diff hyphy_fade.xml @ 0:bab74ad497ee draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hyphy_fade.xml	Thu Jan 17 09:51:50 2019 -0500
@@ -0,0 +1,116 @@
+<?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"/>
+  <version_command>HYPHYMP --version | tail -n 1 | awk '{print
+  $1}'</version_command>
+  <command detect_errors="exit_code"><![CDATA[
+    #if $posteriorEstimationMethod == 3:
+      ln -s '$input_file' fade_input.fa &&
+      ln -s '$input_nhx' fade_input.nhx &&
+      echo `pwd`/fade_input.fa >> tool_params &&
+      echo `pwd`/fade_input.nhx >> tool_params &&
+      echo '$branches' >> tool_params &&
+      echo '$grid_points' >> tool_params &&
+      echo '$substitutionmodel' >> tool_params &&
+      echo '$posteriorEstimationMethod' >> tool_params &&
+      echo '$concentration' >> tool_params &&
+      @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FADE.bf > '$fade_log'
+    #else:
+      ln -s '$input_file' fade_input.fa &&
+      ln -s '$input_nhx' fade_input.nhx &&
+      echo `pwd`/fade_input.fa >> tool_params &&
+      echo `pwd`/fade_input.nhx >> tool_params &&
+      echo '$branches' >> tool_params &&
+      echo '$grid_points' >> tool_params &&
+      echo '$substitutionmodel' >> tool_params &&
+      echo '$posteriorEstimationMethod' >> tool_params &&
+      echo '$mcmc' >> tool_params &&
+      echo '$chain_length' >> tool_params &&
+      echo '$samples' >> tool_params &&
+      echo '$samples_per_chain' >> tool_params &&
+      echo '$concentration' >> tool_params &&
+      @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FADE.bf > '$fade_log'
+    #end if
+    ]]></command>
+  <inputs>
+    <param name="input_file" type="data" format="fasta" label="Input FASTA file"/>
+    <param name="input_nhx" type="data" format="nhx" label="Input newick file"/>
+    <param name="branches" type="select" label="Set of branches to test">
+      <option value="1">All branches</option>
+      <option value="2">Internal branches</option>
+      <option value="3">Leaf branches</option>
+      <option value="4">Unlabeled branches</option>
+    </param>
+    <param name="substitutionmodel" type="select" label="Substitution Model">
+      <option value="1">LG (Generalist empirical model from Le and
+      Gascuel 2008)</option>
+      <option value="2">WAG (Generalist empirical model from Whelon
+      and Goldman 2001)</option>
+      <option value="3">JTT (Generalist empirical model from Jones,
+      Taylor and Thornton 1996)</option>
+      <option value="4">JC69 (Generalist empirical model with equal
+      exhangeability rates among all amino acids)</option>
+      <option value="5">mtMet (Specialist empirical model for
+      metazoan mitochondrial genomes from Le, Dang and Le
+      2007)</option>
+      <option value="6">mtVer (Specialist empirical model for
+      vertebrate mitochondrial gemones from Le, Dang and Le
+      2007)</option>
+      <option value="7">mtInv (Specialist empirical model for
+      invertebrate mitochondrial genomes from Le, Dang and Le
+      2007)</option>
+      <option value="8">gcpREV (Specialist empirical model for
+      green plant chloroplast genomes from Cox and Foster
+      20013)</option>
+      <option value="9">HIVBm (Specialist empirical model for
+      between-host HIV sequences from Nickle et al. 2007)</option>
+      <option value="10">HIVWm (Specialist empirical model for
+      within-host HIV sequences from Nickle et al. 2007)</option>
+      <option value="11">GTR (General time reversible model; 189
+      estimated parameters)</option>
+    </param>
+    <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"/>
+    <param name="branches" type="select" label="Set of branches to test">
+      <option value="1">All branches</option>
+      <option value="2">Internal branches</option>
+      <option value="3">Leaf branches</option>
+      <option value="4">Unlabeled branches</option>
+    </param>
+    <param name="posteriorEstimationMethod" type="select" label="Posterior estimation method">
+      <option value="1">Metropolis-Hastings - Full
+      Metropolis-Hastings MCMC algorithm (slowest, original 2013
+      paper implementation)</option>
+      <option value="2">Collapsed Gibbs - Collapsed Gibbs sampler
+      (intermediate speed)</option>
+      <option value="3">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="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>