--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/glmmpql_en.xml	Fri Aug 03 08:28:22 2018 -0400
@@ -0,0 +1,40 @@
+<tool id="glmmpql" name="Expected temporal trend" version="0.1">
+    <description>of species abundance</description>
+    <requirements>
+        <requirement type="package" version="3.1_131">r-nlme</requirement>
+        <requirement type="package" version="7.3_48">r-mass</requirement>
+        <requirement type="package" version="0.9.10">xorg-libxrender</requirement>
+        <requirement type="package" version="1.2.2">xorg-libsm</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        Rscript '$__tool_directory__/glmmpql.R' '$input1' '$output' '$output2' ]]>
+    </command>
+    <inputs>
+        <param format="tabular" name="input1" type="data" label="Tabular file generated by the ab_index tool"/>
+    </inputs>
+    <outputs>
+        <data format="png" name="output" from_work_dir="output-plot.png" />
+        <data format="tabular" name="output2" from_work_dir="output-glmmpql" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="data_index.tabular"/>
+            <param name="output" value="glmmpql-plot.png"/>
+            <output name="output2" value="glmmpql.tabular"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+    
+.. class:: infomark 
+
+==========================
+Temporal trends of species abundance
+==========================
+
+This tool is an implementation of the glmmpql function from `RegionalGAM package:  https://github.com/RetoSchmucki/regionalGAM/
+This function computes a collated index for each year and estimates the temporal trend.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1111/1365-2664.12561</citation>  
+    </citations>
+</tool>