Mercurial > repos > ecology > pampa_glmcomm

annotate PAMPA_GLM.xml @ 3:97967fbcf6da 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 e8643d3d2e48d2ec7fcb2bd5abf77869a8687422"
author ecology
date Mon, 27 Jul 2020 09:52:47 -0400
parents 11165d05c768
children 44b9069775ca
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0
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1 <tool id="pampa_glmcomm" name="Compute GLM on community data" version="@VERSION@">
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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>
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5 </macros>
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6 <expand macro="GLM_requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 Rscript
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9 '$__tool_directory__/FunctExeCalcGLMGalaxy.r'
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10 '$input_metric'
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11 '$input_unitobs'
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12 '$varint'
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13 '$varrep'
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14 '$varrand'
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15 '$sep'
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16 #if $settings.advanced=='advanced'
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17 $settings.distrib
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18 'FALSE'
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19 #else
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20 'None'
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21 'FALSE'
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22 #end if
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23 'unit'
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24 '$__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 <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"/>
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33 <conditional name="settings">
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34 <expand macro="pampa_advanced_params_select_GLM"/>
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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>
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37 <outputs>
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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>
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41 <tests>
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42 <test>
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43 <param name="input_metric" value="Community_metrics_cropped.tabular"/>
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44 <param name="input_unitobs" value="Unitobs.tabular"/>
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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>
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54 </output>
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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>
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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>
3
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67 <edam_topics>
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68 <edam_topic>topic_0610</edam_topic>
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69 <edam_topic>topic_3050</edam_topic>
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70 </edam_topics>
0
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71 <help><![CDATA[
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72 ==============================================================
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73 Compute GLM on community data with selected interest variables
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74 ==============================================================
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75
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76 **What it does**
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77
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78 This tool from PAMPA toolsuite computes Generalized Linear Models on community data.
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79
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80 It allows user to choose composition of the model :
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81
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82 - Interest variable among numeric or integer variables of the input file
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83
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84 - Response variables among year, site and/or habitat
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85
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86 - Allocation of random effect on year and/or site
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87
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88 |
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89
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90 **Input description**
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91
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92 A tabular file with community data. Must at least contain two or three columns depending on the case :
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93
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94 - ['year' and 'location'] or ['observation.unit']
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95
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96 - At least one community metric
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97
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98 +------------------+---------+---------+-----+
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99 | observation.unit | metric1 | metric2 | ... |
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100 +==================+=========+=========+=====+
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101 | site_yearID | 2 | 0.4 | ... |
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102 +------------------+---------+---------+-----+
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103 | ... | ... | ... | ... |
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104 +------------------+---------+---------+-----+
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105
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106 OR
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107
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108 +------+----------+---------+---------+-----+
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109 | year | location | metric1 | metric2 | ... |
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110 +======+==========+=========+=========+=====+
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111 | 2000 |locationID| 2 | 0.4 | ... |
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112 +------+----------+---------+---------+-----+
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113 | ... | ... | ... | ... | ... |
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114 +------+----------+---------+---------+-----+
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115
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116 The first input may be extracted from the 'Calculate community metrics' tool.
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117
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118 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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119
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120 +--------------------------------+---------+--------+------------+-----+
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121 | observation.unit OR location | ??site? | year | habitat | ... |
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122 +================================+=========+========+============+=====+
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123 | site_yearID OR locationID | site ID | 2000 | habitatID | ... |
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124 +--------------------------------+---------+--------+------------+-----+
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125 | ... | ... | ... | ... | ... |
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126 +--------------------------------+---------+--------+------------+-----+
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127
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128 |
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129
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130 **Output**
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131
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132 Two text files :
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133
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134 - 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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135
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136 - A second text file with simple statistics on the whole dataset.
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137
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138 |
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139
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140 **Source**
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141
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142 Derived from PAMPA scripts (https://wwz.ifremer.fr/pampa/Meth.-Outils/Outils) written by Yves Reecht.
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143
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144 ]]></help>
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145
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146 <expand macro="pampa_bibref" />
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147 </tool>