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comparison 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
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children 61cc30e94df4
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-1:000000000000 0:f0dc3958e65d
1 <tool id="pampa_glmcomm" name="Compute GLM on community data" version="@VERSION@">
2 <description>Compute a GLM of your choice on community data</description>
3 <macros>
4 <import>pampa_macros.xml</import>
5 </macros>
6 <expand macro="GLM_requirements"/>
7 <command detect_errors="exit_code"><![CDATA[
8 Rscript
9 '$__tool_directory__/FunctExeCalcGLMGalaxy.r'
10 '$input_metric'
11 '$input_unitobs'
12 '$varint'
13 '$varrep'
14 '$varrand'
15 '$sep'
16 #if $settings.advanced=='advanced'
17 $settings.distrib
18 'FALSE'
19 #else
20 'None'
21 'FALSE'
22 #end if
23 'unit'
24 '$__tool_directory__/FunctPAMPAGalaxy.r'
25 '$output_summary'
26 '$output_recap'
27 ]]>
28 </command>
29 <inputs>
30 <expand macro="pampa_input_GLM"/>
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."/>
32 <expand macro="pampa_var_GLM"/>
33 <conditional name="settings">
34 <expand macro="pampa_advanced_params_select_GLM"/>
35 </conditional>
36 </inputs>
37 <outputs>
38 <data name="output_summary" from_work_dir="GLMSummary.tabular" format="tabular" label="GLM - Results from your community analysis on ${on_string}"/>
39 <expand macro="pampa_output_GLM"/>
40 </outputs>
41 <tests>
42 <test>
43 <param name="input_metric" value="Community_metrics_cropped.tabular"/>
44 <param name="input_unitobs" value="Unitobs.tabular"/>
45 <param name="varint" value="4"/>
46 <param name="varrep" value="year,site,habitat"/>
47 <param name="varrand" value="site"/>
48 <param name="sep" value="22"/>
49 <param name="advanced" value="simple"/>
50 <output name="output_summary">
51 <assert_contents>
52 <has_n_lines n="9"/>
53 </assert_contents>
54 </output>
55 <output name="output_recap">
56 <assert_contents>
57 <has_n_lines n="413"/>
58 </assert_contents>
59 </output>
60 <output name="output_rate">
61 <assert_contents>
62 <has_n_lines n="51"/>
63 </assert_contents>
64 </output>
65 </test>
66 </tests>
67 <help><![CDATA[
68 ==============================================================
69 Compute GLM on community data with selected interest variables
70 ==============================================================
71
72 **What it does**
73
74 This tool from PAMPA toolsuite computes Generalized Linear Models on community data.
75
76 It allows user to choose composition of the model :
77
78 - Interest variable among numeric or integer variables of the input file
79
80 - Response variables among year, site and/or habitat
81
82 - Allocation of random effect on year and/or site
83
84 |
85
86 **Input description**
87
88 A tabular file with community data. Must at least contain two or three columns depending on the case :
89
90 - ['year' and 'location'] or ['observation.unit']
91
92 - At least one community metric
93
94 +------------------+---------+---------+-----+
95 | observation.unit | metric1 | metric2 | ... |
96 +==================+=========+=========+=====+
97 | site_yearID | 2 | 0.4 | ... |
98 +------------------+---------+---------+-----+
99 | ... | ... | ... | ... |
100 +------------------+---------+---------+-----+
101
102 OR
103
104 +------+----------+---------+---------+-----+
105 | year | location | metric1 | metric2 | ... |
106 +======+==========+=========+=========+=====+
107 | 2000 |locationID| 2 | 0.4 | ... |
108 +------+----------+---------+---------+-----+
109 | ... | ... | ... | ... | ... |
110 +------+----------+---------+---------+-----+
111
112 The first input may be extracted from the 'Calculate community metrics' tool.
113
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.
115
116 +--------------------------------+---------+--------+------------+-----+
117 | observation.unit OR location | ??site? | year | habitat | ... |
118 +================================+=========+========+============+=====+
119 | site_yearID OR locationID | site ID | 2000 | habitatID | ... |
120 +--------------------------------+---------+--------+------------+-----+
121 | ... | ... | ... | ... | ... |
122 +--------------------------------+---------+--------+------------+-----+
123
124 |
125
126 **Output**
127
128 Two text files :
129
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.
131
132 - A second text file with simple statistics on the whole dataset.
133
134 |
135
136 **Source**
137
138 Derived from PAMPA scripts (https://wwz.ifremer.fr/pampa/Meth.-Outils/Outils) written by Yves Reecht.
139
140 ]]></help>
141
142 <expand macro="pampa_bibref" />
143 </tool>