Mercurial > repos > rdvelazquez > hyphy_fubar

changeset 9:55dd19bffb00 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'17327d46ff082448f0a0fc3b6827f5d9d6124a10\n'-dirty
author rdvelazquez
date Tue, 08 Jan 2019 10:59:21 -0500
parents 257d1d617dfb
children da4fd8c3ad0c
files hyphy_fubar.xml macros.xml test-data/relax-in1.fa test-data/relax-in1.nhx test-data/relax-in2.nhx test-data/relax-out1.json
diffstat 6 files changed, 479 insertions(+), 108 deletions(-) [+]
line wrap: on
line diff
--- a/hyphy_fubar.xml	Tue Dec 04 11:13:15 2018 -0500
+++ b/hyphy_fubar.xml	Tue Jan 08 10:59:21 2019 -0500
@@ -1,93 +1,70 @@
 <?xml version="1.0"?>
 <tool id="hyphy_fubar" name="HyPhy-FUBAR" version="@VERSION@+galaxy0">
-  <description>: 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' fubar_input.fa &&
-      ln -s '$input_nhx' fubar_input.nhx &&
-      echo $gencodeid > tool_params &&
-      echo `pwd`/fubar_input.fa >> tool_params &&
-      echo `pwd`/fubar_input.nhx >> tool_params &&
-      echo '$grid_points' >> tool_params &&
-      echo '$posteriorEstimationMethod' >> tool_params &&
-      echo '$concentration' >> tool_params &&
-      @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FUBAR.bf > '$fubar_log'
-    #else:
-      ln -s '$input_file' fubar_input.fa &&
-      ln -s '$input_nhx' fubar_input.nhx &&
-      echo $gencodeid > tool_params &&
-      echo `pwd`/fubar_input.fa >> tool_params &&
-      echo `pwd`/fubar_input.nhx >> tool_params &&
-      echo '$grid_points' >> 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/FUBAR.bf > '$fubar_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="gencodeid" type="select" label="Genetic code">
-      <option value="1">Universal code</option>
-      <option value="2">Vertebrate mitochondrial DNA code</option>
-      <option value="3">Yeast mitochondrial DNA code</option>
-      <option value="4">Mold, Protozoan and Coelenterate mt;
-      Mycloplasma/Spiroplasma</option>
-      <option value="5">Invertebrate mitochondrial DNA
-      code</option>
-      <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear
-      code</option>
-      <option value="7">Echinoderm mitochondrial DNA code</option>
-      <option value="8">Euplotid Nuclear code</option>
-      <option value="9">Alternative Yeast Nuclear code</option>
-      <option value="10">Ascidian mitochondrial DNA code</option>
-      <option value="11">Flatworm mitochondrial DNA code</option>
-      <option value="12">Blepharisma Nuclear code</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>
-    <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"/>
-  </inputs>
-  <outputs>
-    <data name="fubar_log" format="txt"/>
-    <data name="fubar_output" format="json" from_work_dir="fubar_input.fa.FUBAR.json"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="input_file" ftype="fasta" value="fubar-in1.fa"/>
-      <param name="input_nhx" ftype="nhx" value="fubar-in1.nhx"/>
-      <output name="fubar_output" file="fubar-out1.json" compare="sim_size"/>
-    </test>
-  </tests>
-  <help><![CDATA[
+    <description>: Fast Unconstrained Bayesian AppRoximation</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command>
+    <command detect_errors="exit_code">
+    <![CDATA[
+    ln -s '$input_file' fubar_input.fa &&
+    ln -s '$input_nhx' fubar_input.nhx &&
+    echo $gencodeid > tool_params &&
+    echo `pwd`/fubar_input.fa >> tool_params &&
+    echo `pwd`/fubar_input.nhx >> tool_params &&
+    echo '$grid_points' >> tool_params &&
+    echo '$mcmc' >> tool_params &&
+    echo '$chain_length' >> tool_params &&
+    echo '$samples' >> tool_params &&
+    echo '$samples_per_chain' >> tool_params &&
+    echo '$concentration' >> tool_params &&
+    @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FUBAR.bf > '$fubar_log'
+    ]]>
+    </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="gencodeid" type="select" label="Genetic code">
+            <option value="1">Universal code</option>
+            <option value="2">Vertebrate mitochondrial DNA code</option>
+            <option value="3">Yeast mitochondrial DNA code</option>
+            <option value="4">Mold, Protozoan and Coelenterate mt; Mycloplasma/Spiroplasma</option>
+            <option value="5">Invertebrate mitochondrial DNA code</option>
+            <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear code</option>
+            <option value="7">Echinoderm mitochondrial DNA code</option>
+            <option value="8">Euplotid Nuclear code</option>
+            <option value="9">Alternative Yeast Nuclear code</option>
+            <option value="10">Ascidian mitochondrial DNA code</option>
+            <option value="11">Flatworm mitochondrial DNA code</option>
+            <option value="12">Blepharisma Nuclear code</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" />
+    </inputs>
+    <outputs>
+        <data name="fubar_log" format="txt" />
+        <data name="fubar_output" format="json" from_work_dir="fubar_input.fa.FUBAR.json" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" ftype="fasta" value="fubar-in1.fa" />
+            <param name="input_nhx" ftype="nhx" value="fubar-in1.nhx" />
+            <output name="fubar_output" file="fubar-out1.json" compare="sim_size" />
+        </test>
+    </tests>
+    <help>
+        <![CDATA[
 Model-based selection analyses (such as those performed by PAML and HyPhy) can be slow, becoming impractical for large alignments. We present a method to model and detect selection much faster than existing methods and to leverage Bayesian MCMC to robustly account for parameter estimation errors.
