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annotate tools/reconstruction/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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1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
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2 <tool id="met4j_CreateMetaNetwork" name="CreateMetaNetwork" version="2.0.0">
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3 <description>Create a Meta-Network from two sub-networks in SBML format.</description>
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4 <xrefs>
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5 <xref type="bio.tools">met4j</xref>
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6 </xrefs>
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7 <requirements>
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8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh reconstruction.CreateMetaNetwork -n1 "$sbml1FilePath"
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11 -n2 "$sbml2FilePath"
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12 -n1ex "$external1"
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13 -n2ex "$external2"
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14 #if str($n1prefix):
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15 -n1px "$n1prefix"
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16 #end if
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17 #if str($n2prefix):
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18 -n2px "$n2prefix"
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19 #end if
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20 $keepCompartment
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21 $firstIsMeta
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22 #if str($mergingCriterion):
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23 -mc "$mergingCriterion"
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24 #end if
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25 -o "$outputPath"
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26 ]]></command>
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27 <inputs>
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28 <param argument="-n1" format="sbml" label="input SBML file: path to first network, in sbml format." name="sbml1FilePath" optional="false" type="data" value=""/>
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29 <param argument="-n2" format="" label="input SBML file: path to second network, in sbml format." name="sbml2FilePath" optional="false" type="data" value=""/>
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30 <param argument="-n1ex" label="external compartment identifier in first network." name="external1" optional="false" type="text" value="">
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31 <sanitizer invalid_char="_">
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32 <valid initial="string.printable"/>
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33 </sanitizer>
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34 </param>
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35 <param argument="-n2ex" label="external compartment identifier in second network." name="external2" optional="false" type="text" value="">
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36 <sanitizer invalid_char="_">
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37 <valid initial="string.printable"/>
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38 </sanitizer>
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39 </param>
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40 <param argument="-n1px" label="prefix that will be added to first network's entities identifiers" name="n1prefix" optional="true" type="text" value="Net1_">
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41 <sanitizer invalid_char="_">
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42 <valid initial="string.printable"/>
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43 </sanitizer>
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44 </param>
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45 <param argument="-n2px" label="prefix that will be added to second network's entities identifiers" name="n2prefix" optional="true" type="text" value="Net2_">
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46 <sanitizer invalid_char="_">
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47 <valid initial="string.printable"/>
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48 </sanitizer>
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49 </param>
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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"/>
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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"/>
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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">
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53 <option value="by_metanetx">by_metanetx</option>
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54 <option selected="true" value="by_name">by_name</option>
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55 <option value="by_id">by_id</option>
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56 </param>
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57 </inputs>
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58 <outputs>
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59 <data format="sbml" name="outputPath"/>
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60 </outputs>
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61 <tests>
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62 <test>
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63 <param name="sbml1FilePath" value="Human-GEM_pathways.xml"/>
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64 <param name="sbml2FilePath" value="ECOL.xml"/>
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65 <param name="external1" value="s"/>
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66 <param name="external2" value="e"/>
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67 <param name="n1prefix" value="hsa"/>
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68 <param name="n2prefix" value="eco"/>
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69 <param name="mergingCriterion" value="by_metanetx"/>
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70 <output ftype="sbml" name="outputPath">
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71 <assert_contents>
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72 <has_text text="&lt;/sbml&gt;"/>
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73 </assert_contents>
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74 </output>
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75 </test>
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76 </tests>
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77 <help><![CDATA[Create a Meta-Network from two sub-networks in SBML format.
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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>
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79 <citations/>
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80 </tool>