Mercurial > repos > ecology > regionalgam_glmmpql
comparison glmmpql.xml @ 0:f3e1b6d244a6 draft default tip
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
author | ecology |
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date | Thu, 20 Jun 2019 04:03:57 -0400 |
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1 <tool id="regionalgam_glmmpql" name="Expected temporal trend" version="@VERSION@"> | |
2 <description>of species abundance</description> | |
3 <macros> | |
4 <import>regionalgam_macros.xml</import> | |
5 </macros> | |
6 <expand macro="rg_nlme_mass_requirements"/> | |
7 <command detect_errors="exit_code"><![CDATA[ | |
8 Rscript '$__tool_directory__/glmmpql.R' | |
9 '$ab_indices' | |
10 '$output' '$output2' | |
11 ]]> | |
12 </command> | |
13 <inputs> | |
14 <expand macro="rg_ab_indices"/> | |
15 </inputs> | |
16 <outputs> | |
17 <data format="png" name="output" from_work_dir="output-plot.png" /> | |
18 <data format="tabular" name="output2" from_work_dir="output-glmmpql" /> | |
19 </outputs> | |
20 <tests> | |
21 <test> | |
22 <param name="ab_indices" value="s_data_index.tabular"/> | |
23 <output name="output2" ftype="tabular"> | |
24 <assert_contents> | |
25 <has_line_matching expression="5.5.*"/> | |
26 <has_line line=""x""/> | |
27 <has_n_columns n="1"/> | |
28 </assert_contents> | |
29 </output> | |
30 </test> | |
31 </tests> | |
32 <help><![CDATA[ | |
33 ===================================== | |
34 Temporal trends of species abundance | |
35 ===================================== | |
36 | |
37 This tool is an implementation of the glmmpql function from RegionalGAM package: https://github.com/RetoSchmucki/regionalGAM/ | |
38 | |
39 This function computes a collated index for each year and estimates the temporal trend. | |
40 | |
41 A collated index correspond to the expected value for a year, when taking into account the variation contained among sites. | |
42 | |
43 Here we also add an autoregressive term to account for temporal autocorrelation in the time series. | |
44 | |
45 | | |
46 | |
47 **Outputs** | |
48 | |
49 The tool returns the collated index in tabular format. | |
50 | |
51 It also and plot it against year for visualization in an output png file. | |
52 | |
53 ]]></help> | |
54 <expand macro="rg_citation"/> | |
55 </tool> |