diff plot-trend.xml @ 0:58ecd15e6836 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/plot-trend.xml	Thu Jun 20 04:04:43 2019 -0400
@@ -0,0 +1,54 @@
+<tool id="regionalgam_plot_trend" name="Plot abundance" version="@VERSION@">
+    <description>with trend line</description>
+    <macros>
+        <import>regionalgam_macros.xml</import>
+    </macros>
+    <expand macro="rg_nlme_mass_requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        Rscript '$__tool_directory__/plot-trend.R' 
+            '$ab_indices' '$gls_model'  
+            '$output' 
+            '$output_tsv' 
+    ]]>
+    </command>
+    <inputs>
+        <expand macro="rg_ab_indices"/>
+        <expand macro="rg_gls_model"/>
+    </inputs>
+    <outputs>
+        <data format="png" name="output" from_work_dir="output-plot-trend.png" />
+        <data format="tabular" name="output_tsv" from_work_dir="s_trend.tsv" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="ab_indices" value="s_data_index.tabular"/>
+            <param name="gls_model" value="s_gls-adju_rda.rda"/>
+            <output name="output_tsv" ftype="tabular">
+                <assert_contents>
+                    <has_line_matching expression="2003&#009;5.5699.*"/>
+                    <has_line_matching expression="2004&#009;5.6221.*"/>
+                    <has_line_matching expression="2005&#009;5.6915.*"/>
+                    <has_line line="&quot;year&quot;&#009;&quot;collated index&quot;"/>
+                    <has_n_columns n="2"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+==========================
+Plot abundance trend 
+==========================
+
+This tool is an implementation of the plot_trend function from RegionalGAM package: https://github.com/RetoSchmucki/regionalGAM/
+
+This function plot abundance and add a trend line, it is the year effect estimated in the model.
+
+|
+
+**Outputs**
+
+Trend estimation plotted in an image png file, and raw values in a tabular file.
+
+    ]]></help>
+    <expand macro="rg_citation"/>
+</tool>