Mercurial > repos > metexplore > met4j_setecnumbers

annotate SetEcNumbers.xml @ 3:a0ba54d595f0 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 15:32:41 +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_SetEcNumbers" name="SetEcNumbers" version="@TOOL_VERSION@">
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3 <description>Set EC numbers to reactions in a SBML file from a tabulated file containing the reaction ids and the EC numbers</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.SetEcNumbers#if str($colec) != 'nan':
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10 -cec "$colec"
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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
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15 $p
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16 #if str($nSkip):
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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($tab) != 'None':
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21 -tab "$tab"
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22 #end if
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23 #if str($c):
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24 -c "$c"
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25 #end if
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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="-cec" label="[2] number of the column where are the ecs" name="colec" optional="true" type="integer" value="2"/>
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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"/>
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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"/>
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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">
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33 <sanitizer invalid_char="_">
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34 <valid initial="string.printable"/>
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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="_">
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41 <valid initial="string.printable"/>
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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[Set EC numbers to reactions in a SBML file from a tabulated file containing the reaction ids and the EC numbers
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50 The ids must correspond between the tabulated file and the SBML file.
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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 The EC will be written in the SBML file in two locations:
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53 - in the reaction HTML notes (e.g. EC_NUMBER: 2.4.2.14)
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54 - as a reaction MIRIAM annotation (see https://pubmed.ncbi.nlm.nih.gov/16333295/) with ec-code identifiers link (https://registry.identifiers.org/registry/ec-code)
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55 @ATTRIBUTION@]]></help>
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56 <citations>
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57 <citation type="doi">10.1038/nbt1156</citation>
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58 </citations>
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59 </tool>