diff hyphy_fade.xml @ 0:6164d9298db9 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hyphy_fade.xml	Wed Aug 21 12:25:26 2019 -0400
@@ -0,0 +1,67 @@
+<?xml version="1.0"?>
+<tool id="hyphy_fade" name="HyPhy-FADE" version="@VERSION@+galaxy0">
+    <description>: FUBAR* Approach to Directional Evolution (*Fast
+    Unconstrained Bayesian Approximation)</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$input_file' fade_input.fa &&
+        ln -s '$input_nhx' fade_input.nhx &&
+        @HYPHY_INVOCATION@ fade
+            --alignment ./fade_input.fa
+            --tree ./fade_input.nhx
+            --branches '$branches'
+            --model '$model'
+            --method '$posteriorEstimationMethod'
+            --grid '$grid_points'
+            --concentration_parameter '$concentration'
+            #if $posteriorEstimationMethod != "Metropolis-Hastings"
+                --chains '$mcmc'
+                --chain-length '$chain_length'
+                --burn-in '$samples'
+                --samples '$samples_per_chain'
+            #end if
+            > '$fade_log'
+    ]]></command>
+    <inputs>
+        <param name="input_file" type="data" format="fasta" label="Input amino acid FASTA file"/>
+        <param name="input_nhx" type="data" format="nhx" label="Input rooted newick file"/>
+        <expand macro="branches"/>
+        <expand macro="substitution" />
+        <param name="grid_points" type="integer" value="20" min="5" max="50" label="Grid points"/>
+        <param name="mcmc" type="integer" value="5" min="2" max="20" label="Number of MCMC chains"/>
+        <param name="chain_length" type="integer" value="2000000" min="500000" max="50000000" label="Length of each chain"/>
+        <param name="samples" type="integer" value="1000000" min="100000" max="1900000" label="Samples to use for burn-in"/>
+        <param name="samples_per_chain" type="integer" value="100" min="50" max="1000000" label="Samples to draw from each chain"/>
+        <param name="concentration" type="float" value="0.5" min="0.001" max="1" label="Concentration parameter of the Dirichlet prior"/>
+        <expand macro="branches"/>
+        <param name="posteriorEstimationMethod" type="select" label="Posterior estimation method">
+            <option value="Variational-Bayes">Metropolis-Hastings - Full
+            Metropolis-Hastings MCMC algorithm (slowest, original 2013
+            paper implementation)</option>
+            <option value="Collapsed-Gibbs">Collapsed Gibbs - Collapsed Gibbs sampler
+            (intermediate speed)</option>
+            <option value="Metropolis-Hastings">Variational Bayes - 0-th order Variational
+            Bayes approximations (fastest, recommended default)</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="fade_log" format="txt"/>
+        <data name="fade_output" format="hyphy_results.json" from_work_dir="fade_input.fa.FADE.json"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" ftype="fasta" value="fade-in1.fa"/>
+            <param name="input_nhx" ftype="nhx" value="fade-in1.nhx"/>
+            <output name="fade_output" file="fade-out1.json" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+FADE (FUBAR Approach to Directional Evolution) uses the same underlying algorithmic advances as impletented in FUBAR to apply Baysian MCMC accounting of parameter uncertiantiy to detect sites evolving under directional evolution in protien alignments.
+    ]]></help>
+    <expand macro="citations">
+        <citation type="doi">10.1093/molbev/msv022</citation>
+    </expand>
+</tool>