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annotate tools/networkAnalysis/SeedsAndTargets/SeedsAndTargets.xml @ 5:35c9abcd8934 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
author metexplore
date Thu, 12 Jan 2023 13:45:13 +0000
parents ae4c301919c4
children 7a6f2380fc1d
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="met4j_SeedsAndTargets" name="SeedsAndTargets" version="1.2.1">
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3 <description>Identify exogenously acquired compounds, producible compounds exogenously available 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:1.2.1</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 seed" 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 seed and target" 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"/>
4
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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="targetsFilePath" value="SeedsAndTargets-result.tab"/>
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49 <param name="source" value="true"/>
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50 <output ftype="tsv" name="outputPath">
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51 <assert_contents>
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52 <has_n_columns n="1"/>
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53 <has_n_lines n="109"/>
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54 <has_line_matching expression="M_\S+_\w" n="109"/>
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55 </assert_contents>
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56 </output>
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57 </test>
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58 <test>
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59 <param name="inputPath" value="XF_network.sbml"/>
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60 <param name="targetsFilePath" value="SeedsAndTargets-result.tab"/>
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61 <param name="sink" value="true"/>
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62 <param name="useInternal" value="true"/>
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63 <param name="comp" value="e"/>
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64 <output ftype="tsv" name="outputPath">
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65 <assert_contents>
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66 <has_n_columns n="1"/>
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67 <has_n_lines n="5"/>
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68 <has_line_matching expression="^M_\S+_\w" n="5"/>
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69 </assert_contents>
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70 </output>
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71 </test>
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72 <test>
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73 <param name="inputPath" value="XF_network.sbml"/>
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74 <param name="targetsFilePath" value="SeedsAndTargets-result.tab"/>
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75 <param name="sink" value="true"/>
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76 <param name="useBorensteinAlg" value="true"/>
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77 <param name="comp" value="e"/>
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78 <output ftype="tsv" name="outputPath">
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79 <assert_contents>
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80 <has_n_columns n="1"/>
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81 <has_n_lines n="26"/>
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82 <has_line_matching expression="^M_\S+_\w" n="26"/>
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83 </assert_contents>
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84 </output>
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85 </test>
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86 </tests>
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87 <help><![CDATA[Identify exogenously acquired compounds, producible compounds exogenously available and/or dead ends metabolites from metabolic network topology. Metabolic seeds and targets are useful for identifying medium requirements and metabolic capability, and thus enable analysis of metabolic ties within communities of organisms.
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
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88 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.
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
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89 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 seed. 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.
ae4c301919c4 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
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90 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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91 <citations/>
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92 </tool>