annotate CalculatePresAbs.xml @ 1:5b45377f6a75 draft

"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 30ad791ef2452487dc248d4266c0cf14eda79914"

<tool id="pampa_presabs" name="Calculate presence absence table" version="@VERSION@">
    <description>calculate presence absence table from observation data</description>
    <macros>
        <import>pampa_macros.xml</import>
    </macros>
    <expand macro="Pampa_requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        Rscript 
         '$__tool_directory__/FunctExeCalcPresAbsGalaxy.r' 
         '$input'
         '$__tool_directory__/FunctPAMPAGalaxy.r' 
         '$output_presabs'
    ]]>
    </command>
    <inputs>
        <expand macro="pampa_input_calculate"/>
    </inputs>
    <outputs>
        <data name="output_presabs" from_work_dir="TabPresAbs.tabular" format="tabular"/>
    </outputs>
    <tests>
        <test> 
            <param name="input" value="ObservationsSansszcl_cropped.tabular"/>
            <output name="output_presabs" value="Presence_absence_table_sansszcl_cropped.tabular"/>      
        </test>
    </tests>
    <edam_topics>
       <edam_topic>topic_0610</edam_topic>
    </edam_topics>
    <help><![CDATA[
====================================================
Calculate presence absence table from abundance data
====================================================

**What it does**

This tool from PAMPA toolsuite computes an abundance (max and standard deviation if SVR data) and presence absence table at finest aggregation possible from observation data

|

**Input description**

A tabular file with observation data. Must at least contain three columns 'observation.unit' 
which associate year and location or 'year' and 'location', 'species.code' with species ID and 'number' for abundance.

+------------------+--------------+------------+
| observation.unit | species.code |   number   |
+==================+==============+============+
|   site_yearID    |   speciesID  |      4     |
+------------------+--------------+------------+
|        ...       |      ...     |     ...    |
+------------------+--------------+------------+

OR

+------+----------+--------------+------------+
| year | location | species.code |   number   |
+======+==========+==============+============+
| 2000 |locationID|   speciesID  |      4     |
+------+----------+--------------+------------+
|  ... |    ...   |      ...     |     ...    |
+------+----------+--------------+------------+

The data frame may also contain:
 
- 'size.class' field with 'G' representing big individuals in given species, 'M'middle-sized individuals and 'P' small individuals
- 'rotation' field for STAVIRO data

|

**Output**


A tabular file with presence/absence at finest aggregation available (per observation unit per species OR per observation unit per species per size class)


|

**Source**

Derived from PAMPA scripts (https://wwz.ifremer.fr/pampa/Meth.-Outils/Outils) written by Yves Reecht.

  ]]></help>

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