Mercurial > repos > ecology > pampa_glmcomm

annotate pampa_macros.xml @ 0:f0dc3958e65d 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 06:00:31 -0400
parents
children 44b9069775ca
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
1 <macros>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
2 <token name="@VERSION@">0.0.1</token>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
3 <xml name="Pampa_requirements">
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
4 <requirements>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
5 <requirement type="package" version="1.0.2">r-tidyr</requirement>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
6 </requirements>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
7 </xml>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
8 <xml name="GLM_requirements">
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
9 <requirements>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
10 <requirement type="package" version="1.2.2">r-gap</requirement>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
11 <requirement type="package" version="1.0.1">r-glmmtmb</requirement>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
12 <requirement type="package" version="1.4_13">r-multcomp</requirement>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
13 </requirements>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
14 </xml>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
15 <xml name="Plot_requirements">
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
16 <requirements>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
17 <requirement type="package" version="3.1.1">r-ggplot2</requirement>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
18 </requirements>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
19 </xml>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
20 <xml name="pampa_input_calculate">
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
21 <param name="input" type="data" format="tabular" label="Input file" help="Observation data file, with location, year, species and abundance."/>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
22 </xml>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
23 <xml name="pampa_advanced_params_select">
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
24 <param name="advanced" type="select" label="Specify advanced parameters">
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
25 <option value="simple" selected="true">No, use program defaults.</option>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
26 <option value="advanced">Yes, see full parameter list.</option>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
27 </param>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
28 <when value="simple">
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
29 </when>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
30 </xml>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
31 <xml name="pampa_advanced_params_select_GLM">
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
32 <param name="advanced" type="select" label="Specify advanced parameters">
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
33 <option value="simple" selected="true">No, use program defaults.</option>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
34 <option value="advanced">Yes, see full parameter list.</option>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
35 </param>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
36 <when value="simple">
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
37 </when>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
38 <when value="advanced">
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
39 <param name="distrib" type="select" label="Distribution for model">
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
40 <option selected="true" value="None">Auto</option>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
41 <option value="gaussian">Gaussian</option>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
42 <option value="inverse.gaussian">Inverse Gaussian</option>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
43 <option value="poisson">Poisson</option>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
44 <option value="quasipoisson">Quasi-Poisson</option>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
45 <option value="binomial">Binomial</option>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
46 <option value="quasibinomial">Quasi-Binomial</option>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
47 <option value="Gamma">Gamma</option>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
48 </param>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
49 </when>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
50 </xml>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
51 <xml name="pampa_input_GLM">
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
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."/>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
53 <param name="input_unitobs" type="data" format="tabular" label="Unitobs informations file" help="Unitobs file, with all informations available about unitobs."/>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
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."/>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
55 </xml>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
56 <xml name="pampa_var_GLM">
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
57 <param name="varrep" type="select" label="Response variables" help= "Choose the response variables you want to include in your analysis." multiple="true">
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
58 <option selected="true" value="year">Year</option>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
59 <option selected="true" value="site">Site</option>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
60 <option selected="true" value="habitat">Habitat</option>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
61 </param>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
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">
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
63 <option value="year">Year</option>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
64 <option selected="true" value="site">Site</option>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
65 </param>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
66 </xml>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
67 <xml name="pampa_output_GLM">
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
68 <data name="output_recap" from_work_dir="GLMSummaryFull.txt" format="txt" label="Simple statistics on chosen variables on ${on_string}"/>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
69 <data name="output_rate" from_work_dir="RatingGLM.txt" format="txt" label="Your analysis rating file on ${on_string}"/>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
70 </xml>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
71 <xml name="pampa_bibref">
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
72 <citations>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
73 <citation type="bibtex">
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
74 @unpublished{pampayves,
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
75 title={ PAMPA "ressources et biodiversité" scripts },
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
76 author={Yves Reecht},
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
77 url={https://wwz.ifremer.fr/pampa/Meth.-Outils/Outils}
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
78 }
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
79 </citation>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
80 </citations>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
81 </xml>
f0dc3958e65d "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
82 </macros>