Mercurial > repos > ecology > pampa_glmsp
annotate PAMPA_GLM_SP.xml @ 0:0778efa9eb2e draft
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
author | ecology |
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date | Tue, 21 Jul 2020 06:00:51 -0400 |
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children | e972fe2bffee |
rev | line source |
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0
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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1 <tool id="pampa_glmsp" name="Compute GLM on population data" version="@VERSION@"> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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2 <description>Compute a GLM of your choice on population data</description> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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3 <macros> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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4 <import>pampa_macros.xml</import> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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5 </macros> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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6 <expand macro="GLM_requirements"/> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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7 <command detect_errors="exit_code"><![CDATA[ |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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8 Rscript |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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9 '$__tool_directory__/FunctExeCalcGLMSpGalaxy.r' |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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10 '$input_metric' |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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11 '$input_unitobs' |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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12 '$varint' |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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13 '$varrep' |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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14 '$varrand' |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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15 'species.code' |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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16 #if $settings.advanced=='advanced' |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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17 $settings.distrib |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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18 'FALSE' |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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19 #else |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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20 'None' |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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21 'FALSE' |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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22 #end if |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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23 'unitSp' |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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24 '$__tool_directory__/FunctPAMPAGalaxy.r' |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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25 '$output_summary' |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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26 '$output_recap' |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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27 ]]> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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28 </command> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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29 <inputs> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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30 <expand macro="pampa_input_GLM"/> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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31 <expand macro="pampa_var_GLM"/> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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32 <conditional name="settings"> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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33 <expand macro="pampa_advanced_params_select_GLM"/> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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34 </conditional> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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35 </inputs> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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36 <outputs> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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37 |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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38 <data name="output_summary" from_work_dir="GLMSummary.tabular" format="tabular" label="GLM - Results from your population analysis on ${on_string}"/> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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39 <expand macro="pampa_output_GLM"/> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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40 </outputs> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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41 <tests> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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42 <test> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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43 <param name="input_metric" value="Presence_absence_table_sansszcl_cropped.tabular"/> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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44 <param name="input_unitobs" value="Unitobs.tabular"/> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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45 <param name="varint" value="4"/> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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46 <param name="varrep" value="year,site,habitat"/> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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47 <param name="varrand" value="site"/> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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48 <param name="advanced" value="simple"/> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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49 <output name="output_summary"> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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50 <assert_contents> |
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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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51 <has_n_lines n="4"/> |
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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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52 </assert_contents> |
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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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53 </output> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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54 <output name="output_recap"> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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55 <assert_contents> |
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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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56 <has_n_lines n="607"/> |
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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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57 </assert_contents> |
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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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58 </output> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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59 <output name="output_rate"> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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60 <assert_contents> |
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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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61 <has_n_lines n="46"/> |
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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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62 </assert_contents> |
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63 </output> |
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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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64 </test> |
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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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65 </tests> |
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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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66 <help><![CDATA[ |
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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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67 =============================================================== |
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68 Compute GLM on population data with selected interest variables |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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69 =============================================================== |
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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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70 |
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71 **What it does** |
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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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72 |
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73 This tool from PAMPA toolsuite computes Generalized Linear Models on population data. |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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74 |
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75 It allows user to choose composition of the model : |
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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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76 |
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77 - Interest variable among numeric or integer variables of the input file |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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78 |
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79 - Response variables among year, site and/or habitat |
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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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80 |
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81 - Allocation of random effect on year and/or site |
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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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82 |
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83 | |
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84 |
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85 **Input description** |
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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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86 |
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87 A tabular file with population data. Must at least contain three or four columns depending on the case : |
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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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88 |
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89 - ['year' and 'location'] or ['observation.unit'] |
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90 |
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91 - 'species.code' |
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92 |
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93 - At least one population metric |
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94 |
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95 +------------------+--------------+---------+---------+-----+ |
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96 | observation.unit | species.code | metric1 | metric2 | ... | |
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97 +==================+==============+=========+=========+=====+ |
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98 | site_yearID | species code | 2 | 0.4 | ... | |
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99 +------------------+--------------+---------+---------+-----+ |
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100 | ... | ... | ... | ... | ... | |
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101 +------------------+--------------+---------+---------+-----+ |
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102 |
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103 OR |
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104 |
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105 +------+----------+--------------+---------+---------+-----+ |
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106 | year | location | species.code | metric1 | metric2 | ... | |
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107 +======+==========+==============+=========+=========+=====+ |
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108 | 2000 |locationID| species code | 2 | 0.4 | ... | |
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109 +------+----------+--------------+---------+---------+-----+ |
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110 | ... | ... | ... | ... | ... | ... | |
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111 +------+----------+--------------+---------+---------+-----+ |
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112 |
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113 The first input may be extracted from the 'Calculate presence absence' tool. |
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114 |
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115 A tabular file with unitobs or location data which contains at least as much columns as used response variables and separation factor in addition with the 'observation.unit' or 'location' and 'species.code' column. |
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116 |
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117 +--------------------------------+--------------+---------+--------+------------+-----+ |
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118 | observation.unit OR location | species.code | site | year | habitat | ... | |
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119 +================================+==============+=========+========+============+=====+ |
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120 | site_yearID OR locationID | species code | site ID | 2000 | habitatID | ... | |
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121 +--------------------------------+--------------+---------+--------+------------+-----+ |
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122 | ... | ... | ... | ... | ... | ... | |
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123 +--------------------------------+--------------+---------+--------+------------+-----+ |
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124 |
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125 | |
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126 |
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127 **Output** |
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128 |
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129 Two text files : |
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130 |
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131 - A first text file with GLM results. One analysis per species. |
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132 |
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133 - A second text file with simple statistics on the whole dataset. |
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134 |
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135 | |
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136 |
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137 **Source** |
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138 |
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139 Derived from PAMPA scripts (https://wwz.ifremer.fr/pampa/Meth.-Outils/Outils) written by Yves Reecht. |
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140 |
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141 ]]></help> |
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142 |
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143 <expand macro="pampa_bibref" /> |
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144 </tool> |