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author tduigou
date Fri, 18 Nov 2022 16:36:16 +0000
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1 <tool id="rpscore" name="Score Pathway" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
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2 <description>Computes a global score for a heterologous pathway</description>
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3 <macros>
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4 <token name="@VERSION_SUFFIX@">0</token>
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5 <token name="@TOOL_VERSION@">6.0.1</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">rptools</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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11 python -m rptools.rpscore '$pathway' '$scored_pathway'
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12 --no_of_rxns_thres '$adv.no_of_rxns_thres'
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13 --log "error"
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14 ]]></command>
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15 <inputs>
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16 <param name="pathway" type="data" format="sbml" label="Pathway (rpSBML)" />
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17 <section name="adv" title="Advanced Options" expanded="false">
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18 <param argument="no_of_rxns_thres" type="integer" value="10" label="number of reactions above which a pathway is not scored" />
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19 </section>
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20 </inputs>
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21 <outputs>
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22 <data name="scored_pathway" format="sbml" label="${tool.name} - ${pathway.name}" />
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23 </outputs>
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24 <tests>
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25 <test>
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26 <!-- check if identical outputs are produced with default parameters -->
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27 <param name="pathway" value="pathway.xml" />
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28 <output name="scored_pathway" file="scored_pathway.xml" ftype="sbml" compare="diff" sort="true"/>
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29 </test>
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30 </tests>
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31 <help><![CDATA[
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32 Score Pathway
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33 ==============
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35 Computes a global score for a heterologous pathway. The score is calculated from a learning process based on reaction rules score, flux balance analysis and thermodynamics metrics, and the number of reactions in the pathway.
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36
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37 Input
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38 -----
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39
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40 Required:
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41
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42 * **Pathway (rpSBML)**\ : pathway file (rpSBML) with scores (rules, FBA, Thermo...).
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43 * **Scored pathway**\ : pathway file (rpSBML) with global score.
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44
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45 Advanced options:
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46
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47 * **--no_of_rxns_thres**\ :(integer, default: 10) Number of reactions above which pathway are not scored
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48
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49 Acknowledgments
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50 ---------------
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51
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52 * Thomas Duigou
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53
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54 ]]></help>
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55 <creator>
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56 <person givenName="Jean-Loup" familyName="Faulon" email="jean-loup.faulon@inrae.fr" identifier="http://orcid.org/0000-0003-4274-2953" />
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57 <person givenName="Joan" familyName="Hérisson" email="Joan.Herisson@univ-evry.fr" identifier="http://orcid.org/0000-0001-9741-0847" />
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58 </creator>
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59 </tool>