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+++ b/phykit_alignment_tree_based.xml	Mon Mar 28 16:23:18 2022 +0000
@@ -0,0 +1,67 @@
+<tool id="phykit_alignment_tree_based" name="PhyKit - Alignment- and tree-based functions" version="0.1.0" python_template_version="3.5">
+    <requirements>
+        <requirement type="package" version="1.11.7">phykit</requirement>
+    </requirements>
+     <command detect_errors="exit_code"><![CDATA[    
+        #if $tools.tool_selector == "treeness_over_rcv"    
+            phykit treeness_over_rcv -a $tools.input1 -t $tools.input2 > $treeness_rcv;
+        #end if
+        
+
+    ]]></command>
+    <inputs>
+        <conditional name="tools">
+            <param name="tool_selector" type="select" label="Select tool for processing the alignment(s)">
+                <option value="treeness_over_rcv">Calculate treeness/RCV for a given alignment and tree.</option>
+            </param>
+            <when value="treeness_over_rcv">
+                <param name="input1" type="data" format="fasta" multiple="false" label="Alignment file" optional="false" />
+                <param name="input2" type="data" format="newick" multiple="false" label="Tree file" optional="false" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="treeness_rcv" format="tabular" label="Three tab delimited values: col1: treeness/RCV col2: treeness col3: RCV" >
+            <filter>tools['tool_selector']=='treeness_over_rcv'</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="tool_selector" value="treeness_over_rcv" />
+            <param name="input1" value="simple.fa"/>
+            <param name="input2" value="tree_simple.tre"/>
+            <output name="treeness_rcv" file="test_treeness_over_rcv.txt"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Version: 1.11.3
+Citation: Steenwyk et al. 2021, Bioinformatics. doi: 10.1093/bioinformatics/btab096
+Documentation link: https://jlsteenwyk.com/PhyKIT/usage/index.html#alignment-and-tree-based-functions
+Publication link: https://academic.oup.com/bioinformatics/article-abstract/37/16/2325/6131675
+
+PhyKIT helps process and analyze multiple sequence alignments and phylogenies.
+
+Generally, all functions are designed to help understand the contents of alignments
+(e.g., gc content or the number of parsimony informative sites) and the shape
+of trees (e.g., treeness, degree of violation of a molecular clock).
+
+
+Alignment- and tree-based commands
+==================================
+treeness_over_rcv (alias: toverr)
+    - calculates treeness/rcv, treeness, and rcv
+
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+@misc{githubPhyKIT,
+  author = {LastTODO, FirstTODO},
+  year = {TODO},
+  title = {PhyKIT},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/JLSteenwyk/PhyKIT},
+}</citation>
+    </citations>
+</tool>
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