMetaNetwork" version="develop">
3 <description>Create a Meta-Network from two sub-networks in SBML format.</description>
4 <xrefs>
5 <xref type="bio.tools">met4j</xref>
6 </xrefs>
7 <requirements>
8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh reconstruction.CreateMetaNetwork -n1 "$sbml1FilePath"
11 -n2 "$sbml2FilePath"
12 -n1ex "$external1"
13 -n2ex "$external2"
14 #if str($n1prefix):
15 -n1px "$n1prefix"
16 #end if
17 #if str($n2prefix):
18 -n2px "$n2prefix"
19 #end if
20 $keepCompartment
21 $firstIsMeta
22 #if str($mergingCriterion):
23 -mc "$mergingCriterion"
24 #end if
25 -o "$outputPath"
26 ]]></command>
27 <inputs>
28 <param argument="-n1" format="sbml" label="input SBML file: path to first network, in sbml format." name="sbml1FilePath" optional="false" type="data" value=""/>
29 <param argument="-n2" format="" label="input SBML file: path to second network, in sbml format." name="sbml2FilePath" optional="false" type="data" value=""/>
30 <param argument="-n1ex" label="external compartment identifier in first network." name="external1" optional="false" type="text" value="">
31 <sanitizer invalid_char="_">
32 <valid initial="string.printable"/>
33 </sanitizer>
34 </param>
35 <param argument="-n2ex" label="external compartment identifier in second network." name="external2" optional="false" type="text" value="">
36 <sanitizer invalid_char="_">
37 <valid initial="string.printable"/>
38 </sanitizer>
39 </param>
40 <param argument="-n1px" label="prefix that will be added to first network's entities identifiers" name="n1prefix" optional="true" type="text" value="Net1_">
41 <sanitizer invalid_char="_">
42 <valid initial="string.printable"/>
43 </sanitizer>
44 </param>
45 <param argument="-n2px" label="prefix that will be added to second network's entities identifiers" name="n2prefix" optional="true" type="text" value="Net2_">
46 <sanitizer invalid_char="_">
47 <valid initial="string.printable"/>
48 </sanitizer>
49 </param>
50 <param argument="-k" checked="false" falsevalue="" label="keep the original external compartments in the meta-network, otherwise, they will be fused into the new shared external compartment" name="keepCompartment" truevalue="-k" type="boolean" value="false"/>
51 <param argument="-n1meta" checked="false" falsevalue="" label="treat first network as meta-network, allowing more than two sub-models with iterative fusions. This will overwrite shared compartment and pool compounds (which must follow the &quot;pool_&quot; prefix convention) and will ignore --n1prefix argument" name="firstIsMeta" truevalue="-n1meta" type="boolean" value="false"/>
52 <param argument="-mc" label="field used to identify the same metabolites across the two different networks. &quot;by_name&quot;/&quot;by_id&quot; can be used if names/identifiers are consistent and unambiguous across source models, &quot;by_metanetx&quot; can be used if models contains MetaNetX identifiers in annotation field using standard miriam format." name="mergingCriterion" optional="true" type="select" value="by_name">
53 <option value="by_metanetx">by_metanetx</option>
54 <option selected="true" value="by_name">by_name</option>
55 <option value="by_id">by_id</option>
56 </param>
57 </inputs>
58 <outputs>
59 <data format="sbml" name="outputPath"/>
60 </outputs>
61 <tests>
62 <test>
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73 <param name="sbml1FilePath" value="Human-GEM_pathways.xml"/>
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84 <param name="sbml2FilePath" value="ECOL.xml"/>
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95 <param name="external1" value="s"/>
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106 <param name="external2" value="e"/>
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117 <param name="n1prefix" value="hsa"/>
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128 <param name="n2prefix" value="eco"/>
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139 <param name="mergingCriterion" value="by_metanetx"/>
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150 <output ftype="sbml" name="outputPath">
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161 <assert_contents>
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172 <has_text text="&lt;/sbml&gt;"/>
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183 </assert_contents>
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194 </output>
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205 </test>
206 </tests>
207 <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>
209 <citations/>
210 </tool>