Mercurial > repos > metexplore > met4j

annotate tools/attributes/SbmlSetPathwaysFromFile/SbmlSetPathwaysFromFile.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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dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
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1 <?xml version="1.0" encoding="UTF-8"?>
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35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
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2 <tool id="met4j_SbmlSetPathwaysFromFile" name="SbmlSetPathwaysFromFile" version="1.2.1">
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3 <description>Set pathway to reactions in a network from a tabulated file containing the reaction ids and the pathways</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 attributes.SbmlSetPathwaysFromFile#if str($colp) != 'nan':
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11 -cp "$colp"
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12 #end if
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13 #if str($sep):
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14 -sep "$sep"
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15 #end if
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16 #if str($colid) != 'nan':
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17 -ci "$colid"
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18 #end if
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19 $p
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20 #if str($nSkip):
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21 -n "$nSkip"
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22 #end if
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23 -sbml "$sbml"
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24 #if str($tab) != 'None':
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25 -tab "$tab"
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26 #end if
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27 #if str($c):
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28 -c "$c"
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29 #end if
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30 -out "$out"
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31 ]]></command>
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32 <inputs>
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33 <param argument="-cp" label="[2] number of the column where are the pathways" name="colp" optional="true" type="integer" value="2"/>
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34 <param argument="-sep" label="[|] Separator of pathways in the tabulated file" name="sep" optional="true" type="text" value="|">
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35 <sanitizer invalid_char="_">
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36 <valid initial="string.printable"/>
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37 </sanitizer>
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38 </param>
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39 <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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40 <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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41 <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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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="-sbml" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/>
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47 <param argument="-tab" format="tsv" label="Tabulated file" name="tab" optional="true" type="data" value=""/>
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48 <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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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 </inputs>
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54 <outputs>
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55 <data format="sbml" name="out"/>
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56 </outputs>
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57 <tests>
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58 <test>
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59 <param name="sbml" value="toy_model.xml"/>
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60 <param name="tab" value="pathways.tsv"/>
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61 <output ftype="sbml" name="out">
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62 <assert_contents>
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63 <is_valid_xml/>
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64 <has_line_matching expression=".*groups:id=.*" n="3"/>
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65 <has_line_matching expression=".*groups:id=.p1.*" n="1"/>
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66 <has_line_matching expression=".*groups:id=.p2.*" n="1"/>
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67 <has_line_matching expression=".*groups:id=.p3.*" n="1"/>
0
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68 </assert_contents>
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69 </output>
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70 </test>
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71 <test>
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72 <param name="sbml" value="toy_model.xml"/>
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73 <param name="tab" value="pathwaysOtherSep.tsv"/>
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74 <param name="sep" value=" + "/>
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75 <output ftype="sbml" name="out">
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76 <assert_contents>
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77 <is_valid_xml/>
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78 <has_line_matching expression=".*groups:id=.*" n="3"/>
2
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79 <has_line_matching expression=".*groups:id=.p1.*" n="1"/>
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80 <has_line_matching expression=".*groups:id=.p2.*" n="1"/>
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81 <has_line_matching expression=".*groups:id=.p3.*" n="1"/>
0
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82 </assert_contents>
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83 </output>
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84 </test>
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85 </tests>
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86 <help><![CDATA[Set pathway to reactions in a network from a tabulated file containing the reaction ids and the pathways
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87 The ids must correspond between the tabulated file and the SBML file.
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
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88 If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option.
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
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89 Pathways will be written in the SBML file in two ways:- as reaction note (e.g. <p>SUBSYSTEM: purine_biosynthesis</p>)- as SBML group:
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9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
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90 <groups:group groups:id="purine_biosynthesis" groups:kind="classification" groups:name="purine_biosynthesis">
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
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91 <groups:listOfMembers>
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
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92 <groups:member groups:idRef="R_GLUPRT"/>
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
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93 <groups:member groups:idRef="R_RNDR1b"/>
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dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
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94 ...
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
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95 ]]></help>
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9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
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96 <citations/>
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dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
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97 </tool>