 
 Results: By exploiting some commonly used approximations, FUBAR can perform detection of positive selection under a model that allows rich site- to-site rate variation about 30 to 50 times faster than existing random effects likelihood methods, and 10 to 30 times faster than existing fixed effects likelihood methods. We introduce an ultra-fast MCMC routine that allows a flexible prior specification, with no parametric constraints on the prior shape. Furthermore, our method allows us to visualize Bayesian inference for each site, revealing the model supported by the data.
-        ]]></help>
-  <expand macro="citations">
-    <citation type="doi">10.1093/molbev/mst030</citation>
-  </expand>
+        ]]>
+    </help>
+    <expand macro="citations">
+        <citation type="doi">10.1093/molbev/msu400</citation>
+    </expand>
 </tool>
--- a/macros.xml	Tue Dec 04 11:13:15 2018 -0500
+++ b/macros.xml	Tue Jan 08 10:59:21 2019 -0500
@@ -1,25 +1,21 @@
 <?xml version="1.0"?>
 <macros>
-  <xml name="citations">
-    <citations>
-      <citation type="doi">10.1093/bioinformatics/bti079</citation>
-      <yield/>
-    </citations>
-  </xml>
-  <token name="@VERSION@">2.3.14</token>
-  <xml name="requirements">
-    <requirements>
-      <requirement type="package" version="@VERSION@">
-      hyphy</requirement>
-      <yield/>
-    </requirements>
-  </xml>
-  <token name="@HYPHY_INVOCATION@"><![CDATA[export HYPHY=`which HYPHYMP` &&
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1093/bioinformatics/bti079</citation>
+            <yield />
+        </citations>
+    </xml>
+    <token name="@VERSION@">2.3.14</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">hyphy</requirement>
+            <yield />
+        </requirements>
+    </xml>
+    <token name="@HYPHY_INVOCATION@"><![CDATA[export HYPHY=`which HYPHYMP` &&
 export HYPHY_PATH=`dirname \$HYPHY` &&
 export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` &&
-cat tool_params | HYPHYMP LIBPATH=\$HYPHY_LIB ]]></token>
-  <token name="@HYPHYMPI_INVOCATION@"><![CDATA[export HYPHYMPI=`which HYPHYMPI` &&
-export HYPHYMPI_PATH=`dirname \$HYPHYMPI` &&
-export HYPHYMPI_LIB=`readlink -f \$HYPHYMPI_PATH/../lib/hyphy` &&
-cat tool_params | mpirun -np \${GALAXY_SLOTS:-1} HYPHYMPI LIBPATH=\$HYPHYMPI_LIB ]]></token>
-</macros>
+cat tool_params | HYPHYMP LIBPATH=\$HYPHY_LIB ]]>
+    </token>
+</macros>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/relax-in1.fa	Tue Jan 08 10:59:21 2019 -0500
@@ -0,0 +1,20 @@
+>Human
+AAAGAGATTACGAATGCCTTGGAAACCTGGGGTGCCTTGGGTCAGGACATCAACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGACGATATAAAATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAAGAGACTTTCAAGGAAAAAGATACATATAAGCTATTTAAAAATGGAACTCTGAAAATTAAGCAT---CTGAAGACCGATGATCAGGATATCTACAAGGTATCAATATATGATACAAAAGGAAAAAATGTGTTGGAAAAAATATTTGATTTGAAGATTCAAGAGAGGGTCTCAAAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAGGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCAAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGTGTCGAGCCTGTCAGCTGTCCAGAGAAAGGTCTGGAC
+>Chimp
