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annotate build/tools/SetGprs/SetGprs.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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
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2 <tool id="met4j_SetGprs" name="SetGprs" version="2.0.0">
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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:2.0.0</container>
9
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetGprs#if str($colgpr) != 'nan':
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11 -cgpr "$colgpr"
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12 #end if
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13 #if str($colid) != 'nan':
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14 -ci "$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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18 -n "$nSkip"
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19 #end if
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20 -i "$sbml"
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21 #if str($tab) != 'None':
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22 -tab "$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 -o "$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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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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35 <valid initial="string.printable"/>
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36 </sanitizer>
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37 </param>
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38 <param argument="-i" format="sbml" label="Original SBML file" name="sbml" optional="false" type="data" value=""/>
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39 <param argument="-tab" format="tsv" label="Input Tabulated file" name="tab" optional="true" type="data" value=""/>
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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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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 </inputs>
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46 <outputs>
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47 <data format="sbml" name="out"/>
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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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52 <param name="tab" value="gpr.tsv"/>
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53 <output ftype="sbml" name="out">
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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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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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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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61 <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G2.*" n="1"/>
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62 <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G3.*" n="1"/>
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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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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 html notes (GENE_ASSOCIATION: ( XC_0401 ) OR ( XC_3282 ))
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75 - as fbc gene product association (see FBC package specifications: https://doi.org/10.1515/jib-2017-0082)]]></help>
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76 <citations>
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77 <citation type="doi">10.1038/nprot.2011.308</citation>
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78 <citation type="doi">10.1515/jib-2017-0082</citation>
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79 </citations>
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80 </tool>