Mercurial > repos > metexplore > met4j

annotate tools/attributes/SetReferences/SetReferences.xml @ 11:40c15b7467f1 draft default tip

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 61dbdbae896d18b519a470e056cb8b4f98394518
author metexplore
date Thu, 13 Feb 2025 15:08:22 +0000
parents 6a112eaf8f38
children
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_SetReferences" name="SetReferences" version="2.0.1">
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3 <description>Add references to network objects in a SBML file from a tabulated file containing the metabolite ids and the references</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:2.0.1</container>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetReferences#if str($colRef) != 'nan':
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11 -cr "$colRef"
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12 #end if
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13 -ref "$ref"
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14 #if str($colid):
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15 -ci "$colid"
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16 #end if
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17 $p
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18 $s
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19 #if str($o):
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20 -t "$o"
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21 #end if
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22 #if str($nSkip):
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23 -n "$nSkip"
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24 #end if
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25 -i "$sbml"
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26 #if str($tab) != 'None':
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27 -tab "$tab"
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28 #end if
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29 #if str($c):
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30 -c "$c"
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31 #end if
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32 -o "$out"
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33 ]]></command>
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34 <inputs>
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35 <param argument="-cr" label="[2] number of the column where are the references" name="colRef" optional="true" type="integer" value="2"/>
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36 <param argument="-ref" label="Name of the reference. Must exist in identifiers.org (https://registry.identifiers.org/registry)" name="ref" optional="false" type="text" value="">
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37 <sanitizer invalid_char="_">
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38 <valid initial="string.printable"/>
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39 </sanitizer>
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40 </param>
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41 <param argument="-ci" label="[1] number of the column where are the object ids" name="colid" optional="true" type="text" value="1">
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42 <sanitizer invalid_char="_">
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43 <valid initial="string.printable"/>
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44 </sanitizer>
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45 </param>
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46 <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix R_ to reactions and M_ to metabolites" name="p" truevalue="-p" type="boolean" value="false"/>
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47 <param argument="-s" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the suffix _comparmentID to metabolites" name="s" truevalue="-s" type="boolean" value="false"/>
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48 <param argument="-t" label="[REACTION] Object type in the column id : REACTION;METABOLITE;GENE;PATHWAY" name="o" optional="true" type="text" value="REACTION">
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49 <sanitizer invalid_char="_">
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50 <valid initial="string.printable"/>
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51 </sanitizer>
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52 </param>
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53 <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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54 <sanitizer invalid_char="_">
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55 <valid initial="string.printable"/>
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56 </sanitizer>
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57 </param>
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58 <param argument="-i" format="sbml" label="Original SBML file" name="sbml" optional="false" type="data" value=""/>
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59 <param argument="-tab" format="tsv" label="Input Tabulated file" name="tab" optional="true" type="data" value=""/>
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60 <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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61 <sanitizer invalid_char="_">
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62 <valid initial="string.printable"/>
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63 </sanitizer>
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64 </param>
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65 </inputs>
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66 <outputs>
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67 <data format="sbml" name="out"/>
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68 </outputs>
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69 <tests>
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70 <test>
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71
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72 <param name="sbml" value="toy_model.xml"/>
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74 <param name="tab" value="refs.tsv"/>
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75
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76 <param name="ref" value="InChi"/>
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77
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78 <param name="o" value="METABOLITE"/>
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79
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80 <output ftype="sbml" name="out">
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81
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82 <assert_contents>
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83
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84 <is_valid_xml/>
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85
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86 <has_line_matching expression=".*C2H6O.*" n="3"/>
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87
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88 <has_line_matching expression=".*C6H8O6.*" n="1"/>
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89
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90 </assert_contents>
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92 </output>
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93
9
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94 </test>
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95 </tests>
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96 <help><![CDATA[Add references to network objects in a SBML file from a tabulated file containing the metabolite ids and the references
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97 Reference name given as parameter (-ref) must correspond to an existing id in the registry of identifiers.org (https://registry.identifiers.org/registry)
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98 The corresponding key:value pair will be written as metabolite or reaction MIRIAM annotation (see https://pubmed.ncbi.nlm.nih.gov/16333295/)]]></help>
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99 <citations>
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100 <citation type="doi">10.1038/nbt1156</citation>
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101 </citations>
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102 </tool>