--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CalculateCommunityMetrics.xml	Tue Jul 21 06:00:10 2020 -0400
@@ -0,0 +1,96 @@
+<tool id="pampa_communitymetrics" name="Calculate community metrics" version="@VERSION@">
+    <description>calculate community metrics from abundance data</description>
+    <macros>
+        <import>pampa_macros.xml</import>
+    </macros>
+    <expand macro="Pampa_requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        Rscript 
+         '$__tool_directory__/FunctExeCalcCommIndexesGalaxy.r' 
+         '$input'
+         '$indexes'
+         '$__tool_directory__/FunctPAMPAGalaxy.r' 
+         '$output_community'
+    ]]>
+    </command>
+    <inputs>
+        <expand macro="pampa_input_calculate"/>
+        <param name="indexes" type="select" label="Choose the community metrics you want to compute" help="Presence/absence, Species richness, Simpson and Shannon index are systematically computed." multiple="true">
+            <option selected="true" value="all">All</option>
+            <option value="simpson.l">1-Simpson</option>
+            <option value="pielou">Pielou</option>
+            <option value="hill">Hill</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output_community" from_work_dir="TabCommunityIndexes.tabular" format="tabular"/>
+    </outputs>
+    <tests>
+        <test> 
+            <param name="input" value="ObservationsSansszcl_cropped.tabular"/>
+            <param name="indexes" value="all"/>
+            <output name="output_community" value="Community_metrics_cropped.tabular"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+===============================================
+Calculate community metrics from abundance data
+===============================================
+
+**What it does**
+
+This tool from PAMPA toolsuite computes community metrics from abundance data:
+
+- Specific richness
+- Shannon index
+- Simpson index
+- Pielou index
+- Hill index
+- Relative richness
+
+|
+
+**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 every metrics selected computed per observation unit
+
+|
+
+**Source**
+
+Derived from PAMPA scripts (https://wwz.ifremer.fr/pampa/Meth.-Outils/Outils) written by Yves Reecht.
+
+  ]]></help>
+
+  <expand macro="pampa_bibref" />
+</tool>