Mercurial > repos > tduigou > rpscore
annotate rpscore.xml @ 1:da8ae7fa5ed3 draft
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author | tduigou |
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date | Thu, 10 Feb 2022 12:17:38 +0000 |
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children | eddae32301bd |
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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> |