Mercurial > repos > metexplore > met4j_setchemicalformulas

annotate SetChemicalFormulas.xml @ 2:c1a0a6d9766a draft default tip

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planemo upload for repository https://forge.inrae.fr/metexplore/met4j-galaxy commit 71335d4a636672d264cc4f443c07856907571928
author metexplore
date Fri, 21 Nov 2025 10:23:19 +0000
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1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
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2 <tool id="met4j_SetChemicalFormulas" name="SetChemicalFormulas" version="@TOOL_VERSION@">
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3 <description>Set Formula to network metabolites from a tabulated file containing the metabolite ids and the formulas</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.SetChemicalFormulas#if str($colformula) != 'nan':
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10 -cf "$colformula"
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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 $s
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17 #if str($nSkip):
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18 -n "$nSkip"
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19 #end if
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20 -i "$sbml"
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21 #if str($tab) != 'None':
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22 -tab "$tab"
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23 #end if
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24 #if str($c):
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25 -c "$c"
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26 #end if
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27 -o "$out"
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28 ]]></command>
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29 <inputs>
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30 <param argument="-cf" label="[2] number of the column where are the formulas" name="colformula" optional="true" type="integer" value="2"/>
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31 <param argument="-ci" label="[1] number of the column where are the metabolite ids" name="colid" optional="true" type="integer" value="1"/>
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32 <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix M_ to metabolite ids" name="p" truevalue="-p" type="boolean" value="false"/>
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33 <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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34 <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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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="-i" format="sbml" label="Original SBML file" name="sbml" optional="false" type="data" value=""/>
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40 <param argument="-tab" format="tsv" label="Input Tabulated file" name="tab" optional="true" type="data" value=""/>
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41 <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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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 </inputs>
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47 <outputs>
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48 <data format="sbml" name="out"/>
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49 </outputs>
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50 <tests>
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51 <test>
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52 <param name="sbml" value="toy_model.xml"/>
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53 <param name="tab" value="formula.tsv"/>
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54 <output ftype="sbml" name="out">
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55 <assert_contents>
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56 <is_valid_xml/>
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57 <has_line_matching expression=".*CH6O6.*" n="2"/>
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58 <has_line_matching expression=".*CH12O4.*" n="2"/>
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59 </assert_contents>
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60 </output>
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61 </test>
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62 <test expect_failure="true">
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63 <param name="sbml" value="toy_model.xml"/>
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64 <param name="tab" value="formulaBad.tsv"/>
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65 </test>
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66 </tests>
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67 <help><![CDATA[Set Formula to network metabolites from a tabulated file containing the metabolite ids and the formulas
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68 The ids must correspond between the tabulated file and the SBML file.
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69 If prefix or suffix is different in the SBML file, use the -p or the -s options.
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70 The formula will be written in the SBML file in two locations:+
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71 - in the metabolite HTML notes (e.g. formula: C16H29O2)
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72 - as a fbc attribute (e.g. fbc:chemicalFormula="C16H29O2")
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73 @ATTRIBUTION@]]></help>
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74 <citations>
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75 <citation type="doi">10.1515/jib-2017-0082</citation>
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76 </citations>
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77 </tool>