Mercurial > repos > metexplore > met4j

annotate tools/networkAnalysis/SeedsAndTargets/SeedsAndTargets.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_SeedsAndTargets" name="SeedsAndTargets" version="2.0.0">
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3 <description>Identify exogenously acquired compounds, exogenously available producible compounds and/or dead ends metabolites from metabolic network topology</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 networkAnalysis.SeedsAndTargets -i "$inputPath"
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11 #if str($inputSide) != 'None':
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12 -sc "$inputSide"
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13 #end if
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14 #if str($comp):
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15 -c "$comp"
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16 #end if
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17 $source
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18 $sink
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19 $notsource
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20 $notsink
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21 $keepIsolated
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22 $useBorensteinAlg
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23 $useInternal
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24 -o "$outputPath"
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25 ]]></command>
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26 <inputs>
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27 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
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28 <param argument="-sc" format="txt" label="input side compound file" name="inputSide" optional="true" type="data" value=""/>
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29 <param argument="-c" label="selected compartment(s), as model identifiers, separated by &quot;+&quot; sign if more than one" name="comp" optional="true" type="text" value="">
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30 <sanitizer invalid_char="_">
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31 <valid initial="string.printable"/>
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32 </sanitizer>
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33 </param>
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34 <param argument="-s" checked="false" falsevalue="" label="export seeds" name="source" truevalue="-s" type="boolean" value="false"/>
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35 <param argument="-t" checked="false" falsevalue="" label="export targets" name="sink" truevalue="-t" type="boolean" value="false"/>
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36 <param argument="-!s" checked="false" falsevalue="" label="export nodes that are not seeds" name="notsource" truevalue="-!s" type="boolean" value="false"/>
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37 <param argument="-!t" checked="false" falsevalue="" label="export nodes that are not targets" name="notsink" truevalue="-!t" type="boolean" value="false"/>
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38 <param argument="-is" checked="false" falsevalue="" label="do not ignore isolated nodes, consider isolated both seeds and targets" name="keepIsolated" truevalue="-is" type="boolean" value="false"/>
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39 <param argument="-B" checked="false" falsevalue="" label="use Borenstein Algorithm. Please cite Borenstein et al. 2008 Large-scale reconstruction and phylogenetic analysis of metabolic environments https://doi.org/10.1073/pnas.0806162105), ignore internal option" name="useBorensteinAlg" truevalue="-B" type="boolean" value="false"/>
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40 <param argument="-in" checked="false" falsevalue="" label="if an external compartment is defined, adjust degree by considering internal counterpart" name="useInternal" truevalue="-in" type="boolean" value="false"/>
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41 </inputs>
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42 <outputs>
5
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43 <data format="tsv" name="outputPath"/>
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44 </outputs>
5
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45 <tests>
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46 <test>
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47 <param name="inputPath" value="XF_network.sbml"/>
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48 <param name="source" value="true"/>
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49 <output ftype="tsv" name="outputPath">
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50 <assert_contents>
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51 <has_n_columns n="1"/>
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52 <has_n_lines n="109"/>
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53 <has_line_matching expression="M_\S+_\w" n="109"/>
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54 </assert_contents>
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55 </output>
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56 </test>
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57 <test>
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58 <param name="inputPath" value="XF_network.sbml"/>
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59 <param name="sink" value="true"/>
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60 <param name="useInternal" value="true"/>
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61 <param name="comp" value="e"/>
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62 <output ftype="tsv" name="outputPath">
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63 <assert_contents>
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64 <has_n_columns n="1"/>
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65 <has_n_lines n="5"/>
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66 <has_line_matching expression="^M_\S+_\w" n="5"/>
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67 </assert_contents>
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68 </output>
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69 </test>
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70 <test>
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71 <param name="inputPath" value="XF_network.sbml"/>
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72 <param name="sink" value="true"/>
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73 <param name="useBorensteinAlg" value="true"/>
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74 <param name="comp" value="e"/>
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75 <output ftype="tsv" name="outputPath">
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76 <assert_contents>
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77 <has_n_columns n="1"/>
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78 <has_n_lines n="26"/>
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79 <has_line_matching expression="^M_\S+_\w" n="26"/>
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80 </assert_contents>
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81 </output>
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82 </test>
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83 </tests>
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84 <help><![CDATA[Identify exogenously acquired compounds, exogenously available producible compounds and/or dead ends metabolites from metabolic network topology
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85 Metabolic seeds and targets are useful for identifying medium requirements and metabolic capability, and thus enable analysis of metabolic ties within communities of organisms.
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86 This application can use seed definition and SCC-based detection algorithm by Borenstein et al. or, alternatively, degree-based sink and source detection with compartment adjustment.
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87 The first method (see Borenstein et al. 2008 Large-scale reconstruction and phylogenetic analysis of metabolic environments https://doi.org/10.1073/pnas.0806162105) consider strongly connected components rather than individual nodes, thus, members of cycles can be considered as seeds. A sink from an external compartment can however be connected to a non sink internal counterpart, thus highlighting what could end up in the external compartment rather than what must be exported.
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88 The second approach is neighborhood based and identify sources and sinks. Since "real" sinks and sources in intracellular compartment(s) may be involved in transport/exchange reactions reversible by default, thus not allowing extracellular source or sink, an option allows to take the degree (minus extracellular neighbors) of intracellular counterparts.]]></help>
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89 <citations>
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90 <citation type="doi">10.1073/pnas.0806162105</citation>
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91 </citations>
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92 </tool>