+GAAGAGATTACGAATGCCTTGGAAACCTGGGGTGCCTTGGGTCAGGACATCAACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGACGATATAAAATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAAGAGACTTTCAAGGAAAAAGATACATATAAGCTATTTAAAAATGGAACTCTGAAAATTAAGCAT---CTGAAGACCGATGATCAGGATATCTACAAGGTATCAATATATGATACAAAAGGAAAAAATGTGTTGGAAAAAATATTTGATTTGAAGATTCAAGAGAGGGTCTCAAAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAGGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCAAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGTGTCGAGCCTGTCAGCTGTCCAGAGAAAGGTCTGGAC
+>Baboon
+AAAGAGATTAGGAATGCTTTGGAAACCTGGGGAGCGCTGGGTCAGGACATCGACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGATGATATAAAATGGGAGAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAGGAGACTTTCGAGGAAAAAGATGCATATAAGCTATTTAAAAACGGAACTCTGAAAATTAAGCAT---CTGAAGATCCATGATCAGGATAGCTACAAGGTATCAATATACGATACAAAAGGAAAAAATGTGTTGGAAAAAACATTTGATTTGAAGATTCAAGAGAGGGTCTCAGAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAAGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCGAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGGATGGAGACTGTCAGCTGTCCAGAGAAAGGTCTGGAC
+>RhMonkey
+AAAGAGATTAGGAATGCTTTGGAAACCTGGGGAGCGCTGGGTCAGGACATCGACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGATGATATAAGATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAGGAGACTTTCGAGGAAAAAGATGCATATAAGCTATTTAAAAACGGAACTCTGAAAAYTAAGCAT---CTGAAGATCCATGATCAGGATAGCTACAAGGTATCAATATACGATACAAAAGGAAAAAATGTGTTGGAAAAAACATTTGATTTGAAGATTCAAGAGAGGGTCTCAGAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAAGTAATGAATGGAACTGRCCCCGAATTAAACCTGTATCAAGATGGGAAACATGTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCGAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGGATGGAGACTGTCAGCTGTCCAGAGAAAGGTCTGGAC
+>Cow
+------------GAAAGCATTGTCGTCTGGGGTGCCCTGGATCATGACCTCAACCTGGACATTCCTGGTTTTCCAAGAAGTGATATAGTGGCAGATATAAAATGGAACAGA------AACAAAAACAAGATTGCACGAATAAAGAAAGATATGCCACTTCACAATGAAATGGACAAATATGATATGTTTACAAATGGAACTCTGAAAATTAAAACT---CTGATGAGAAACGATAGTGGTCTCTATGAGGTAGAGGTTTATGATTCAAATGGAGTAAACCTACTGAGCAAAAAATTTGATTTGAAGATTCAAGAGATGCTCTCAGGACCTGAAATTAACTGGATCTGTACCAACAGAACTGTGAGCTGCAAGGTAGAAAATGGAAGTAATCCTAAATTACAACTGTTTTTAAATACGACCCGTGTCAAACAAGATCATGGGAAGCTCATCACCTACACGTGGAACACCAGATGGAATAAAACATTCAAGTGCGTGGCGAGTAACCATGTCGATAGCAAAGTCAGCATAGAGATCGCCGTGTGTCCAGATGAAGGTCTGGAT
+>Pig
+---------------ACTGAGGTTGTCTGGGGCATCGTGGATCAAGACATCAACCTGGACATTCCTGAACTTTCAAAACATGATAACGTAGATCATATACGATGGCAGAAG------AATGAAAACAAGATCGCAGAATTTAAAAAAAACAAAGAAACTCACCCTGTGAAAGACACATACATGATGTTACCAAATGGAACTCTGAGAATTAAAGAT---CTGAAGAGAGATGATGAGGGTATCTACAAGGTAACTGTCTATGCTACGGATGGAAAACACATGCTGGAGAGAAAATTTGATTTGCCGATTCTAGATGGGGTCTCAAAACCTGTAATCTCCTGGAGCTGTGCCGACAAAACGGTGACCTGTGAGGTAGCAGAAGGAAGTGACCCTAAGTTAAAACTGTATGTAAATAAGTCCACTGCCAGAGAAGGTCGTCAGAAGGTCATCCTGTGGAAGTGGAACACCAAATGGAGCACATTATTCAAGTGTGTGGCCAGTAACAACGCCAGTGAGCAAATCAGCATGGTGACCATCAGTTGTACGGGGCAAGGTCTGGAT
+>Horse
