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annotate build/tools/ChokePoint/ChokePoint.xml @ 7:1436e9cde9c9 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
author metexplore
date Tue, 04 Jul 2023 10:21:26 +0000
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="met4j_ChokePoint" name="ChokePoint" version="1.4.0">
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3 <description>Compute the Choke points of a metabolic network.</description>
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4 <xrefs>
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5 <xref type="bio.tools">met4j</xref>
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6 </xrefs>
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7 <requirements>
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1436e9cde9c9 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
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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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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ChokePoint -i "$inputPath"
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11 -o "$outputPath"
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12 ]]></command>
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13 <inputs>
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14 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
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15 </inputs>
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16 <outputs>
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17 <data format="tsv" name="outputPath"/>
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18 </outputs>
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19 <tests>
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20 <test>
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21 <param name="inputPath" value="XF_network.sbml"/>
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22 <output ftype="tsv" name="outputPath">
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23 <assert_contents>
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24 <has_n_lines n="695"/>
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25 <has_n_columns n="3"/>
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26 <has_line_matching expression="R_ADEtex.*adenine_transport_via_diffusion__extracellular_to_periplasm_.*M_ade_e &lt;==&gt; M_ade_p" n="1"/>
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27 <has_line_matching expression="R_AGDC_r.*R_AGDC_r.*M_acgam6p_c \+ M_h2o_c --&gt; M_ac_c \+ M_gam6p_c" n="1"/>
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28 </assert_contents>
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29 </output>
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30 </test>
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31 </tests>
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32 <help><![CDATA[Compute the Choke points of a metabolic network.
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33 Choke points constitute an indicator of lethality and can help identifying drug target Choke points are reactions that are required to consume or produce one compound. Targeting of choke point can lead to the accumulation or the loss of some metabolites, thus choke points constitute an indicator of lethality and can help identifying drug target
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34 See : Syed Asad Rahman, Dietmar Schomburg; Observing local and global properties of metabolic pathways: ‘load points’ and ‘choke points’ in the metabolic networks. Bioinformatics 2006; 22 (14): 1767-1774. doi: 10.1093/bioinformatics/btl181]]></help>
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35 <citations/>
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36 </tool>