diff hyphy_relax.xml @ 5:7827dfb71693 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"

--- a/hyphy_relax.xml	Mon Feb 17 14:52:33 2020 -0500
+++ b/hyphy_relax.xml	Thu Feb 20 18:16:06 2020 -0500
@@ -24,11 +24,11 @@
     <inputs>
         <expand macro="inputs"/>
         <expand macro="gencode"/>
-        <param name="analysisType" type="select" label="Analysis Type">
+        <param argument="--model" name="analysisType" type="select" label="Analysis Type" >
             <option value="All">All</option>
             <option value="Minimal">Minimal</option>
         </param>
-        <param name="treeAnnotations" type="select" label="Tree Annotations">
+        <param name="treeAnnotations" type="select" label="Tree Annotations" help = "Is there one or two sets of annotated branches in the Newick file?">
             <option value="1">TEST only</option>
             <option value="2">TEST and REFERENCE</option>
         </param>
@@ -45,11 +45,66 @@
         </test>
     </tests>
     <help><![CDATA[
-RELAX is a hypothesis testing framework that asks whether the strength of natural selection has been relaxed or intensified along a specified set of test branches. RELAX is therefore not a suitable method for explicitly testing for positive selection. Instead, RELAX is most useful for identifying trends and/or shifts in the stringency of natural selection on a given gene.
+RELAX: a test for selection differences
+=======================================
+
+What question does this method answer?
+--------------------------------------
+
+Is there ev- idence the strength of selection has been relaxed (or conversely intensified) on a specified group of lineages (TEST)
+relative to a set of reference lineages (RELAX)? Importantly, RELAX is not designed to detect diversifying selection specifically.
+We note that the RELAX framework can perform both this specific hypothesis test as well as fit a suite of descriptive models which address,
+or example, overall rate differences between test and reference branches or lineage-specific inferences of selection relaxation.
+
+Recommended Applications
+------------------------
+
+1. Testing for a systematic shift (relaxation / intensification) in the distribution of selection pressure associated with major biological transitions such as hosting switching in viruses, lifestyle evolution in bacteria (i.e. transition from free-living to endosymbiotic lifestyle
+2. Comparing selective regimes between two subsets of branches in the tree, e.g. to investigate selective differences due an environmental/phenotypic changes.
+
+
+Brief description
+-----------------
+
+RELAX (a random effects test of selection relaxation) uses a random
+effects branch-site model framework to test whether a set of 'Test'
+branches evolves under relaxed selection relative to a set of
+'Reference' branches (R), as measured by the relaxation parameter (K).
+
+Input
+-----
 
-See the online documentation_ for more information.
+    1. A *FASTA* sequence alignment.
+    2. A phylogenetic tree in the *Newick* format that is further partitioned into one or two groups (_TEST_ or _TEST_ and _REFERENCE_). See http://hyphy.org/tutorials/phylotree/
+
+Note: the names of sequences in the alignment must match the names of the sequences in the tree.
+
+
+Output
+------
+
+A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
+
+A custom visualization module for viewing these results is available (see http://vision.hyphy.org/RELAX for an example)
+
+Further reading
+---------------
 
-.. _documentation: http://hyphy.org/methods/selection-methods/#relax
+http://hyphy.org/methods/selection-methods/#RELAX
+
+
+Tool options
+------------
+::
+
+
+    --code             Which genetic code to use
+
+    --model            Which type of test to run
+                            All : fit 4 different models [default]
+                            Minimal: only perform a 2-model test of relaxation/intensification  [faster]
+
+
     ]]></help>
     <expand macro="citations">
         <citation type="doi">10.1093/molbev/msu400</citation>