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annotate pampa_macros.xml @ 2:f1bfdeb5ebfe draft

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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit e8643d3d2e48d2ec7fcb2bd5abf77869a8687422"
author ecology
date Mon, 27 Jul 2020 09:46:51 -0400
parents c9dfe4e20a45
children 8d8aec182fb1
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c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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1 <macros>
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2 <token name="@VERSION@">0.0.1</token>
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3 <xml name="Pampa_requirements">
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4 <requirements>
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5 <requirement type="package" version="1.0.2">r-tidyr</requirement>
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6 </requirements>
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7 </xml>
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8 <xml name="GLM_requirements">
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9 <requirements>
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10 <requirement type="package" version="1.2.2">r-gap</requirement>
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11 <requirement type="package" version="1.0.1">r-glmmtmb</requirement>
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12 <requirement type="package" version="1.4_13">r-multcomp</requirement>
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13 </requirements>
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14 </xml>
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15 <xml name="Plot_requirements">
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16 <requirements>
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17 <requirement type="package" version="3.1.1">r-ggplot2</requirement>
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18 </requirements>
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19 </xml>
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20 <xml name="pampa_input_calculate">
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21 <param name="input" type="data" format="tabular" label="Input file" help="Observation data file, with location, year, species and abundance."/>
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22 </xml>
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23 <xml name="pampa_advanced_params_select">
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24 <param name="advanced" type="select" label="Specify advanced parameters">
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25 <option value="simple" selected="true">No, use program defaults.</option>
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26 <option value="advanced">Yes, see full parameter list.</option>
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27 </param>
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28 <when value="simple">
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29 </when>
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30 </xml>
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31 <xml name="pampa_advanced_params_select_GLM">
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32 <param name="advanced" type="select" label="Specify advanced parameters">
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33 <option value="simple" selected="true">No, use program defaults.</option>
c9dfe4e20a45 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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34 <option value="advanced">Yes, see full parameter list.</option>
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35 </param>
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36 <when value="simple">
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37 </when>
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38 <when value="advanced">
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39 <param name="distrib" type="select" label="Distribution for model">
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40 <option selected="true" value="None">Auto</option>
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41 <option value="gaussian">Gaussian</option>
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42 <option value="inverse.gaussian">Inverse Gaussian</option>
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43 <option value="poisson">Poisson</option>
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44 <option value="quasipoisson">Quasi-Poisson</option>
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45 <option value="binomial">Binomial</option>
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46 <option value="quasibinomial">Quasi-Binomial</option>
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47 <option value="Gamma">Gamma</option>
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48 </param>
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49 </when>
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50 </xml>
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51 <xml name="pampa_input_GLM">
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52 <param name="input_metric" type="data" format="tabular" label="Input metrics file" help="Metrics data file, with location, year, and metrics informations that can be used as interest variable."/>
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53 <param name="input_unitobs" type="data" format="tabular" label="Unitobs informations file" help="Unitobs file, with all informations available about unitobs."/>
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54 <param name="varint" type="data_column" data_ref="input_metric" label="Interest variable from metrics file" help= "Choose the field of the interest variable."/>
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55 </xml>
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56 <xml name="pampa_var_GLM">
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57 <param name="varrep" type="select" label="Response variables" help= "Choose the response variables you want to include in your analysis." multiple="true">
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58 <option selected="true" value="year">Year</option>
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59 <option selected="true" value="site">Site</option>
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60 <option selected="true" value="habitat">Habitat</option>
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61 </param>
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62 <param name="varrand" type="select" label="Random effect ?" help="Allocate a random effect on site or year makes your model more reliable as random events on a peculiar site or year can affect populations, it takes account of pseudoreplication. However, avoid applying it on a less than 10 levels variable (less than 10 different sites and/or year)." multiple="true">
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63 <option value="year">Year</option>
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64 <option selected="true" value="site">Site</option>
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65 </param>
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66 </xml>
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67 <xml name="pampa_output_GLM">
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68 <data name="output_recap" from_work_dir="GLMSummaryFull.txt" format="txt" label="Simple statistics on chosen variables on ${on_string}"/>
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69 <data name="output_rate" from_work_dir="RatingGLM.txt" format="txt" label="Your analysis rating file on ${on_string}"/>
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70 </xml>
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71 <xml name="pampa_bibref">
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72 <citations>
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73 <citation type="bibtex">
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74 @unpublished{pampayves,
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75 title={ PAMPA "ressources et biodiversité" scripts },
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76 author={Yves Reecht},
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77 url={https://wwz.ifremer.fr/pampa/Meth.-Outils/Outils}
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78 }
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79 </citation>
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80 </citations>
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81 </xml>
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82 </macros>