diff hyphy_gard.xml @ 5:6283babe736e draft

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

--- a/hyphy_gard.xml	Mon Feb 17 14:51:29 2020 -0500
+++ b/hyphy_gard.xml	Thu Feb 20 18:14:24 2020 -0500
@@ -10,13 +10,13 @@
         @HYPHYMPI@ gard
             --alignment ./gard_input.fa
             --type '$datatype.value'
-            #if str($datatype.value) == 'Codon':
+            #if str($datatype.value) == 'codon':
                 --code '$datatype.gencodeid'
-            #elif str($datatype.value) == 'Protein':
+            #elif str($datatype.value) == 'amino-acid':
                 --model '$datatype.model'
             #end if
-            --rv '$rate_cond.rate'
-            #if str($rate_cond.rate) != 'None':
+            #if str($rate_cond.rate):
+                --rv '$rate_cond.rate'
                 --rate-classes '$rate_classes'
             #end if
             --output '$translated'
@@ -26,31 +26,31 @@
     <inputs>
         <param name="input_file" type="data" format="fasta" label="Input FASTA file"/>
         <conditional name="datatype">
-            <param name="value" type="select" label="Type of data">
+            <param argument="--type" name="value" type="select" label="Alignment kind">
                 <option value="nucleotide">Nucleotide</option>
-                <option value="protein">Amino acid</option>
+                <option value="amino-acid">Amino acid</option>
                 <option value="codon">Codon</option>
             </param>
-            <when value="Nucleotide"/>
-            <when value="Protein">
+            <when value="nucleotide"/>
+            <when value="amino-acid">
                 <expand macro="substitution" />
             </when>
-            <when value="Codon">
+            <when value="codon">
                 <expand macro="gencode" />
             </when>
         </conditional>
         <conditional name="rate_cond">
-            <param name="rate" type="select" label="Rate variation">
-                <option value="None">None</option>
+            <param argument="--rv" name="rate" type="select" label="Rate variation">
+                <option value="">None</option>
                 <option value="GDD">General Discrete</option>
                 <option value="Gamma">Beta-Gamma</option>
             </param>
-            <when value="None"/>
+            <when value=""/>
             <when value="GDD">
-                <param name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes"/>
+                <param argument="--rate-classes" name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes" />
             </when>
             <when value="Gamma">
-                <param name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes"/>
+                <param argument="--rate-classes" name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes" />
             </when>
         </conditional>
     </inputs>
@@ -66,11 +66,85 @@
         </test>
     </tests>
     <help><![CDATA[
-GARD (Genetic Algorithm for Recombination Detection) is a method to screen a multiple sequence analysis for the presence of recombination and is extremely useful as a pre-processing step for selection inference. Because recombinant sequences cannot be adequately described with a single phylogenetic history, selection inference on recombinant data often leads to a significant increase in false positives. GARD alleviates this concern by comprehensively screening an alignment for recombination breakpoints and inferring a unique phylogenetic history for each detected recombination block.
+
+GARD : Genetic Algorithms for Recombination Detection.
+======================================================
+
+What does this do?
+------------------
+
+This tools screens an alignment of sequences for evidence of recombination in one or more sequences.
+The main idea is that if sufficient recombination has occurred, then no single phylogenetic tree will
+properly fit the entire length of the alignment and instead a separate tree will be preferred for each *nonrecombinant* segment.
+
+Brief description
+-----------------
+
+This analysis implements a heuristic approach to screening alignments of sequences for
+recombination, by using the CHC genetic algorithm (GA) to search for
+phylogenetic incongruence among different partitions of the data. The
+number of partitions is determined using a step-up procedure, while the
+placement of breakpoints is searched for with the GA. The best fitting
+model (based on c-AIC) is returned; and additional post-hoc tests run to
+distinguish topological incongruence from rate-variation.
+
+For each identified breakpoint, the support for its placement is calculated, and for each
+non-recombinant fragment, a phylogenetic tree is inferred (using neighbor joining) and returned.
+
+Input
+-----
+
+A *FASTA* sequence alignment
+
+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/GARD for an example)
+
 
-See the online documentation_ for more information.
+Tool options
+------------
+::
+
+
+    --type              type of alignment to screen
+                        Nucleotide [default].
+                            Assumes aligned nucleotide data and screens the alignment using
+                            the general time reversible model of sequence evolution.
+                            This is the fastest option
+                        Protein
+                            Assumes aligned aminoacid sequences. One of several protein
+                            substitution models may be used to screen the alignment.
+                        Codon
+                            Assumes an in-frame coding sequence alignment.
+                            The Muse-Gaut 94 (GTR) model will be used to screen the alignment.
+                            Selecting this option will dramatically increase run times.
+
 
-.. _documentation: http://hyphy.org/methods/selection-methods/#gard
+    --code              Genetic code/translation table to use (for codon alignments).
+                        Default value: Universal
+
+    --model             The substitution model to use (for protein alignments).
+                        default value: JTT
+
+    --rv                The discrete distribution to use for modeling site to site rate variation.
+
+                        None [default]
+                            No rate variation. This is the fastest option in terms of run time, but
+                            using it can result in false positives if there is significant site-to-site
+                            rate variation
+                        GDD
+                            Use the general discrete distribution on N bins
+                        Beta-Gamma
+                            Use a discretized gamma with weights partitioned by a discretized beta
+                            (see doi.org/10.1093/molbev/msi009)
+
+    --rate-classes      How many site rate classes to use (if GDD or Beta-Gamma are selected)
+                        default value: 4
+
+
     ]]></help>
     <expand macro="citations">
         <citation type="doi">10.1093/molbev/msl051</citation>