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annotate wrap.xml @ 0:f818d489ca7d draft

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Tue, 07 Dec 2021 15:53:15 +0000
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1 <tool id="rpscore" name="Score Pathway" version="5.9.2">
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2 <description>Computes a global score for a heterologous pathway.</description>
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3 <requirements>
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4 <requirement type="package" version="5.9.2">rptools</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 python -m rptools.rpscore '$pathway' '$scored_pathway'
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8 --no_of_rxns_thres '$adv.no_of_rxns_thres'
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9 --log '$adv.log_level'
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10 ]]></command>
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11 <inputs>
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12 <param name="pathway" type="data" format="xml" label="Pathway (rpSBML)" />
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13 <section name="adv" title="Advanced Options" expanded="false">
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14 <param name="no_of_rxns_thres" type="integer" value="10" label="number of reactions above which a pathway is not scored" />
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15 <param name="log_level" type="select" label="Log level">
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16 <option value="debug" >debug</option>
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17 <option value="info" >info</option>
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18 <option value="warning" >warning</option>
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19 <option value="error" selected="true">error</option>
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20 <option value="critical" >critical</option>
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21 </param>
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22 </section>
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23 </inputs>
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24 <outputs>
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25 <data name="scored_pathway" format="xml" label="${tool.name} - ${pathway.name}" />
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26 </outputs>
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27 <tests>
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28 <test>
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29 <!-- test 1: check if identical outputs are produced with default parameters -->
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30 <param name="pathway" value="pathway.xml" />
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31 <output name="scored_pathway" file="scored_pathway.xml" ftype="xml" compare="diff" sort="true"/>
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32 </test>
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33 </tests>
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34 <help><![CDATA[
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35 rpscore
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36 =========
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37
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38
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39 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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40
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41
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42 Input
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43 -----
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44
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45 Required:
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46
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47 * **infile**\ : (string) Pathway file (rpSBML) with scores (rules, FBA, Thermo...)
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48 * **outfile**\ : (string) Path to write pathway file (rpSBML) with global score
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49
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50 Advanced options:
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51
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52 * **--no_of_rxns_thres**\ :(integer, default: 10) Number of reactions above which pathway are not scored (too long)
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53 * **--log**: (string, default=error) Set the log level, choices are 'debug', 'info', 'warning', 'error', 'critical'
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54
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55 Version
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56 ----------
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57
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58 5.9.2
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59
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60 Authors
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61 -------
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62
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63 * **Jean-Loup Faulon**
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64 * **Joan Hérisson**
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65
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66 Acknowledgments
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67 ---------------
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68
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69 * Thomas Duigou
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70 ]]></help>
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71 </tool>