diff macros.xml @ 5:6283babe736e draft

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

--- a/macros.xml	Mon Feb 17 14:51:29 2020 -0500
+++ b/macros.xml	Thu Feb 20 18:14:24 2020 -0500
@@ -6,6 +6,8 @@
     </xml>
     <xml name="substitution">
         <param name="model" type="select" label="Substitution model">
+            <option value="GTR">GTR - General time reversible
+            model</option>
             <option value="LG">LG - Generalist empirical model from
             Le and Gascuel (2008)</option>
             <option value="HIVBm">HIVBm - Specialist empirical model
@@ -26,10 +28,43 @@
             for invertebrate mitochondrial genomes</option>
             <option value="gcpREV">gcpREV - Specialist empirical
             model for green plant chloroplast genomes</option>
-            <option value="GTR">GTR - General time reversible
-            model</option>
         </param>
     </xml>
+
+    <xml name="conditional_posteriorEstimationMethod">
+        <conditional name="posteriorEstimationMethod">
+            <param argument="--method" type="select" label="Posterior estimation method">
+                <option value="Variational-Bayes">0-th order Variational Bayes approximation</option>
+                <option value="Metropolis-Hastings">Full Metropolis-Hastings MCMC algorithm</option>
+                <option value="Collapsed-Gibbs">Collapsed Gibbs sampler</option>
+            </param>
+            <when value="Variational-Bayes">
+            </when>
+            <when value="Metropolis-Hastings">
+                <expand macro="mcmc_options" />
+            </when>
+            <when value="Collapsed-Gibbs">
+                <expand macro="mcmc_options" />
+            </when>
+        </conditional>
+    </xml>
+
+    <token name="@posteriorEstimationMethod_cmd@">
+            #if $posteriorEstimationMethod.method != "Variational-Bayes"
+                --chains '$posteriorEstimationMethod.chains'
+                --chain-length '$posteriorEstimationMethod.chain_length'
+                --burn-in '$posteriorEstimationMethod.samples'
+                --samples '$posteriorEstimationMethod.samples_per_chain'
+            #end if
+    </token>
+
+    <xml name="mcmc_options">
+        <param argument="--chains" type="integer" value="5" min="2" max="20" label="Number of MCMC chains" />
+        <param argument="--chain-length" name="chain_length" type="integer" value="2000000" min="500000" max="50000000" label="Length of each chain" />
+        <param argument="--burn-in" name="samples" type="integer" value="1000000" min="100000" max="1900000" label="Samples to use for burn-in" />
+        <param argument="--samples" name="samples_per_chain" type="integer" value="100" min="50" max="1000000" label="Samples to draw from each chain" />
+    </xml>
+
     <xml name="gencode">
         <param name="gencodeid" type="select" label="Genetic code">
             <option value="Universal">Universal code</option>
@@ -62,27 +97,28 @@
             <option value="All">All branches</option>
             <option value="Internal">Internal branches</option>
             <option value="Leaves">Leaf branches</option>
-            <option value="'Unlabeled-branches'">Unlabeled
-            branches</option>
+            <option value="'Unlabeled-branches'">Unlabeled branches</option>
         </param>
     </xml>
     <xml name="citations">
         <citations>
-            <citation type="doi">10.1093/bioinformatics/bti079</citation>
+            <citation type="doi">10.1093/molbev/msz197</citation>
             <yield/>
         </citations>
     </xml>
-    <token name="@VERSION@">2.5.3</token>
+    <token name="@VERSION@">2.5.4</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@VERSION@">
-            hyphy</requirement>
+            <requirement type="package" version="@VERSION@">hyphy</requirement>
             <yield/>
         </requirements>
     </xml>
     <token name="@HYPHYMPI@">\${GALAXY_MPIRUN:-mpirun -np \${GALAXY_SLOTS:-1}} HYPHYMPI</token>
-    <token name="@HYPHY_ENVIRONMENT@"><![CDATA[export HYPHY=`which hyphy` &&
-export HYPHY_PATH=`dirname \$HYPHY` &&
-export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` &&]]></token>
-    <token name="@HYPHY_INVOCATION@"><![CDATA[@HYPHY_ENVIRONMENT@ hyphy LIBPATH=\$HYPHY_LIB ]]></token>
+    <token name="@HYPHY_ENVIRONMENT@"><![CDATA[
+        export HYPHY=`which hyphy` &&
+        export HYPHY_PATH=`dirname \$HYPHY` &&
+        export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` &&]]></token>
+    <token name="@HYPHY_INVOCATION@"><![CDATA[
+        @HYPHY_ENVIRONMENT@ hyphy LIBPATH=\$HYPHY_LIB
+    ]]></token>
 </macros>