diff ab_index_en.xml @ 0:5b126f770671 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ab_index_en.xml	Fri Aug 03 08:28:22 2018 -0400
@@ -0,0 +1,39 @@
+<tool id="ab_index" name="Abundance index" version="0.1">
+    <description>computation across species, sites and years</description>
+    <requirements>
+        <requirement type="package" version="3.4">r</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        Rscript '$__tool_directory__/ab_index.R' '$__tool_directory__/dennis_gam_initial_functions.R' '$input1' '$input2' '$output' ]]>
+    </command>
+    <inputs>
+        <param format="tabular,csv" name="input1" type="data" label="Count file" help="The file must contain the SPECIES, SITE, YEAR, MONTH, DAY and COUNT columns. CSV file separator ',' or tab."/>
+        <param format="tabular" name="input2" type="data" label="Flight curve output"/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output" from_work_dir="data.index" />
+    </outputs>
+    <tests>
+        <test> <!-- FAILED -->
+            <param name="input1" value="gatekeeper_CM"/>
+            <param name="input2" value="flight_curve_result.tabular"/>
+            <output name="output" value="data_index.tabular"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark 
+
+==========================
+Compute abundance index
+==========================
+
+This tool is an implementation of the abundance_index function from `RegionalGAM package:  https://github.com/RetoSchmucki/regionalGAM/
+
+This function compute the Abundance Index across sites and years from your dataset and the regional flight curve.
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1111/1365-2664.12561</citation>  
+    </citations>
+</tool>