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comparison PAMPA_GLM.xml @ 5:8db02073b671 draft

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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit cd938a05cb066b16f2518159fa0ff5e3ed8a2b2b"
author ecology
date Mon, 26 Apr 2021 16:05:19 +0000
parents 44b9069775ca
children b40fecef616b
comparison
equal deleted inserted replaced
4:44b9069775ca 5:8db02073b671
32 #end if 32 #end if
33 ]]> 33 ]]>
34 </command> 34 </command>
35 <inputs> 35 <inputs>
36 <expand macro="pampa_input_GLM"/> 36 <expand macro="pampa_input_GLM"/>
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."/> 37 <param name="sep" type="data_column" data_ref="input_unitobs" use_header_names="true" 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."/>
38 <expand macro="pampa_var_GLM"/> 38 <expand macro="pampa_var_GLM"/>
39 <conditional name="settings"> 39 <conditional name="settings">
40 <expand macro="pampa_advanced_params_select_GLM"/> 40 <expand macro="pampa_advanced_params_select_GLM"/>
41 </conditional> 41 </conditional>
42 </inputs> 42 </inputs>
108 108
109 - Response variables among year, site and/or habitat 109 - Response variables among year, site and/or habitat
110 110
111 - Allocation of random effect on year and/or site 111 - Allocation of random effect on year and/or site
112 112
113 - (optional) Separation factor to compute several GLMs
114
113 | 115 |
114 116
115 **Input description** 117 **Input description**
116 118
117 A tabular file with community data. Must at least contain two or three columns depending on the case : 119 A tabular file with community data. Must at least contain two or three columns depending on the case :
118 120
119 - ['year' and 'location'] or ['observation.unit'] 121 - ['year' and 'location'] or ['observation.unit']
120 122
121 - At least one community metric 123 - At least one community metric
122 124
123 +------------------+---------+---------+-----+ 125 +----------------------+---------+---------+-----+
124 | observation.unit | metric1 | metric2 | ... | 126 | observation.unit | metric1 | metric2 | ... |
125 +==================+=========+=========+=====+ 127 +======================+=========+=========+=====+
126 | site_yearID | 2 | 0.4 | ... | 128 | year_locationID | 2 | 0.4 | ... |
127 +------------------+---------+---------+-----+ 129 +----------------------+---------+---------+-----+
128 | ... | ... | ... | ... | 130 | ... | ... | ... | ... |
129 +------------------+---------+---------+-----+ 131 +----------------------+---------+---------+-----+
130 132
131 OR 133 OR
132 134
133 +------+----------+---------+---------+-----+ 135 +------+----------+---------+---------+-----+
134 | year | location | metric1 | metric2 | ... | 136 | year | location | metric1 | metric2 | ... |
138 | ... | ... | ... | ... | ... | 140 | ... | ... | ... | ... | ... |
139 +------+----------+---------+---------+-----+ 141 +------+----------+---------+---------+-----+
140 142
141 The first input may be extracted from the 'Calculate community metrics' tool. 143 The first input may be extracted from the 'Calculate community metrics' tool.
142 144
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. 145 A tabular file with observation unit data which contains at least as much columns as used response variables and separation factor in addition with the 'observation.unit' column.
144 146
145 +--------------------------------+---------+--------+------------+-----+ 147 +----------------------+---------+--------+------------+-----+
146 | observation.unit OR location | site | year | habitat | ... | 148 | observation.unit | site | year | habitat | ... |
147 +================================+=========+========+============+=====+ 149 +======================+=========+========+============+=====+
148 | site_yearID OR locationID | site ID | 2000 | habitatID | ... | 150 | year_locationID | site ID | 2000 | habitatID | ... |
149 +--------------------------------+---------+--------+------------+-----+ 151 +----------------------+---------+--------+------------+-----+
150 | ... | ... | ... | ... | ... | 152 | ... | ... | ... | ... | ... |
151 +--------------------------------+---------+--------+------------+-----+ 153 +----------------------+---------+--------+------------+-----+
152 154
153 The site may represent the same entity as the location or represent an aggregation of several locations 155 The site may represent the same entity as the location or represent an aggregation of several locations
154 156
155 | 157 |
156 158
157 **Output** 159 **Output**
158 160
159 Two text files : 161 Three text files :
160 162
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. 163 - A first tabular 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.
162 164
163 - A second text file with simple statistics on the whole dataset. 165 - A second text file with simple statistics on the whole dataset.
166
167 - A third text file with ratings of your analysis based on several criterias.
164 168
165 | 169 |
166 170
167 **Source** 171 **Source**
168 172