Mercurial > repos > metexplore > met4j_sbml2tab

annotate Sbml2Tab.xml @ 3:afc9b623aa3e 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 15:31:53 +0000
parents be58dd7c74ee
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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897bc123f6c5 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"?>
897bc123f6c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
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2 <tool id="met4j_Sbml2Tab" name="Sbml2Tab" version="@TOOL_VERSION@">
897bc123f6c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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3 <description>Create a tabulated file listing reaction attributes from a SBML file</description>
897bc123f6c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
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4 <macros>
897bc123f6c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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5 <import>macros.xml</import>
897bc123f6c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
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6 </macros>
897bc123f6c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
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7 <expand macro="bio_tools"/>
897bc123f6c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
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8 <expand macro="requirements"/>
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be58dd7c74ee 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 convert.Sbml2Tab#if str($i):
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897bc123f6c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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10 -irr "$i"
897bc123f6c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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11 #end if
897bc123f6c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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12 #if str($r):
897bc123f6c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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13 -rev "$r"
897bc123f6c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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14 #end if
897bc123f6c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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15 -i "$in"
897bc123f6c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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16 -o "$out"
897bc123f6c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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17 ]]></command>
897bc123f6c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
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18 <inputs>
897bc123f6c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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19 <param argument="-irr" label="[--&gt;] String for irreversible reaction" name="i" optional="true" type="text" value="--&gt;">
897bc123f6c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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20 <sanitizer invalid_char="_">
897bc123f6c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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21 <valid initial="string.printable"/>
897bc123f6c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
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22 </sanitizer>
897bc123f6c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
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23 </param>
897bc123f6c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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24 <param argument="-rev" label="[&lt;==&gt;] String for reversible reaction" name="r" optional="true" type="text" value="&lt;==&gt;">
897bc123f6c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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25 <sanitizer invalid_char="_">
897bc123f6c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
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26 <valid initial="string.printable"/>
897bc123f6c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
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27 </sanitizer>
897bc123f6c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
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28 </param>
897bc123f6c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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29 <param argument="-i" format="sbml" label="Sbml file" name="in" optional="false" type="data" value=""/>
897bc123f6c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
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30 </inputs>
897bc123f6c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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31 <outputs>
897bc123f6c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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32 <data format="tsv" name="out"/>
897bc123f6c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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33 </outputs>
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afc9b623aa3e planemo upload for repository https://forge.inrae.fr/metexplore/met4j-galaxy commit e757d0398a8407d983f1ef3f900b31cafc26e170
metexplore
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34 <tests/>
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897bc123f6c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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35 <help><![CDATA[Create a tabulated file listing reaction attributes from a SBML file
897bc123f6c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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36 @ATTRIBUTION@]]></help>
897bc123f6c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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37 <citations/>
897bc123f6c5 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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38 </tool>