Mercurial > repos > ecology > stoc_maketable
comparison makeTableAnalyse.xml @ 0:22a784d2b0e0 draft
"planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
author | ecology |
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date | Thu, 02 Apr 2020 03:33:29 -0400 |
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1 <tool id="stoceps_maketablecarrer" name="Preprocess population data" version="@VERSION@"> | |
2 <description>for evolution trend analyzes</description> | |
3 <macros> | |
4 <import>stoceps_macros.xml</import> | |
5 </macros> | |
6 <expand macro="reshape_requirements"/> | |
7 <command detect_errors="exit_code"><![CDATA[ | |
8 Rscript | |
9 '$__tool_directory__/ExemakeTableAnalyseGalaxy.r' | |
10 '$input' | |
11 '$__tool_directory__/FunctTrendSTOCGalaxy.r' | |
12 '$output' | |
13 ]]> | |
14 </command> | |
15 <inputs> | |
16 <param name="input" type="data" format="tabular" label="Input file" help="Population count file, with location, date, species and abundance."/> | |
17 </inputs> | |
18 <outputs> | |
19 <data name="output" from_work_dir="Datatransformedforfiltering_trendanalysis.tabular" format="tabular"/> | |
20 </outputs> | |
21 <tests> | |
22 <test> | |
23 <param name="input" value="data_FrenchBBS_squarre_dataSTOCallSp_France_trend_2001_2017_ALAARV-PARCAE_2001_2018.tabular"/> | |
24 <output name="output" file="Datatransformedforfiltering_trendanalysis.tabular"/> | |
25 </test> | |
26 </tests> | |
27 <help><![CDATA[ | |
28 =============================== | |
29 STOC preprocess population data | |
30 =============================== | |
31 | |
32 **What it does** | |
33 | |
34 Reshape the data for the next steps of STOC analyzes by adding zero count to sites that are in the dataset, for species having no count data for those sites. | |
35 | |
36 | |
37 | | |
38 | |
39 **Input description** | |
40 | |
41 A tabular file with abundance per year, per site and per species with no or few zero abundance. | |
42 | |
43 The data file can be extracted from the STOC database on demand : romain.lorrilliere@mnhn.fr | |
44 | |
45 The table needs the following structure (at least these 4 fours columns) : | |
46 | |
47 +-----------+---------+----------+---------+ | |
48 | carre | annee | espece | abond | | |
49 +===========+=========+==========+=========+ | |
50 | carreId1 | 2019 | especeId | 12 | | |
51 +-----------+---------+----------+---------+ | |
52 | ... | ... | ... | ... | | |
53 +-----------+---------+----------+---------+ | |
54 | |
55 | | |
56 | |
57 **Output** | |
58 | |
59 A tabular file transformed, with one column indicating the year, one indicating the site, and one column for each species abundance. | |
60 | |
61 This file is ready for the next filtering steps. | |
62 | |
63 | | |
64 | |
65 **Source** | |
66 | |
67 UnPublished script available at http://www.vigienature.fr/sites/vigienature/files/atoms/files/analysestoceps_0.zip | |
68 | |
69 First version written by romain.lorrilliere@mnhn.fr | |
70 ]]></help> | |
71 | |
72 <expand macro="stoceps_bibref" /> | |
73 </tool> |