diff hyphy_prime.xml @ 0:725ef5f6d749 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hyphy_prime.xml	Fri Mar 27 13:15:01 2020 -0400
@@ -0,0 +1,132 @@
+<?xml version="1.0"?>
+<tool id="hyphy_prime" name="HyPhy-PRIME" version="@VERSION@+galaxy0">
+    <description>Property Informed Models of Evolution</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$input_file' prime_input.fa &&
+        ln -s '$input_nhx' prime_input.nhx &&
+        @HYPHYMPI@ prime
+            --alignment ./prime_input.fa
+            --tree ./prime_input.nhx
+            --code '$gencodeid'
+            --branches '$branches'
+            --pvalue '$p_value'
+            --properties '$prop_set'
+            --output '$prime_output'
+            > '$prime_log'
+            ;
+        @CATCH_MPIERR@
+    ]]></command>
+    <inputs>
+        <expand macro="inputs"/>
+        <expand macro="gencode"/>
+        <expand macro="branches"/>
+        <param name="prop_set" type="select" label="Biochemical properties to use">
+            <option value="Atchley">Atchley</option>
+            <option value="LCAP">LCAP</option>
+        </param>
+        <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value threshold"/>
+    </inputs>
+    <outputs>
+        <data name="prime_log" format="txt"/>
+        <data name="prime_output" format="hyphy_results.json" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" ftype="fasta" value="prime-in1.fa"/>
+            <param name="input_nhx" ftype="nhx" value="prime-in1.nhx"/>
+            <param name="branches" value="All"/>
+            <param name="p_value" value="0.1"/>
+            <param name="prop_set" value="Atchley"/>
+            <output name="prime_output" file="prime-out1.json" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+PRIME: Property Informed Model of Evolution
+===========================================
+
+What question does this method answer?
+--------------------------------------
+
+Does evolution at specific sites in a coding alignment preserve or alter some biochemical properties?
+
+Recommended Applications
+------------------------
+
+Identify biochemical evolutionary constraints or changes with site level resolution: e.g. site 23 is
+evolving to conserve residue polarity, but alter it's volume.
+
+
+Brief description
+-----------------
+
+Most methods of coding sequence analysis do not take direct account of the fact that
+the rate at which amino-acids are exchanged is different depending on the amino-acids.
+While this seems obvious (e.g. radical changes should happen slower), there are many technical reasons
+for why the standard assumption of "one-rate for all residues" holds.
+
+
+Given a set of N amino-acid properties, fit a site-level model where non-synonymous rates
+depend on how much a non-synonymous substitution changes the properties
+of the residue, beta (X,Y) = Exp (log_omega - lambda_1 * diff_1 (X,Y )-
+lambda_2 * diff_2 (X,Y) -...). When lambda_k > 0, changes in property k
+are disfavored and when lambda_k < 0 -- they are promoted. At each site,
+N+1 tests are performed (one for each property, and an omnibus test).
+
+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.
+
+
+Output
+------
+
+A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
+
+A custom visualization module for viewing these results will soon be available at http://vision.hyphy.org/
+
+Further reading
+---------------
+
+http://hyphy.org/methods/selection-methods/#PRIME
+
+
+Tool options
+------------
+::
+
+
+    --code              Which genetic code to use
+
+    --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
+
+     --properties       Which property set to use
+                            Atchley : Use the five properties derived from a factor analysis of 500 amino-acid properties [Table 2 in PNAS (2005) 102(18) 6395-6400 doi: 10.1073/pnas.0408677102]
+                            LCAP: Use the five properties defined in the Conant and Stadler LCAP model [Mol Biol Evol (2009) 26 (5): 1155-1161. doi: 10.1093/molbev/msp031]
+
+
+    ]]></help>
+    <!--<expand macro="citations">
+        <citation type="doi">10.1371/journal.pgen.1002764</citation>
+    </expand>-->
+</tool>
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