Mercurial > repos > ecology > pampa_glmcomm

annotate PAMPA_GLM.xml @ 4:44b9069775ca draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
author ecology
date Sun, 22 Nov 2020 18:40:23 +0000
parents 97967fbcf6da
children 8db02073b671
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f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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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>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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3 <macros>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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4 <import>pampa_macros.xml</import>
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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 '$__tool_directory__/FunctExeCalcGLMGalaxy.r'
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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10 '$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'
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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17 $settings.distrib
4
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18 $settings.rdata
0
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19 #else
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20 'None'
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21 'false'
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22 #end if
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23 'unit'
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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24 '$__tool_directory__/FunctPAMPAGalaxy.r'
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25 '$output_summary'
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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26 '$output_recap'
4
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27 '$output_rate'
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28 #if $settings.advanced=='advanced'
44b9069775ca "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
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29 #if $settings.rdata=='true'
44b9069775ca "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
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30 '$output_GLM'
44b9069775ca "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
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31 #end if
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32 #end if
0
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33 ]]>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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34 </command>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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35 <inputs>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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36 <expand macro="pampa_input_GLM"/>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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37 <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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38 <expand macro="pampa_var_GLM"/>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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39 <conditional name="settings">
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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40 <expand macro="pampa_advanced_params_select_GLM"/>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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41 </conditional>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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42 </inputs>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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43 <outputs>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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44 <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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45 <expand macro="pampa_output_GLM"/>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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46 </outputs>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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47 <tests>
4
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48 <test expect_num_outputs="4">
0
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49 <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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50 <param name="input_unitobs" value="Unitobs.tabular"/>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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51 <param name="varint" value="4"/>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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52 <param name="varrep" value="year,site,habitat"/>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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53 <param name="varrand" value="site"/>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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54 <param name="sep" value="22"/>
4
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55 <param name="advanced" value="advanced"/>
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56 <param name="distrib" value="None"/>
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57 <param name="rdata" value="true"/>
0
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58 <output name="output_summary">
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59 <assert_contents>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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60 <has_n_lines n="9"/>
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61 </assert_contents>
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62 </output>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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63 <output name="output_recap">
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64 <assert_contents>
4
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65 <has_n_lines n="412"/>
0
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66 </assert_contents>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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67 </output>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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68 <output name="output_rate">
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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69 <assert_contents>
4
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70 <has_n_lines n="50"/>
0
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71 </assert_contents>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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72 </output>
4
44b9069775ca "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
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73 <output_collection name="output_GLM" type="list" count="3">
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74 <element name="GLM_HR" ftype="Rdata">
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75 <assert_contents>
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76 <has_size value="185018" delta="10000"/>
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77 </assert_contents>
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78 </element>
44b9069775ca "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
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79 <element name="GLM_RE" ftype="Rdata">
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80 <assert_contents>
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81 <has_size value="168685" delta="10000"/>
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82 </assert_contents>
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83 </element>
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84 <element name="global_GLM" ftype="Rdata">
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85 <assert_contents>
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86 <has_size value="195910" delta="10000"/>
44b9069775ca "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
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87 </assert_contents>
44b9069775ca "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
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88 </element>
44b9069775ca "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
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89 </output_collection>
0
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90 </test>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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91 </tests>
3
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92 <edam_topics>
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93 <edam_topic>topic_0610</edam_topic>
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94 <edam_topic>topic_3050</edam_topic>
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95 </edam_topics>
0
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96 <help><![CDATA[
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97 ==============================================================
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98 Compute GLM on community data with selected interest variables
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99 ==============================================================
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100
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101 **What it does**
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102
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103 This tool from PAMPA toolsuite computes Generalized Linear Models on community data.
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104
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105 It allows user to choose composition of the model :
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106
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107 - Interest variable among numeric or integer variables of the input file
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108
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109 - Response variables among year, site and/or habitat
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110
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111 - Allocation of random effect on year and/or site
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112
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113 |
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114
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115 **Input description**
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116
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117 A tabular file with community data. Must at least contain two or three columns depending on the case :
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118
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119 - ['year' and 'location'] or ['observation.unit']
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120
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121 - At least one community metric
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122
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123 +------------------+---------+---------+-----+
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124 | observation.unit | metric1 | metric2 | ... |
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125 +==================+=========+=========+=====+
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126 | site_yearID | 2 | 0.4 | ... |
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127 +------------------+---------+---------+-----+
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128 | ... | ... | ... | ... |
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129 +------------------+---------+---------+-----+
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130
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131 OR
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132
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133 +------+----------+---------+---------+-----+
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134 | year | location | metric1 | metric2 | ... |
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135 +======+==========+=========+=========+=====+
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136 | 2000 |locationID| 2 | 0.4 | ... |
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137 +------+----------+---------+---------+-----+
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138 | ... | ... | ... | ... | ... |
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139 +------+----------+---------+---------+-----+
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140
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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141 The first input may be extracted from the 'Calculate community metrics' tool.
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142
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143 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.
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144
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145 +--------------------------------+---------+--------+------------+-----+
4
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146 | observation.unit OR location | site | year | habitat | ... |
0
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147 +================================+=========+========+============+=====+
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148 | site_yearID OR locationID | site ID | 2000 | habitatID | ... |
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149 +--------------------------------+---------+--------+------------+-----+
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150 | ... | ... | ... | ... | ... |
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151 +--------------------------------+---------+--------+------------+-----+
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152
4
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153 The site may represent the same entity as the location or represent an aggregation of several locations
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154
0
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155 |
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156
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157 **Output**
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158
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159 Two text files :
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160
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161 - 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.
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162
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163 - A second text file with simple statistics on the whole dataset.
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164
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165 |
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166
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167 **Source**
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168
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169 Derived from PAMPA scripts (https://wwz.ifremer.fr/pampa/Meth.-Outils/Outils) written by Yves Reecht.
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170
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171 ]]></help>
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172 <expand macro="pampa_bibref" />
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173 </tool>