Mercurial > repos > iuc > phyloseq_plot_richness

diff phyloseq_plot_richness.xml @ 0:92b82deaaed1 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
author: iuc
date: Thu, 03 Mar 2022 13:28:55 +0000
children: 1ff178d1757e
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phyloseq_plot_richness.xml	Thu Mar 03 13:28:55 2022 +0000
@@ -0,0 +1,38 @@
+<tool id="phyloseq_plot_richness" name="Phyloseq: plot alpha diverstiy measure" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+  <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+Rscript '${__tool_directory__}/phyloseq_plot_richness.R' 
+--input '$input' 
+--output '$output'
+    ]]></command>
+    <inputs>
+        <expand macro="phyloseq_input"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="pdf"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="output.phyloseq" ftype="phyloseq"/>
+            <output name="output" ftype="pdf">
+                <assert_contents>
+                    <has_text text="%PDF"/>
+                    <has_text text="%%EOF"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Accepts a dataset containing a phyloseq object created from a dada2 taxonomy table and a dada2 sequence table,
+estimates a number of alpha-diversity metrics, and generates a colored plot that includes the alpha diverstiy measure
+of each sample. 
+    </help>
+    <expand macro="citations"/>
+</tool>
+