+------------AAGAATATCACCATCTTGGGTGCCCTGGAACGTGATATCAACCTGGACATTCCTGCTTTTCAAATGAGTGAGCATGTAGAAGATATACAATGGAGCAAA------GGAAAAACCAAGATTGCAAAATTCAAAAATGGCAGTATGACTTTCCAGAAAGATAAAACATACGAGGTATTAAAAAATGGAACTCTGAAAATTAAACAT---CTGGAGAGAATTCATGAAGGTACCTACAAGGTAGACGCATATGATAGTGATGGAAAAAATGTGTTGGAGGAAACATTTCATTTGAGCCTTCTAGAGATGGTCTCAAAACCTAATATCTCCTGGAGCTGCACCAACACCACCCTGACCTGCGAGGTGACAAAAGGAACTGACTTTGAGTTAAAACTCTATCTAAATGGGAGAATGATCCAAAAAAGTCCTCGCAAAGTCATCGTATACAAGCGGGCCAGCAACCAAATTGCGTCCTTCAAGTGCACAGCCAATAACACAGTCAGCGAGGAAAGCAGCTCTGTGGTCATCAGGTGTACAGAGAAAGGTCTGGAT
+>Cat
+---------GCAAATGATGATATCGTCTGGGGTACCCTGGGTCAGGACATCAACCTGGACATTCCTGATTCTCAA---GGGATTAATATAGATGATATACACTGGGAAAAA------GGCAAGAAGAAGGTGGCGAGGTTCCAAATTAGCAACAAGCCTAAGAATCCAGATGAAAAATATAATGTGTCAATGAATGGAACTCTGAAAATTAAACAT---CTGATGCTAGAAGACTGCGATACCTACAAGGTTGTTATATACGATAAGGATGGAAAGAATGTGTTGGATAAAACATTTCAGCTGAAGATTCAAGAGAAGGTCTCAACGCCTAACATCGACTGGAATTGTATCAACAAAACCCTGGTCTGTAAGGTATCAAATGGAACAGACCCTGAATTAAAACTGTACGTAAATGGGACCAGTATCAAGCCCGTTTCTTCGAAGTTCAGCACATACAGGTTTATAAACAAGCAGAAGATATTAGTCAACTGCACGGCAGAAAACAAAGTCAGCAAGGAAAGCGACGTGAAGATGATCACTTGTTCAGAGAAGGGTCTGGAC
+>Mouse
+---------AGAGACAATGAGACCATCTGGGGTGTCTTGGGTCATGGCATCACCCTGAACATCCCCAACTTTCAAATGACTGATGATATTGATGAGGTGCGATGGGTAAGG------AGGGGCACCCTGGTCGCAGAGTTTAAAAGGAAGAAGCCACCTTTTTTGATATCAGAAACGTATGAGGTCTTAGCAAACGGATCCCTGAAGATAAAGAAGCCGATGATGAGAAACGACAGTGGCACCTATAATGTAATGGTGTATGGCACAAATGGGATGACTAGGCTGGAGAAGGACCTGGACGTGAGGATTCTGGAGAGGGTCTCAAAGCCCATGATCCACTGGGAATGCCCCAACACAACCCTGACCTGTGCGGTCTTGCAAGGGACAGATTTTGAACTGAAGCTGTATCAAGGGGAAACACTACTCAATAGTCTCCCCCAGAAGAACATGAGTTACCAGTGG---ACCAACCTGAACGCACCATTCAAGTGTGAGGCGATAAACCCGGTCAGCAAGGAGTCTAAGATGGAAGTTGTTAACTGTCCAGAGAAAGGTCTGTCC
+>Rat
+---------AGAGACAGTGGGACCGTCTGGGGTGCCCTGGGTCATGGCATCAACCTGAACATCCCTAACTTTCAAATGACTGATGATATTGATGAGGTGCGATGGGAGAGG------GGGAGCACCCTGGTTGCCGAGTTTAAAAGGAAGATGAAGCCTTTTTTGAAATCGGGAGCATTTGAGATCTTAGCAAATGGAGACTTGAAGATAAAGAAT---CTGACAAGAGATGACAGTGGCACCTATAATGTAACGGTATACAGCACAAATGGGACACGTATCCTGGACAAGGCACTGGACTTGAGGATTCTAGAGATGGTCTCAAAGCCGATGATCTACTGGGAGTGCAGCAACGCAACCCTGACCTGTGAGGTCTTGGAAGGAACAGATGTTGAACTAAAGCTGTACCAAGGAAAGGAGCATCTCAGGAGCCTCCGTCAGAAGACCATGAGTTACCAGTGG---ACCAACCTGAGAGCACCGTTTAAGTGCAAGGCGGTAAACAGGGTCAGCCAGGAGTCTGAGATGGAAGTTGTCAACTGTCCAGAGAAAGGTCTGCCC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/relax-in1.nhx	Tue Jan 08 10:59:21 2019 -0500
@@ -0,0 +1,1 @@
+((((Pig{TEST}:0.147969,Cow{TEST}:0.21343){TEST}:0.085099,Horse:0.165787,Cat:0.264806){TEST}:0.058611,((RhMonkey{REFERENCE}:0.002015,Baboon{REFERENCE}:0.003108){REFERENCE}:0.022733,(Human{REFERENCE}:0.004349,Chimp{REFERENCE}:0.000799):0.011873){REFERENCE}:0.101856){REFERENCE}:0.340802,Rat{REFERENCE}:0.050958,Mouse{REFERENCE}:0.09795);
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/relax-in2.nhx	Tue Jan 08 10:59:21 2019 -0500
@@ -0,0 +1,1 @@
+((((Pig{TEST}:0.147969,Cow{TEST}:0.21343){TEST}:0.085099,Horse:0.165787,Cat:0.264806){TEST}:0.058611,((RhMonkey:0.002015,Baboon:0.003108):0.022733,(Human:0.004349,Chimp:0.000799):0.011873):0.101856):0.340802,Rat:0.050958,Mouse:0.09795);
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/relax-out1.json	Tue Jan 08 10:59:21 2019 -0500
@@ -0,0 +1,376 @@
+{
+ "analysis":{
