diff hyphy_slac.xml @ 6:25782236e47e draft

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

--- a/hyphy_slac.xml	Mon Feb 17 14:54:08 2020 -0500
+++ b/hyphy_slac.xml	Thu Feb 20 18:13:33 2020 -0500
@@ -22,8 +22,8 @@
         <expand macro="inputs"/>
         <expand macro="gencode"/>
         <expand macro="branches"/>
-        <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value"/>
-        <param name="number_of_samples" type="integer" value="100" min="0" max="100000" label="Number of samples used to assess ancestral reconstruction uncertainty"/>
+        <param argument="--pvalue" name="p_value" type="float" value=".1" min="0" max="1" label="P-value"  />
+        <param argument="--samples" name="number_of_samples" type="integer" value="100" min="0" max="100000" label="Number of samples used to assess ancestral reconstruction uncertainty"/>
     </inputs>
     <outputs>
         <data name="slac_log" format="txt"/>
@@ -37,12 +37,83 @@
         </test>
     </tests>
     <help><![CDATA[
-SLAC (Single-Likelihood Ancestor Counting) uses a combination of maximum-likelihood and counting approaches to infer nonsynonymous and synonymous substitution rates on a per-site basis for a given coding alignment and corresponding phylogeny. SLAC assumes that the selection pressure for each site is constant along the entire phylogeny.
+SLAC : Single Likelihood Ancestor Counting
+==========================================
+
+What question does this method answer?
+--------------------------------------
+
+Which site(s) in a gene are subject to pervasive, i.e. consistently across the entire phylogeny, diversifying selection?
+
+Recommended Applications
+------------------------
+
+The phenomenon of pervasive selection is generally most prevalent in pathogen evolution and any biological system influenced by evolutionary arms race dynamics
+(or balancing selection), including adaptive immune escape by viruses. As such, SLAC is ideally suited to identify sites under positive selection which
+represent candidate sites subject to strong selective pressures across the entire phylogeny.
+SLAC provides legacy functionality as a counting-based method adapted for phylogenetic applications.
+In general, this method will be the least statistically robust (compared to FEL or FUBAR), but it is the most directly interpretable.
+
+Brief description
+-----------------
+
+SLAC (Single Likelihood Ancestor Counting) uses a maximum likelihood
+ancestral state reconstruction and minimum path substitution counting to
+estimate site - level dS and dN, and applies a simple binomial - based
+test to test if dS differs drom dN. The estimates aggregate information
+over all branches, so the signal is derived from pervasive
+diversification or conservation. A subset of branches can be selected
+for testing as well.
+
+Input
+-----
+
+1. A *FASTA* sequence alignment.
+2. A phylogenetic tree in the *Newick* format
+
+Note: the names of sequences in the alignment must match the names of the sequences in the tree.
+
 
-See the online documentation_ for more information.
+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/SLAC for an example)
+
+Further reading
+---------------
+
+http://hyphy.org/methods/selection-methods/#SLAC
+
+
+Tool options
+------------
+::
+
+
+    --code              Which genetic code to use
 
-.. _documentation: http://hyphy.org/methods/selection-methods/#slac
-    ]]></help>
+    --branches          Which branches should be tested for selection?
+                            All [default] : test all branches
+
+                            Internal : test only internal branches (suitable for
+                            intra-host pathogen evolution for example, where terminal branches
+                            may contain polymorphism data)
+
+                            Leaves: test only terminal (leaf) branches
+
+                            Unlabeled: if the Newick string is labeled using the {} notation,
+                            test only branches without explicit labels
+                            (see http://hyphy.org/tutorials/phylotree/)
+
+     --pvalue           The significance level used to determine significance
+
+     --samples          Draw this many alternative ancestral state reconstructions
+                        to evaluate uncertainty
+
+  ]]>
+  </help>
     <expand macro="citations">
         <citation type="doi">10.1093/molbev/msi105</citation>
     </expand>