diff plot_trend_en.xml @ 0:5b126f770671 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plot_trend_en.xml	Fri Aug 03 08:28:22 2018 -0400
@@ -0,0 +1,40 @@
+<tool id="plot_trend" name="Plot abundance" version="0.1">
+    <description>with trend line</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="1.1.2">xorg-libsm</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        Rscript '$__tool_directory__/plot_trend.R' '$input1' '$input2' '$output' ]]>
+    </command>
+    <inputs>
+        <param format="tabular" name="input1" type="data" label="File generated by the ab_index tool"/>
+        <param format="rdata" name="input2" type="data" label="gls model" help="Rdata File"/>
+    </inputs>
+    <outputs>
+        <data format="png" name="output" from_work_dir="output-plot-trend.png" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="data_index.tabular"/>
+            <param name="input2" value="gls-adju_rda.rda"/>
+            <output name="output" value="trend.png"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark 
+
+==========================
+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.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1111/1365-2664.12561</citation>  
+    </citations>
+</tool>