Mercurial > repos > metexplore > met4j
annotate build/tools/SBMLwizard/SBMLwizard.xml @ 7:1436e9cde9c9 draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
| author | metexplore |
|---|---|
| date | Tue, 04 Jul 2023 10:21:26 +0000 |
| parents | |
| children | 1274e2a62479 |
| rev | line source |
|---|---|
|
7
1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
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1 <?xml version="1.0" encoding="UTF-8"?> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
diff
changeset
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2 <tool id="met4j_SBMLwizard" name="SBMLwizard" version="1.4.0"> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
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3 <description>General SBML model processing</description> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
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4 <xrefs> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
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changeset
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5 <xref type="bio.tools">met4j</xref> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
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changeset
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6 </xrefs> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
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7 <requirements> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
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8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.4.0</container> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
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9 </requirements> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
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changeset
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10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.SBMLwizard -s "$inputPath" |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
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11 #if str($inputSide) != 'None': |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
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12 -rc "$inputSide" |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
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13 #end if |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
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14 $removeIsolated |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
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changeset
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15 #if str($inputReactions) != 'None': |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
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changeset
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16 -rr "$inputReactions" |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
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17 #end if |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
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changeset
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18 $removeNoFlux |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
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changeset
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19 #if str($mergingStrat): |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
diff
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20 -mc "$mergingStrat" |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
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changeset
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21 #end if |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
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22 $removeDuplicated |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
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23 #if str($exchangeCompToRemove): |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
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changeset
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24 -rEX "$exchangeCompToRemove" |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
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changeset
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25 #end if |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
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changeset
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26 -o "$outputPath" |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
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changeset
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27 ]]></command> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
diff
changeset
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28 <inputs> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
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changeset
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29 <param argument="-s" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
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changeset
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30 <param argument="-rc" format="txt" label="file containing identifiers of compounds to remove from the metabolic network" name="inputSide" optional="true" type="data" value=""/> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
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changeset
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31 <param argument="-ric" checked="false" falsevalue="" label="remove isolated compounds (not involved in any reaction)" name="removeIsolated" truevalue="-ric" type="boolean" value="false"/> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
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32 <param argument="-rr" format="txt" label="file containing identifiers of reactions to remove from the metabolic network" name="inputReactions" optional="true" type="data" value=""/> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
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33 <param argument="-r0" checked="false" falsevalue="" label="remove reactions with lower and upper flux bounds both set to 0.0" name="removeNoFlux" truevalue="-r0" type="boolean" value="false"/> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
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34 <param argument="-mc" label="merge compartments using the provided strategy. No merge by default. "by_name" can be used if names are consistent and unambiguous across compartments, "by_id" can be used if compartment suffix is present in compounds identifiers (id in form "xxx_y" with xxx as base identifier and y as compartment label)." name="mergingStrat" optional="true" type="select" value="no"> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
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35 <option selected="true" value="no">no</option> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
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36 <option value="by_name">by_name</option> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
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37 <option value="by_id">by_id</option> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
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38 </param> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
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39 <param argument="-rdr" checked="false" falsevalue="" label="remove duplicated reactions (same reactants, same GPR)" name="removeDuplicated" truevalue="-rdr" type="boolean" value="false"/> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
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40 <param argument="-rEX" label="remove exchange reactions and species from given exchange compartment identifier" name="exchangeCompToRemove" optional="true" type="text" value=""> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
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41 <sanitizer invalid_char="_"> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
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42 <valid initial="string.printable"/> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
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43 </sanitizer> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
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44 </param> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
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45 </inputs> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
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46 <outputs> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
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47 <data format="sbml" name="outputPath"/> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
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48 </outputs> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
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49 <tests> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
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50 <test> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
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51 <param name="inputPath" value="Human-GEM_pathways.xml"/> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
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52 <param name="removeIsolated" value="true"/> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
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53 <param name="removeNoFlux" value="true"/> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents:
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54 <param name="mergingStrat" value="by_id"/> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
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55 <param name="removeDuplicated" value="true"/> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
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56 <param name="exchangeCompToRemove" value="s"/> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
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57 <output ftype="sbml" name="outputPath"> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
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58 <assert_contents> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
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59 <has_text text="</sbml>"/> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
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60 </assert_contents> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
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61 </output> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
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62 </test> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
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63 <test> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
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64 <param name="inputPath" value="XF_network.sbml"/> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
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65 <param name="removeIsolated" value="true"/> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
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66 <param name="removeNoFlux" value="true"/> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
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67 <param name="removeDuplicated" value="true"/> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
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68 <param name="inputSide" value="XF_network_C_Side.tab"/> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
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69 <param name="inputReactions" value="XF_network_R_Seed.tab"/> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
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70 <output ftype="sbml" name="outputPath"> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
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71 <assert_contents> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
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72 <has_text text="</sbml>"/> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
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73 </assert_contents> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
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74 </output> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
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75 </test> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
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76 </tests> |
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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
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77 <help><![CDATA[General SBML model processing including compound removal (such as side compounds or isolated compounds), reaction removal (ex. blocked or exchange reaction), and compartment merging]]></help> |
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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
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78 <citations/> |
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1436e9cde9c9
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
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79 </tool> |