+   "info":"RELAX (a random effects test of selection relaxation) uses a random effects branch-site model framework to test whether a set of 'Test' branches evolves under relaxed selection relative to a set of 'Reference' branches (R), as measured by the relaxation parameter (K).\n                                                Version 2.1 adds a check for stability in K estimates to try to mitigate convergence problems",
+   "version":"2.1",
+   "citation":"RELAX: Detecting Relaxed Selection in a Phylogenetic Framework (2015). Mol Biol Evol 32 (3): 820-832",
+   "authors":"Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group",
+   "contact":"spond@temple.edu",
+   "requirements":"in-frame codon alignment and a phylogenetic tree, with at least two groups of branches defined using the {} notation (one group can be defined as all unlabeled branches)"
+  },
+ "input":{
+   "file name":"/Users/ryanvelazquez/Documents/misc/galaxy items/tools-iuc/tools/hyphy/test-data/relax-in1.fa",
+   "number of sequences":10,
+   "number of sites":187,
+   "partition count":1,
+   "trees":{
+     "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.085099,Horse:0.165787,Cat:0.264806)Node2:0.058611,((RhMonkey:0.002015,Baboon:0.003108)Node9:0.022733,(Human:0.004349,Chimp:0.000799)Node12:0.011873)Node8:0.101856)Node1:0.340802,Rat:0.050958,Mouse:0.09795)"
+    }
+  },
+ "fits":{
+   "Nucleotide GTR":{
+     "Log Likelihood":-3531.964032193222,
+     "estimated parameters":24,
+     "AIC-c":7112.142925621896,
+     "Equilibrium frequencies":[
+      [0.3563279857397504],
+      [0.1837789661319073],
+      [0.2402852049910873],
+      [0.2196078431372549]
+      ],
+     "Rate Distributions":{
+       "Substitution rate from nucleotide A to nucleotide C":0.5465757107930838,
+       "Substitution rate from nucleotide A to nucleotide G":1,
+       "Substitution rate from nucleotide A to nucleotide T":0.264131123736109,
+       "Substitution rate from nucleotide C to nucleotide G":0.4861812992450388,
+       "Substitution rate from nucleotide C to nucleotide T":1.017887589835735,
+       "Substitution rate from nucleotide G to nucleotide T":0.3021773696987065
+      },
+     "display order":0
+    },
+   "MG94xREV with separate rates for branch sets":{
+     "Log Likelihood":-3458.097783887836,
+     "estimated parameters":33,
+     "AIC-c":6983.417789997894,
+     "Equilibrium frequencies":[
+      [0.04785168648208005],
+      [0.03911346079312019],
+      [0.04842054060317301],
+      [0.04069665666515385],
+      [0.01817010744778396],
+      [0.01485205303123071],
+      [0.01838611113045968],
+      [0.01545321970309948],
+      [0.0190138898893362],
+      [0.01554175184587827],
+      [0.01923992433904378],
+      [0.01617083546230154],
+      [0.02796925133965702],
+      [0.02286176927319543],
+      [0.02830174586718859],
+      [0.02378714529482007],
+      [0.01687870337957799],
+      [0.01379647304851128],
+      [0.01707935503225849],
+      [0.01435491300079667],
+      [0.006409133648843443],
+      [0.005238757839512795],
+      [0.006485324528555602],
+      [0.005450807083377185],
+      [0.006706760641638982],
+      [0.005482034985409045],
+      [0.006786489669196017],
+      [0.005703931360295163],
