Mercurial > repos > ecology > stoc_maketable

comparison makeTableAnalyse.xml @ 0:22a784d2b0e0 draft

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"planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
author ecology
date Thu, 02 Apr 2020 03:33:29 -0400
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-1:000000000000 0:22a784d2b0e0
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>