Mercurial > repos > metexplore > met4j_setcharges

annotate SetCharges.xml @ 2:8f767bc45914 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 10:23:12 +0000
parents 921a828bd368
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
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1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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2 <tool id="met4j_SetCharges" name="SetCharges" version="@TOOL_VERSION@">
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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3 <description>Set charge to metabolites in a SBML file from a tabulated file containing the metabolite ids and the charges</description>
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4 <macros>
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5 <import>macros.xml</import>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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6 </macros>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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7 <expand macro="bio_tools"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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8 <expand macro="requirements"/>
1
921a828bd368 planemo upload for repository https://forge.inrae.fr/metexplore/met4j-galaxy commit 6bb33ff0ff022029543e5e5ace7d16418715aa1c
metexplore
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9 <command detect_errors="exit_code"><![CDATA[met4j attributes.SetCharges#if str($colcharge) != 'nan':
0
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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10 -cc "$colcharge"
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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11 #end if
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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12 #if str($colid) != 'nan':
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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13 -ci "$colid"
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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14 #end if
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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15 $p
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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16 $s
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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17 #if str($nSkip):
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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18 -n "$nSkip"
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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19 #end if
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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20 -i "$sbml"
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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21 #if str($tab) != 'None':
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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22 -tab "$tab"
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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23 #end if
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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24 #if str($c):
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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25 -c "$c"
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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26 #end if
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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27 -o "$out"
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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28 ]]></command>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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29 <inputs>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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30 <param argument="-cc" label="[2] number of the column where are the charges" name="colcharge" optional="true" type="integer" value="2"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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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"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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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"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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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"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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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">
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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35 <sanitizer invalid_char="_">
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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36 <valid initial="string.printable"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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37 </sanitizer>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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38 </param>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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39 <param argument="-i" format="sbml" label="Original SBML file" name="sbml" optional="false" type="data" value=""/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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40 <param argument="-tab" format="tsv" label="Input Tabulated file" name="tab" optional="true" type="data" value=""/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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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="#">
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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42 <sanitizer invalid_char="_">
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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43 <valid initial="string.printable"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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44 </sanitizer>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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45 </param>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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46 </inputs>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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47 <outputs>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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48 <data format="sbml" name="out"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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49 </outputs>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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50 <tests>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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51 <test>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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52 <param name="sbml" value="toy_model.xml"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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53 <param name="tab" value="charges.tsv"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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54 <output ftype="sbml" name="out">
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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55 <assert_contents>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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56 <is_valid_xml/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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57 <has_line_matching expression=".*fbc:charge=.2.*" n="1"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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58 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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59 </assert_contents>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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60 </output>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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61 </test>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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62 <test>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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63 <param name="sbml" value="toy_model.xml"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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64 <param name="tab" value="chargesWithComment.tsv"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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65 <output ftype="sbml" name="out">
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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66 <assert_contents>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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67 <is_valid_xml/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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68 <has_line_matching expression=".*fbc:charge=.2.*" n="1" negate="true"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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69 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/>
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70 </assert_contents>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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71 </output>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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72 </test>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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73 <test>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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74 <param name="sbml" value="toy_model.xml"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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75 <param name="tab" value="charges.tsv"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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76 <param name="nSkip" value="1"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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77 <output ftype="sbml" name="out">
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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78 <assert_contents>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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79 <is_valid_xml/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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80 <has_line_matching expression=".*fbc:charge=.2.*" n="1" negate="true"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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81 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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82 </assert_contents>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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83 </output>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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84 </test>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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85 <test>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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86 <param name="sbml" value="toy_model.xml"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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87 <param name="tab" value="charges.tsv"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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88 <param name="ci" value="2"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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89 <param name="cc" value="3"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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90 <output ftype="sbml" name="out">
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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91 <assert_contents>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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92 <is_valid_xml/>
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93 <has_line_matching expression=".*fbc:charge=.2.*" n="1"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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94 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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95 </assert_contents>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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96 </output>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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97 </test>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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98 <test>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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99 <param name="sbml" value="XF_network.sbml"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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100 <param name="tab" value="chargesXF.tsv"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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101 <param name="p" value="true"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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102 <param name="s" value="true"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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103 <output ftype="sbml" name="out">
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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104 <assert_contents>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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105 <is_valid_xml/>
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106 <has_line_matching expression=".*fbc:charge=.-1000.*" n="3"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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107 </assert_contents>
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108 </output>
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109 </test>
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110 </tests>
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111 <help><![CDATA[Set charge to metabolites in a SBML file from a tabulated file containing the metabolite ids and the charges
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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112 The charge must be a number. The ids must correspond between the tabulated file and the SBML file.
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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113 If prefix or suffix is different in the SBML file, use the -p or the -s options.
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114 The charge will be written in the SBML file in two locations:+
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115 - in the reaction notes (e.g. charge: -1)
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116 - as fbc attribute (e.g. fbc:charge="1")
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117 @ATTRIBUTION@]]></help>
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118 <citations>
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119 <citation type="doi">10.1515/jib-2017-0082</citation>
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120 </citations>
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121 </tool>