Mercurial > repos > ecology > pampa_glmcomm

annotate PAMPA_GLM.xml @ 0:f0dc3958e65d draft

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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
author ecology
date Tue, 21 Jul 2020 06:00:31 -0400
parents
children 61cc30e94df4
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0
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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1 <tool id="pampa_glmcomm" name="Compute GLM on community data" version="@VERSION@">
f0dc3958e65d "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 community data</description>
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3 <macros>
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4 <import>pampa_macros.xml</import>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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5 </macros>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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6 <expand macro="GLM_requirements"/>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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7 <command detect_errors="exit_code"><![CDATA[
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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8 Rscript
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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9 '$__tool_directory__/FunctExeCalcGLMGalaxy.r'
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10 '$input_metric'
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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11 '$input_unitobs'
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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12 '$varint'
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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13 '$varrep'
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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14 '$varrand'
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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15 '$sep'
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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16 #if $settings.advanced=='advanced'
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17 $settings.distrib
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18 'FALSE'
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19 #else
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20 'None'
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21 'FALSE'
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22 #end if
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23 'unit'
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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24 '$__tool_directory__/FunctPAMPAGalaxy.r'
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25 '$output_summary'
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26 '$output_recap'
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27 ]]>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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28 </command>
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29 <inputs>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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30 <expand macro="pampa_input_GLM"/>
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31 <param name="sep" type="data_column" data_ref="input_unitobs" force_select="false" label="Separation factor of your analysis from unitobs file" help= "Choose the field of the separation factor, for each level of this factor, one GLM will be computed."/>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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32 <expand macro="pampa_var_GLM"/>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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33 <conditional name="settings">
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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34 <expand macro="pampa_advanced_params_select_GLM"/>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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35 </conditional>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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36 </inputs>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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37 <outputs>
f0dc3958e65d "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 community analysis on ${on_string}"/>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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39 <expand macro="pampa_output_GLM"/>
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40 </outputs>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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41 <tests>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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42 <test>
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43 <param name="input_metric" value="Community_metrics_cropped.tabular"/>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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44 <param name="input_unitobs" value="Unitobs.tabular"/>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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45 <param name="varint" value="4"/>
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46 <param name="varrep" value="year,site,habitat"/>
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47 <param name="varrand" value="site"/>
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48 <param name="sep" value="22"/>
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49 <param name="advanced" value="simple"/>
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50 <output name="output_summary">
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51 <assert_contents>
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52 <has_n_lines n="9"/>
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53 </assert_contents>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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54 </output>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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55 <output name="output_recap">
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56 <assert_contents>
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57 <has_n_lines n="413"/>
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58 </assert_contents>
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59 </output>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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60 <output name="output_rate">
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61 <assert_contents>
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62 <has_n_lines n="51"/>
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63 </assert_contents>
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64 </output>
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65 </test>
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66 </tests>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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67 <help><![CDATA[
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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68 ==============================================================
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69 Compute GLM on community data with selected interest variables
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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70 ==============================================================
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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71
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72 **What it does**
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73
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74 This tool from PAMPA toolsuite computes Generalized Linear Models on community data.
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75
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76 It allows user to choose composition of the model :
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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77
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78 - Interest variable among numeric or integer variables of the input file
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79
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80 - Response variables among year, site and/or habitat
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81
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82 - Allocation of random effect on year and/or site
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83
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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84 |
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85
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86 **Input description**
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87
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88 A tabular file with community data. Must at least contain two or three columns depending on the case :
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89
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90 - ['year' and 'location'] or ['observation.unit']
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91
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92 - At least one community metric
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93
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94 +------------------+---------+---------+-----+
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95 | observation.unit | metric1 | metric2 | ... |
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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96 +==================+=========+=========+=====+
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97 | site_yearID | 2 | 0.4 | ... |
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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98 +------------------+---------+---------+-----+
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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99 | ... | ... | ... | ... |
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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100 +------------------+---------+---------+-----+
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101
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102 OR
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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103
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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104 +------+----------+---------+---------+-----+
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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105 | year | location | metric1 | metric2 | ... |
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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106 +======+==========+=========+=========+=====+
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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107 | 2000 |locationID| 2 | 0.4 | ... |
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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108 +------+----------+---------+---------+-----+
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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109 | ... | ... | ... | ... | ... |
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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110 +------+----------+---------+---------+-----+
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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111
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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112 The first input may be extracted from the 'Calculate community metrics' tool.
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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113
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114 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' column.
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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115
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116 +--------------------------------+---------+--------+------------+-----+
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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117 | observation.unit OR location | ??site? | year | habitat | ... |
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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118 +================================+=========+========+============+=====+
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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119 | site_yearID OR locationID | site ID | 2000 | habitatID | ... |
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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120 +--------------------------------+---------+--------+------------+-----+
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121 | ... | ... | ... | ... | ... |
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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122 +--------------------------------+---------+--------+------------+-----+
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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123
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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124 |
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125
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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126 **Output**
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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127
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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128 Two text files :
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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129
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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130 - A first text file with GLM results. When a separation factor is selected, one analysis is computed for every level and the last analysis is on the whole dataset.
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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131
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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132 - A second text file with simple statistics on the whole dataset.
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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133
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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134 |
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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135
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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136 **Source**
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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137
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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138 Derived from PAMPA scripts (https://wwz.ifremer.fr/pampa/Meth.-Outils/Outils) written by Yves Reecht.
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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139
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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140 ]]></help>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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141
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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142 <expand macro="pampa_bibref" />
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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143 </tool>