Mercurial > repos > ecology > pampa_glmsp
comparison pampa_macros.xml @ 2:6c14021f678e draft
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
author | ecology |
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date | Sun, 22 Nov 2020 18:40:40 +0000 |
parents | 0778efa9eb2e |
children | c12897ba5f83 |
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1:e972fe2bffee | 2:6c14021f678e |
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1 <macros> | 1 <macros> |
2 <token name="@VERSION@">0.0.1</token> | 2 <token name="@VERSION@">0.0.2</token> |
3 <xml name="Pampa_requirements"> | 3 <xml name="Pampa_requirements"> |
4 <requirements> | 4 <requirements> |
5 <requirement type="package" version="1.0.2">r-tidyr</requirement> | 5 <requirement type="package" version="1.0.2">r-tidyr</requirement> |
6 </requirements> | 6 </requirements> |
7 </xml> | 7 </xml> |
8 <xml name="GLM_requirements"> | 8 <xml name="GLM_requirements"> |
9 <requirements> | 9 <requirements> |
10 <requirement type="package" version="1.2.2">r-gap</requirement> | 10 <requirement type="package" version="1.2.2">r-gap</requirement> |
11 <requirement type="package" version="1.0.1">r-glmmtmb</requirement> | 11 <requirement type="package" version="1.0.1">r-glmmtmb</requirement> |
12 <requirement type="package" version="1.4_13">r-multcomp</requirement> | 12 <requirement type="package" version="1.4_13">r-multcomp</requirement> |
13 <requirement type="package" version="0.3.3.0">r-dharma</requirement> | |
13 </requirements> | 14 </requirements> |
14 </xml> | 15 </xml> |
15 <xml name="Plot_requirements"> | 16 <xml name="Plot_requirements"> |
16 <requirements> | 17 <requirements> |
17 <requirement type="package" version="3.1.1">r-ggplot2</requirement> | 18 <requirement type="package" version="3.1.1">r-ggplot2</requirement> |
19 <requirement type="package" version="1.3_25">r-boot</requirement> | |
18 </requirements> | 20 </requirements> |
19 </xml> | 21 </xml> |
20 <xml name="pampa_input_calculate"> | 22 <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."/> | 23 <param name="input" type="data" format="tabular" label="Input file" help="Observation data file, with location, year, species and abundance."/> |
22 </xml> | 24 </xml> |
44 <option value="quasipoisson">Quasi-Poisson</option> | 46 <option value="quasipoisson">Quasi-Poisson</option> |
45 <option value="binomial">Binomial</option> | 47 <option value="binomial">Binomial</option> |
46 <option value="quasibinomial">Quasi-Binomial</option> | 48 <option value="quasibinomial">Quasi-Binomial</option> |
47 <option value="Gamma">Gamma</option> | 49 <option value="Gamma">Gamma</option> |
48 </param> | 50 </param> |
51 <param name="rdata" type="boolean" checked="yes" label="GLM object(s) as .Rdata output ?"/> | |
49 </when> | 52 </when> |
50 </xml> | 53 </xml> |
51 <xml name="pampa_input_GLM"> | 54 <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."/> | 55 <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."/> | 56 <param name="input_unitobs" type="data" format="tabular" label="Unitobs informations file" help="Unitobs file, with all informations available about unitobs."/> |
65 </param> | 68 </param> |
66 </xml> | 69 </xml> |
67 <xml name="pampa_output_GLM"> | 70 <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}"/> | 71 <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}"/> | 72 <data name="output_rate" from_work_dir="RatingGLM.txt" format="txt" label="Your analysis rating file on ${on_string}"/> |
73 <collection type="list" name="output_GLM"> | |
74 <discover_datasets pattern="(?P<designation>.+)\.Rdata" visible="false" format="Rdata"/> | |
75 <filter> settings['advanced'] == 'advanced' and settings['rdata']</filter> | |
76 </collection> | |
70 </xml> | 77 </xml> |
71 <xml name="pampa_bibref"> | 78 <xml name="pampa_bibref"> |
72 <citations> | 79 <citations> |
73 <citation type="bibtex"> | 80 <citation type="bibtex"> |
74 @unpublished{pampayves, | 81 @unpublished{pampayves, |