Mercurial > repos > metexplore > met4j_setids

annotate SetIds.xml @ 3:d80ba6cbcf39 draft default tip

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planemo upload for repository https://forge.inrae.fr/metexplore/met4j-galaxy commit e757d0398a8407d983f1ef3f900b31cafc26e170
author metexplore
date Wed, 21 Jan 2026 15:32:56 +0000
parents 6c8c9af89afe
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c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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2 <tool id="met4j_SetIds" name="SetIds" version="@TOOL_VERSION@">
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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3 <description>Set new ids to network objects in a SBML file from a tabulated file containing the old ids and the new ids</description>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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4 <macros>
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5 <import>macros.xml</import>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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6 </macros>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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7 <expand macro="bio_tools"/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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8 <expand macro="requirements"/>
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9 <command detect_errors="exit_code"><![CDATA[met4j attributes.SetIds#if str($colname) != 'nan':
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c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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10 -cnew "$colname"
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11 #end if
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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12 #if str($colid):
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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13 -ci "$colid"
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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14 #end if
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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15 $p
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16 $s
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17 #if str($o):
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18 -t "$o"
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19 #end if
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20 #if str($nSkip):
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21 -n "$nSkip"
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22 #end if
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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23 -i "$sbml"
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24 #if str($tab) != 'None':
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25 -tab "$tab"
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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26 #end if
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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27 #if str($c):
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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28 -c "$c"
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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29 #end if
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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30 -o "$out"
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31 ]]></command>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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32 <inputs>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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33 <param argument="-cnew" label="[2] number of the column where are the new ids" name="colname" optional="true" type="integer" value="2"/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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34 <param argument="-ci" label="[1] number of the column where are the object ids" name="colid" optional="true" type="text" value="1">
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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35 <sanitizer invalid_char="_">
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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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="-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"/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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40 <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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41 <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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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="-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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47 <sanitizer invalid_char="_">
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48 <valid initial="string.printable"/>
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49 </sanitizer>
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50 </param>
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51 <param argument="-i" format="sbml" label="Original SBML file" name="sbml" optional="false" type="data" value=""/>
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52 <param argument="-tab" format="tsv" label="Input Tabulated file" name="tab" optional="true" type="data" value=""/>
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53 <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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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 </inputs>
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59 <outputs>
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60 <data format="sbml" name="out"/>
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61 </outputs>
3
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62 <tests/>
0
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63 <help><![CDATA[Set new ids to network objects in a SBML file from a tabulated file containing the old ids and the new ids
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64 The ids must correspond between the tabulated file and the SBML file.
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65 If prefix or suffix is different in the SBML file, use the -p or the -s options.
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66 @ATTRIBUTION@]]></help>
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67 <citations/>
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68 </tool>