Mercurial > repos > metexplore > met4j_setgprs

annotate SetGprs.xml @ 3:d8b1f69da790 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 15:32:48 +0000
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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="@TOOL_VERSION@">
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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 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="bio_tools"/>
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8 <expand macro="requirements"/>
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9 <command detect_errors="exit_code"><![CDATA[met4j attributes.SetGprs#if str($colgpr) != 'nan':
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bec7aabab3c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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10 -cgpr "$colgpr"
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11 #end if
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12 #if str($colid) != 'nan':
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13 -ci "$colid"
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14 #end if
bec7aabab3c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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15 $p
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16 #if str($nSkip):
bec7aabab3c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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17 -n "$nSkip"
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18 #end if
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19 -i "$sbml"
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20 #if str($tab) != 'None':
bec7aabab3c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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21 -tab "$tab"
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22 #end if
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23 #if str($c):
bec7aabab3c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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24 -c "$c"
bec7aabab3c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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25 #end if
bec7aabab3c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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26 -o "$out"
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27 ]]></command>
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28 <inputs>
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29 <param argument="-cgpr" label="[2] number of the column where are the gprs" name="colgpr" optional="true" type="integer" value="2"/>
bec7aabab3c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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30 <param argument="-ci" label="[1] number of the column where are the reaction ids" name="colid" optional="true" type="integer" value="1"/>
bec7aabab3c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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31 <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"/>
bec7aabab3c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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32 <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">
bec7aabab3c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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33 <sanitizer invalid_char="_">
bec7aabab3c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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34 <valid initial="string.printable"/>
bec7aabab3c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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35 </sanitizer>
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36 </param>
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37 <param argument="-i" format="sbml" label="Original SBML file" name="sbml" optional="false" type="data" value=""/>
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38 <param argument="-tab" format="tsv" label="Input Tabulated file" name="tab" optional="true" type="data" value=""/>
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39 <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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40 <sanitizer invalid_char="_">
bec7aabab3c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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41 <valid initial="string.printable"/>
bec7aabab3c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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42 </sanitizer>
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43 </param>
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44 </inputs>
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45 <outputs>
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46 <data format="sbml" name="out"/>
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47 </outputs>
3
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48 <tests/>
0
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49 <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
bec7aabab3c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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50 The ids must correspond between the tabulated file and the SBML file.
bec7aabab3c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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51 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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52 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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53 (The GPR will be written in the SBML file in two locations:
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54 - in the reaction html notes (GENE_ASSOCIATION: ( XC_0401 ) OR ( XC_3282 ))
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55 - as fbc gene product association (see FBC package specifications: https://doi.org/10.1515/jib-2017-0082)
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56 @ATTRIBUTION@]]></help>
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57 <citations>
3
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58 <citation type="doi">10.1515/jib-2017-0082</citation>
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59 <citation type="doi">10.1038/nprot.2011.308</citation>
0
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60 </citations>
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61 </tool>