--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phyloseq_plot_ordination.xml	Thu Mar 03 13:28:30 2022 +0000
@@ -0,0 +1,89 @@
+<tool id="phyloseq_plot_ordination" name="Phyloseq: plot ordination" 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 '${__tool_directory__}/phyloseq_plot_ordination.R' 
+--input '$input' 
+--method '$method'
+--distance '$distance'
+--type '$type'
+--output '$output'
+    ]]></command>
+    <inputs>
+        <expand macro="phyloseq_input"/>
+        <param name="method" type="select" label="Ordination method">
+            <option value="DCA" selected="true">DCA</option>
+            <option value="CCA">CCA</option>
+            <option value="RDA">RDA</option>
+            <option value="CAP">CAP</option>
+            <option value="NMDS">NMDS</option>
+            <option value="MDS">MDS</option>
+            <option value="PCoA">PCoA</option>
+        </param>
+        <param name="distance" type="select" label="Distance method" help="Utilized only if a distance matrix is required by the Ordination method selected above">
+            <option value="bray" selected="true">bray</option>
+            <option value="canberra">canberra</option>
+            <option value="euclidean">euclidean</option>
+            <option value="gower">gower</option>
+            <option value="horn">horn</option>
+            <option value="jaccard">jaccard</option>
+            <option value="kulczynski">kulczynski</option>
+            <option value="manhattan">manhattan</option>
+            <option value="maximum">maximum</option>
+            <option value="minkowski">minkowski</option>
+            <option value="morisita">morisita</option>
+            <option value="mountford">mountford</option>
+        </param>
+        <param name="type" type="select" label="Plot type">
+            <option value="biplot" selected="true">biplot</option>
+            <option value="samples">samples</option>
+            <option value="scree">scree</option>
+            <option value="species">species</option>
+            <option value="split">split</option>
+        </param>
+    </inputs>
+    <expand macro="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,
+and generates an ordination plot of the samples.
+
+**Options**
+
+ **Ordination method**
+
+  * **DCA** - Performs detrended correspondence analysis using decorana.
+  * **CCA** - Performs correspondence analysis, or optionally, constrained correspondence analysis (a.k.a. canonical correspondence analysis) via vegan cca.
+  * **RDA** - Performs redundancy analysis, or optionally principal components analysis, via vegan rda.
+  * **CAP** - [Partial] Constrained Analysis of Principal Coordinates or distance-based RDA, via vegan capscale.
+  * **NMDS** - Performs Non-metric MultiDimenstional Scaling of a sample-wise ecological distance matrix onto a user-specified number of axes (k).  
+  * **MDS/PCoA** - Performs principal coordinate analysis (also called principle coordinate decomposition, multidimensional scaling (MDS), or classical scaling) of a distance matrix including two correction methods for negative eigenvalues.
+
+ **Distance method** - Utilized only if a distance matrix is required by the Ordination method documented above.
+
+ **Plot type**
+
+  * **biplot** - Produces a combined plot with both taxa and samples.
+  * **samples** - Produces a single plot of just the samples of the ordination.
+  * **scree** - Produces an ordered bar plot of the normalized eigenvalues associated with each ordination axis.
+  * **species** - Produces a single plot of just the species of the ordination.
+  * **split** - Produces a plot with both taxa and samples separated in two facet panels respectively.
+    </help>
+    <expand macro="citations"/>
+</tool>
+