Mercurial > repos > metexplore > met4j

annotate build/tools/SbmlSetIdsFromFile/SbmlSetIdsFromFile.xml @ 6:7a6f2380fc1d draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
author metexplore
date Wed, 17 May 2023 13:26:37 +0000
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children 1436e9cde9c9
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6
7a6f2380fc1d 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_SbmlSetIdsFromFile" name="SbmlSetIdsFromFile" version="1.3.0">
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3 <description>Set new ids to network objects from a tabulated file containing the old ids and the new ids</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.SbmlSetIdsFromFile#if str($colname) != 'nan':
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11 -cnew "$colname"
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12 #end if
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13 #if str($colid):
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14 -ci "$colid"
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15 #end if
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16 $p
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17 $s
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18 #if str($o):
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19 -o "$o"
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20 #end if
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21 #if str($nSkip):
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22 -n "$nSkip"
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23 #end if
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24 -sbml "$sbml"
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25 #if str($tab) != 'None':
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26 -tab "$tab"
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27 #end if
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28 #if str($c):
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29 -c "$c"
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30 #end if
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31 -out "$out"
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32 ]]></command>
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33 <inputs>
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34 <param argument="-cnew" label="[2] number of the column where are the new ids" name="colname" optional="true" type="integer" value="2"/>
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35 <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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36 <sanitizer invalid_char="_">
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37 <valid initial="string.printable"/>
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38 </sanitizer>
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39 </param>
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40 <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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41 <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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42 <param argument="-o" label="[REACTION] Object type in the column id : REACTION;METABOLITE;GENE;PATHWAY" name="o" optional="true" type="text" value="REACTION">
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43 <sanitizer invalid_char="_">
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44 <valid initial="string.printable"/>
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45 </sanitizer>
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46 </param>
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47 <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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48 <sanitizer invalid_char="_">
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49 <valid initial="string.printable"/>
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50 </sanitizer>
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51 </param>
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52 <param argument="-sbml" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/>
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53 <param argument="-tab" format="tsv" label="Tabulated file" name="tab" optional="true" type="data" value=""/>
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54 <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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55 <sanitizer invalid_char="_">
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56 <valid initial="string.printable"/>
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57 </sanitizer>
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58 </param>
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59 </inputs>
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60 <outputs>
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61 <data format="sbml" name="out"/>
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62 </outputs>
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63 <tests>
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64 <test>
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65 <param name="sbml" value="toy_model.xml"/>
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66 <param name="tab" value="idMetabolites.tsv"/>
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67 <param name="o" value="METABOLITE"/>
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68 <output ftype="sbml" name="out">
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69 <assert_contents>
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70 <is_valid_xml/>
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71 <has_line_matching expression=".*id=.metaboliteA.*" n="1"/>
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72 <has_line_matching expression=".*id=.metaboliteB.*" n="1"/>
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73 </assert_contents>
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74 </output>
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75 </test>
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76 <test>
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77 <param name="sbml" value="toy_model.xml"/>
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78 <param name="tab" value="idReactions.tsv"/>
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79 <output ftype="sbml" name="out">
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80 <assert_contents>
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81 <is_valid_xml/>
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82 <has_line_matching expression=".*id=.reaction1.*" n="1"/>
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83 <has_line_matching expression=".*id=.reaction2.*" n="1"/>
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84 </assert_contents>
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85 </output>
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86 </test>
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87 <test>
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88 <param name="sbml" value="XF_network.sbml"/>
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89 <param name="tab" value="idPathways.tsv"/>
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90 <param name="o" value="PATHWAY"/>
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91 <output ftype="sbml" name="out">
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92 <assert_contents>
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93 <is_valid_xml/>
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94 <has_line_matching expression=".*groups:id=.CEB.*" n="1"/>
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95 <has_line_matching expression=".*groups:id=.NSP.*" n="1"/>
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96 </assert_contents>
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97 </output>
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98 </test>
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99 <test>
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100 <param name="sbml" value="XF_network.sbml"/>
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101 <param name="tab" value="idGenes.tsv"/>
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102 <param name="o" value="GENE"/>
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103 <output ftype="sbml" name="out">
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104 <assert_contents>
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105 <is_valid_xml/>
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106 <has_line_matching expression=".*fbc:id=.G1.*" n="1"/>
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107 <has_line_matching expression=".*fbc:id=.G2.*" n="1"/>
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108 </assert_contents>
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109 </output>
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110 </test>
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111 <test>
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112 <param name="sbml" value="XF_network.sbml"/>
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113 <param name="tab" value="idCompartments.tsv"/>
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114 <param name="o" value="COMPARTMENT"/>
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115 <output ftype="sbml" name="out">
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116 <assert_contents>
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117 <is_valid_xml/>
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118 <has_line_matching expression=".*id=.cytosol.*" n="1"/>
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119 <has_line_matching expression=".*id=.extra.*" n="1"/>
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120 </assert_contents>
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121 </output>
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122 </test>
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123 </tests>
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124 <help><![CDATA[Set new ids to network objects from a tabulated file containing the old ids and the new ids
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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125 The ids must correspond between the tabulated file and the SBML file.
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126 If prefix or suffix is different in the SBML file, use the -p or the -s options.
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127 ]]></help>
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128 <citations/>
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129 </tool>