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annotate rpscore.xml @ 1:3af8a501f1b5 draft

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Thu, 10 Feb 2022 12:11:57 +0000
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1 <tool id="rpscore" name="Score Pathway" version="@TOOL_VERSION@" profile="19.09">
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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="@TOOL_VERSION@">5.12.1</token>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">rptools</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code"><![CDATA[
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10 python -m rptools.rpscore '$pathway' '$scored_pathway'
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11 --no_of_rxns_thres '$adv.no_of_rxns_thres'
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12 --log "error"
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13 ]]></command>
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14 <inputs>
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15 <param name="pathway" type="data" format="xml" label="Pathway (rpSBML)" />
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16 <section name="adv" title="Advanced Options" expanded="false">
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17 <param name="no_of_rxns_thres" type="integer" value="10" label="number of reactions above which a pathway is not scored" />
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18 </section>
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19 </inputs>
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20 <outputs>
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21 <data name="scored_pathway" format="xml" label="${tool.name} - ${pathway.name}" />
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22 </outputs>
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23 <tests>
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24 <test>
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25 <!-- test 1: check if identical outputs are produced with default parameters -->
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26 <param name="pathway" value="pathway.xml" />
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27 <output name="scored_pathway" file="scored_pathway.xml" ftype="xml" compare="diff" sort="true"/>
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28 </test>
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29 </tests>
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30 <help><![CDATA[
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31 rpscore
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32 =========
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33
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34
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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
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38 Input
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39 -----
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40
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41 Required:
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42
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43 * **infile**\ : (string) Pathway file (rpSBML) with scores (rules, FBA, Thermo...)
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44 * **outfile**\ : (string) Path to write pathway file (rpSBML) with global score
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45
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46 Advanced options:
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47
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48 * **--no_of_rxns_thres**\ :(integer, default: 10) Number of reactions above which pathway are not scored (too long)
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49
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50 Version
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51 ----------
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52
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53 5.12.1
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54
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55 Authors
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56 -------
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57
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58 * **Jean-Loup Faulon**
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59 * **Joan Hérisson**
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60
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61 Acknowledgments
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62 ---------------
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63
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64 * Thomas Duigou
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65 ]]></help>
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66 </tool>