Mercurial > repos > ecology > pampa_communitymetrics

comparison pampa_macros.xml @ 5:5bd7ddd7601f 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 04381ca7162ec3ec68419e308194b91d11cacb04"
author ecology
date Mon, 16 Nov 2020 11:02:24 +0000
parents ddd5b2e74b8b
children 2cd0a5a321c2
comparison
equal deleted inserted replaced
4:5873ac1a5a44 5:5bd7ddd7601f
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&lt;designation&gt;.+)\.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,