view makeTableAnalyse.xml @ 0:22a784d2b0e0 draft

"planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"

<tool id="stoceps_maketablecarrer" name="Preprocess population data" version="@VERSION@">
    <description>for evolution trend analyzes</description>
    <macros>
        <import>stoceps_macros.xml</import>
    </macros>
    <expand macro="reshape_requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        Rscript 
         '$__tool_directory__/ExemakeTableAnalyseGalaxy.r' 
         '$input'
         '$__tool_directory__/FunctTrendSTOCGalaxy.r' 
         '$output'
    ]]>
    </command>
    <inputs>
        <param name="input" type="data" format="tabular" label="Input file" help="Population count file, with location, date, species and abundance."/>
    </inputs>
    <outputs>
        <data name="output" from_work_dir="Datatransformedforfiltering_trendanalysis.tabular" format="tabular"/>
    </outputs>
    <tests>
        <test> 
            <param name="input" value="data_FrenchBBS_squarre_dataSTOCallSp_France_trend_2001_2017_ALAARV-PARCAE_2001_2018.tabular"/>
            <output name="output" file="Datatransformedforfiltering_trendanalysis.tabular"/>
        </test>
    </tests>
    <help><![CDATA[
===============================
STOC preprocess population data
===============================

**What it does**

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.


|

**Input description**

A tabular file with abundance per year, per site and per species with no or few zero abundance.

The data file can be extracted from the STOC database on demand : [e-mail]

The table needs the following structure (at least these 4 fours columns) :

+-----------+---------+----------+---------+
|   carre   |  annee  |  espece  |  abond  |
+===========+=========+==========+=========+
| carreId1  |   2019  | especeId |   12    |  
+-----------+---------+----------+---------+
|    ...    |   ...   |   ...    |   ...   |
+-----------+---------+----------+---------+

|

**Output**

A tabular file transformed, with one column indicating the year, one indicating the site, and one column for each species abundance.

This file is ready for the next filtering steps.

|

**Source**

UnPublished script available at http://www.vigienature.fr/sites/vigienature/files/atoms/files/analysestoceps_0.zip

First version written by [e-mail]
  ]]></help>

  <expand macro="stoceps_bibref" />
</tool>