diff flight-curve.xml @ 0:fff507f00b2b draft default tip

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/flight-curve.xml	Thu Jun 20 04:03:07 2019 -0400
@@ -0,0 +1,58 @@
+<tool id="regionalgam_flight_curve" name="Flight curve" version="@VERSION@">
+    <description>compute the regional expected pattern of abundance</description>
+    <macros>
+        <import>regionalgam_macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="1.8_28">r-mgcv</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        Rscript '$__tool_directory__/flight-curve.R' 
+            '$__tool_directory__/dennis-gam-initial-functions.R' 
+            '$count_file' 
+            $minvisit 
+            $minoccur 
+            '$output' 
+    ]]>
+    </command>
+    <inputs>
+        <expand macro="rg_count_file"/>
+        <param name="minvisit" type="integer" value="3" min="0" label="Minimum number of visits" help="Subset the data with a minimum number of visits." />
+        <param name="minoccur" type="integer" value="2" min="0" label="Minimum number of occurences" help="Subset the data with a minimum number of occurences."/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output" from_work_dir="pheno" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="count_file" value="gatekeeper_CM_200320042005"/>
+            <param name="minvisit" value="3"/>
+            <param name="minoccur" value="2"/>
+            <output name="output" ftype="tabular">
+                <assert_contents>
+                    <has_line line="&quot;species&quot;&#009;&quot;year&quot;&#009;&quot;week&quot;&#009;&quot;DAYNO&quot;&#009;&quot;DAYNO_adj&quot;&#009;&quot;nm&quot;"/>
+                    <has_n_columns n="6"/>
+                    <has_text_matching expression="&quot;Pyronia&#032;tithonus&quot;&#009;2003&#009;[0-9]&#009;[0-9]&#009;[0-9]&#009;[0-9]"/>
+                </assert_contents>
+            </output>   
+        </test>
+    </tests>
+    <help><![CDATA[
+==========================
+Regional phenology
+==========================
+
+This tool is an implementation of the flight_curve function RegionalGAM package:  https://github.com/RetoSchmucki/regionalGAM/
+
+This function computes the annual phenology on a specific region.
+
+The output tabular file can be used to impute expected count values with the abundance index computation tool. 
+
+|
+
+**Outputs**
+
+Regional expected pattern computation in a tabular file.
+    ]]></help>
+    <expand macro="rg_citation"/>
+</tool>