Mercurial > repos > lcottret > met4j
annotate tools/convert/Kegg2Sbml/Kegg2Sbml.xml @ 0:3cdcfdae8bd2 draft default tip
"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
author | lcottret |
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date | Tue, 31 May 2022 07:45:16 +0000 |
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3cdcfdae8bd2
"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
lcottret
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1 <?xml version="1.0" encoding="UTF-8"?> |
3cdcfdae8bd2
"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
lcottret
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2 <tool id="met4j_Kegg2Sbml" name="Kegg2Sbml" version="0.11.0"> |
3cdcfdae8bd2
"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
lcottret
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3 <description>Build a SBML file from KEGG organism-specific pathways. Uses Kegg API.</description> |
3cdcfdae8bd2
"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
lcottret
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4 <xrefs> |
3cdcfdae8bd2
"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
lcottret
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5 <xref type="bio.tools">met4j</xref> |
3cdcfdae8bd2
"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
lcottret
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6 </xrefs> |
3cdcfdae8bd2
"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
lcottret
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7 <requirements> |
3cdcfdae8bd2
"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
lcottret
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8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container> |
3cdcfdae8bd2
"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
lcottret
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9 </requirements> |
3cdcfdae8bd2
"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
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10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Kegg2Sbml#if str($org): |
3cdcfdae8bd2
"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
lcottret
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11 -org "$org" |
3cdcfdae8bd2
"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
lcottret
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12 #end if |
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"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
lcottret
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13 -sbml "$sbml" |
3cdcfdae8bd2
"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
lcottret
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14 ]]></command> |
3cdcfdae8bd2
"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
lcottret
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15 <inputs> |
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"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
lcottret
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16 <param argument="-org" label="[] Kegg org id. Must be 3 letters (" name="org" optional="true" type="text" value=""> |
3cdcfdae8bd2
"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
lcottret
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17 <sanitizer invalid_char="_"> |
3cdcfdae8bd2
"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
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18 <valid initial="string.printable"/> |
3cdcfdae8bd2
"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
lcottret
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19 </sanitizer> |
3cdcfdae8bd2
"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
lcottret
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20 </param> |
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"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
lcottret
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21 </inputs> |
3cdcfdae8bd2
"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
lcottret
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22 <outputs> |
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"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
lcottret
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23 <data format="sbml" name="sbml"/> |
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"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
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24 </outputs> |
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"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
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25 <tests> |
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"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
lcottret
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26 <test maxseconds="600"> |
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"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
lcottret
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27 <param name="org" value="buc"/> |
3cdcfdae8bd2
"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
lcottret
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28 <output ftype="sbml" name="sbml"> |
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"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
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29 <assert_contents> |
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"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
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30 <is_valid_xml/> |
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"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
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31 |
3cdcfdae8bd2
"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
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32 </assert_contents> |
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"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
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33 </output> |
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"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
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34 </test> |
3cdcfdae8bd2
"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
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35 </tests> |
3cdcfdae8bd2
"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
lcottret
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36 <help><![CDATA[Build a SBML file from KEGG organism-specific pathways. Uses Kegg API. |
3cdcfdae8bd2
"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
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37 Errors returned by this program could be due to Kegg API dysfunctions or limitations. Try later if this problem occurs.]]></help> |
3cdcfdae8bd2
"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
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38 </tool> |