Mercurial > repos > ecology > pampa_glmsp

annotate PAMPA_GLM_SP.xml @ 0:0778efa9eb2e 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 07f1028cc764f920b1e6419c151f04ab4e3600fa"
author ecology
date Tue, 21 Jul 2020 06:00:51 -0400
parents
children e972fe2bffee
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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>
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4 <import>pampa_macros.xml</import>
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5 </macros>
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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[
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8 Rscript
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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9 '$__tool_directory__/FunctExeCalcGLMSpGalaxy.r'
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10 '$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"
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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'
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15 'species.code'
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16 #if $settings.advanced=='advanced'
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17 $settings.distrib
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18 'FALSE'
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19 #else
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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20 'None'
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21 'FALSE'
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22 #end if
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23 'unitSp'
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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24 '$__tool_directory__/FunctPAMPAGalaxy.r'
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25 '$output_summary'
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26 '$output_recap'
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27 ]]>
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28 </command>
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29 <inputs>
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30 <expand macro="pampa_input_GLM"/>
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31 <expand macro="pampa_var_GLM"/>
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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
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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>
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42 <test>
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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"/>
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46 <param name="varrep" value="year,site,habitat"/>
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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"/>
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49 <output name="output_summary">
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50 <assert_contents>
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51 <has_n_lines n="4"/>
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52 </assert_contents>
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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">
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55 <assert_contents>
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56 <has_n_lines n="607"/>
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57 </assert_contents>
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58 </output>
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59 <output name="output_rate">
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60 <assert_contents>
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61 <has_n_lines n="46"/>
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62 </assert_contents>
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63 </output>
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64 </test>
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65 </tests>
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66 <help><![CDATA[
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67 ===============================================================
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68 Compute GLM on population data with selected interest variables
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69 ===============================================================
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70
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71 **What it does**
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72
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73 This tool from PAMPA toolsuite computes Generalized Linear Models on population data.
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74
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75 It allows user to choose composition of the model :
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76
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77 - Interest variable among numeric or integer variables of the input file
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78
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79 - Response variables among year, site and/or habitat
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80
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81 - Allocation of random effect on year and/or site
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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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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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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 +==================+==============+=========+=========+=====+
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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98 | site_yearID | species code | 2 | 0.4 | ... |
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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99 +------------------+--------------+---------+---------+-----+
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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100 | ... | ... | ... | ... | ... |
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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101 +------------------+--------------+---------+---------+-----+
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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102
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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103 OR
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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104
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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105 +------+----------+--------------+---------+---------+-----+
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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106 | year | location | species.code | metric1 | metric2 | ... |
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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107 +======+==========+==============+=========+=========+=====+
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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108 | 2000 |locationID| species code | 2 | 0.4 | ... |
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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109 +------+----------+--------------+---------+---------+-----+
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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110 | ... | ... | ... | ... | ... | ... |
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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111 +------+----------+--------------+---------+---------+-----+
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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112
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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113 The first input may be extracted from the 'Calculate presence absence' tool.
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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114
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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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.
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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116
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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117 +--------------------------------+--------------+---------+--------+------------+-----+
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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118 | observation.unit OR location | species.code | site | year | habitat | ... |
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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119 +================================+==============+=========+========+============+=====+
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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120 | site_yearID OR locationID | species code | site ID | 2000 | habitatID | ... |
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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121 +--------------------------------+--------------+---------+--------+------------+-----+
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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122 | ... | ... | ... | ... | ... | ... |
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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123 +--------------------------------+--------------+---------+--------+------------+-----+
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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124
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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125 |
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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126
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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127 **Output**
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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128
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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129 Two text files :
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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130
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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131 - A first text file with GLM results. One analysis per species.
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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132
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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133 - A second text file with simple statistics on the whole dataset.
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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134
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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135 |
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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136
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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137 **Source**
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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138
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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139 Derived from PAMPA scripts (https://wwz.ifremer.fr/pampa/Meth.-Outils/Outils) written by Yves Reecht.
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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140
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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141 ]]></help>
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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142
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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143 <expand macro="pampa_bibref" />
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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144 </tool>