--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CalculatePresAbs.xml	Tue Jul 21 05:59:49 2020 -0400
@@ -0,0 +1,83 @@
+<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>
+    <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>