Mercurial > repos > metexplore > met4j
annotate build/tools/SbmlSetGprsFromFile/SbmlSetGprsFromFile.xml @ 6:7a6f2380fc1d draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
author | metexplore |
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date | Wed, 17 May 2023 13:26:37 +0000 |
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children | 1436e9cde9c9 |
rev | line source |
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6
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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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1 <?xml version="1.0" encoding="UTF-8"?> |
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2 <tool id="met4j_SbmlSetGprsFromFile" name="SbmlSetGprsFromFile" version="1.3.0"> |
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3 <description>Create a new SBML file from an original sbml file and a tabulated file containing reaction ids and Gene association written in a cobra way</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:1.3.0</container> |
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9 </requirements> |
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10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetGprsFromFile#if str($colgpr) != 'nan': |
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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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11 -cgpr "$colgpr" |
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12 #end if |
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13 #if str($colid) != 'nan': |
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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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14 -ci "$colid" |
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15 #end if |
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16 $p |
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17 #if str($nSkip): |
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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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18 -n "$nSkip" |
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19 #end if |
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20 -sbml "$sbml" |
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21 #if str($tab) != 'None': |
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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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22 -tab "$tab" |
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23 #end if |
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24 #if str($c): |
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25 -c "$c" |
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26 #end if |
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27 -out "$out" |
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28 ]]></command> |
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29 <inputs> |
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30 <param argument="-cgpr" label="[2] number of the column where are the gprs" name="colgpr" optional="true" type="integer" value="2"/> |
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31 <param argument="-ci" label="[1] number of the column where are the reaction ids" name="colid" optional="true" type="integer" value="1"/> |
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32 <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix R_ to reactions" name="p" truevalue="-p" type="boolean" value="false"/> |
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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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33 <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0"> |
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34 <sanitizer invalid_char="_"> |
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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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35 <valid initial="string.printable"/> |
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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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36 </sanitizer> |
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37 </param> |
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38 <param argument="-sbml" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/> |
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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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39 <param argument="-tab" format="tsv" label="Tabulated file" name="tab" optional="true" type="data" value=""/> |
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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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40 <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won't be read" name="c" optional="true" type="text" value="#"> |
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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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41 <sanitizer invalid_char="_"> |
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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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42 <valid initial="string.printable"/> |
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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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43 </sanitizer> |
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44 </param> |
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45 </inputs> |
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46 <outputs> |
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47 <data format="sbml" name="out"/> |
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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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48 </outputs> |
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49 <tests> |
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50 <test> |
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51 <param name="sbml" value="toy_model.xml"/> |
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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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52 <param name="tab" value="gpr.tsv"/> |
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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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53 <output ftype="sbml" name="out"> |
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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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54 <assert_contents> |
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55 <is_valid_xml/> |
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56 <has_line_matching expression=".*fbc:id=.G1.*" n="1"/> |
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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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57 <has_line_matching expression=".*fbc:id=.G2.*" n="1"/> |
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58 <has_line_matching expression=".*fbc:id=.G3.*" n="1"/> |
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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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59 <has_line_matching expression=".*fbc:id=.G4.*" n="1"/> |
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60 <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G1.*" n="1"/> |
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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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61 <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G2.*" n="1"/> |
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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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62 <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G3.*" n="1"/> |
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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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63 <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G4.*" n="1"/> |
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64 <has_line_matching expression=".*fbc:and.*" n="2"/> |
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65 </assert_contents> |
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66 </output> |
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67 </test> |
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68 </tests> |
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69 <help><![CDATA[Create a new SBML file from an original sbml file and a tabulated file containing reaction ids and Gene association written in a cobra way |
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70 The ids must correspond between the tabulated file and the SBML file. |
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71 If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option. |
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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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72 GPR must be written in a cobra way in the tabulated file as described in Schellenberger et al 2011 Nature Protocols 6(9):1290-307 |
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73 (The GPR will be written in the SBML file in two locations: |
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74 - in the reaction notes <p>GENE_ASSOCIATION: ( XC_0401 ) OR ( XC_3282 )</p> |
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75 - as fbc gene product association :<fbc:geneProductAssociation> |
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76 <fbc:or> |
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77 <fbc:geneProductRef fbc:geneProduct="XC_3282"/> |
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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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78 <fbc:geneProductRef fbc:geneProduct="XC_0401"/> |
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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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79 </fbc:or> |
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80 </fbc:geneProductAssociation> |
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81 ]]></help> |
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82 <citations/> |
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83 </tool> |