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comparison pampa_macros.xml @ 0:c9dfe4e20a45 draft

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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
author ecology
date Tue, 21 Jul 2020 05:59:49 -0400
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children 8d8aec182fb1
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-1:000000000000 0:c9dfe4e20a45
1 <macros>
2 <token name="@VERSION@">0.0.1</token>
3 <xml name="Pampa_requirements">
4 <requirements>
5 <requirement type="package" version="1.0.2">r-tidyr</requirement>
6 </requirements>
7 </xml>
8 <xml name="GLM_requirements">
9 <requirements>
10 <requirement type="package" version="1.2.2">r-gap</requirement>
11 <requirement type="package" version="1.0.1">r-glmmtmb</requirement>
12 <requirement type="package" version="1.4_13">r-multcomp</requirement>
13 </requirements>
14 </xml>
15 <xml name="Plot_requirements">
16 <requirements>
17 <requirement type="package" version="3.1.1">r-ggplot2</requirement>
18 </requirements>
19 </xml>
20 <xml name="pampa_input_calculate">
21 <param name="input" type="data" format="tabular" label="Input file" help="Observation data file, with location, year, species and abundance."/>
22 </xml>
23 <xml name="pampa_advanced_params_select">
24 <param name="advanced" type="select" label="Specify advanced parameters">
25 <option value="simple" selected="true">No, use program defaults.</option>
26 <option value="advanced">Yes, see full parameter list.</option>
27 </param>
28 <when value="simple">
29 </when>
30 </xml>
31 <xml name="pampa_advanced_params_select_GLM">
32 <param name="advanced" type="select" label="Specify advanced parameters">
33 <option value="simple" selected="true">No, use program defaults.</option>
34 <option value="advanced">Yes, see full parameter list.</option>
35 </param>
36 <when value="simple">
37 </when>
38 <when value="advanced">
39 <param name="distrib" type="select" label="Distribution for model">
40 <option selected="true" value="None">Auto</option>
41 <option value="gaussian">Gaussian</option>
42 <option value="inverse.gaussian">Inverse Gaussian</option>
43 <option value="poisson">Poisson</option>
44 <option value="quasipoisson">Quasi-Poisson</option>
45 <option value="binomial">Binomial</option>
46 <option value="quasibinomial">Quasi-Binomial</option>
47 <option value="Gamma">Gamma</option>
48 </param>
49 </when>
50 </xml>
51 <xml name="pampa_input_GLM">
52 <param name="input_metric" type="data" format="tabular" label="Input metrics file" help="Metrics data file, with location, year, and metrics informations that can be used as interest variable."/>
53 <param name="input_unitobs" type="data" format="tabular" label="Unitobs informations file" help="Unitobs file, with all informations available about unitobs."/>
54 <param name="varint" type="data_column" data_ref="input_metric" label="Interest variable from metrics file" help= "Choose the field of the interest variable."/>
55 </xml>
56 <xml name="pampa_var_GLM">
57 <param name="varrep" type="select" label="Response variables" help= "Choose the response variables you want to include in your analysis." multiple="true">
58 <option selected="true" value="year">Year</option>
59 <option selected="true" value="site">Site</option>
60 <option selected="true" value="habitat">Habitat</option>
61 </param>
62 <param name="varrand" type="select" label="Random effect ?" help="Allocate a random effect on site or year makes your model more reliable as random events on a peculiar site or year can affect populations, it takes account of pseudoreplication. However, avoid applying it on a less than 10 levels variable (less than 10 different sites and/or year)." multiple="true">
63 <option value="year">Year</option>
64 <option selected="true" value="site">Site</option>
65 </param>
66 </xml>
67 <xml name="pampa_output_GLM">
68 <data name="output_recap" from_work_dir="GLMSummaryFull.txt" format="txt" label="Simple statistics on chosen variables on ${on_string}"/>
69 <data name="output_rate" from_work_dir="RatingGLM.txt" format="txt" label="Your analysis rating file on ${on_string}"/>
70 </xml>
71 <xml name="pampa_bibref">
72 <citations>
73 <citation type="bibtex">
74 @unpublished{pampayves,
75 title={ PAMPA "ressources et biodiversité" scripts },
76 author={Yves Reecht},
77 url={https://wwz.ifremer.fr/pampa/Meth.-Outils/Outils}
78 }
79 </citation>
80 </citations>
81 </xml>
82 </macros>