+      [0.009865581170012171],
+      [0.008064021368173151],
+      [0.009982861811889655],
+      [0.008390428826966174],
+      [0.03287895020631181],
+      [0.02687490503171972],
+      [0.033269810543681],
+      [0.0279627207822247],
+      [0.01248470225271473],
+      [0.01020486315060615],
+      [0.01263311863778268],
+      [0.01061792547971484],
+      [0.01306446616325414],
+      [0.01067875601941112],
+      [0.01321977470017749],
+      [0.01111100011404158],
+      [0.01921770557551369],
+      [0.01570834862514353],
+      [0.01944616295744266],
+      [0.01634417558076203],
+      [0.01975257768318274],
+      [0.02055210293142003],
+      [0.009176034326710849],
+      [0.007500393094996483],
+      [0.00928511773266342],
+      [0.007803986567571961],
+      [0.00784869593340758],
+      [0.009716299514778986],
+      [0.008166387662818644],
+      [0.01412467213650941],
+      [0.01154535713247913],
+      [0.01429258425298098],
+      [0.01201267864744234]
+      ],
+     "Rate Distributions":{
+       "non-synonymous/synonymous rate ratio for *Reference*":[
+        [0.5998337130511077, 1]
+        ],
+       "non-synonymous/synonymous rate ratio for *Test*":[
+        [1.554836363231672, 1]
+        ],
+       "non-synonymous/synonymous rate ratio for *Unclassified*":[
+        [1.323008542237338, 1]
+        ]
+      },
+     "display order":1
+    },
+   "RELAX alternative":{
+     "Log Likelihood":-3427.641466344699,
+     "estimated parameters":41,
+     "AIC-c":6939.166958947604,
+     "Rate Distributions":{
+       "Test":{
+         "0":{
+           "omega":0,
+           "proportion":0.2911071539848986
+          },
+         "1":{
+           "omega":0,
+           "proportion":0.2693397808592169
+          },
+         "2":{
+           "omega":5.424306690747749,
+           "proportion":0.4395530651558845
+          }
+        },
+       "Reference":{
+         "0":{
+           "omega":0,
+           "proportion":0.2911071539848986
+          },
+         "1":{
+           "omega":0,
+           "proportion":0.2693397808592169
+          },
+         "2":{
+           "omega":1.812613591933097,
+           "proportion":0.4395530651558845
+          }
+        }
+      },
+     "display order":2
+    },
+   "RELAX null":{
+     "Log Likelihood":-3434.619492705835,
+     "estimated parameters":40,
+     "AIC-c":6951.032315100023,
+     "Rate Distributions":{
+       "Test":{
+         "0":{
+           "omega":0.1293481638748959,
+           "proportion":0.4017058334895309
+          },
+         "1":{
+           "omega":0.2021540589664449,
+           "proportion":0.2729236995381347
+          },
+         "2":{
+           "omega":3.767190802229909,
+           "proportion":0.3253704669723343
+          }
+        },
+       "Reference":{
+         "0":{
+           "omega":0.1293481638748959,
+           "proportion":0.4017058334895309
+          },
+         "1":{
+           "omega":0.2021540589664449,
+           "proportion":0.2729236995381347
+          },
+         "2":{
+           "omega":3.767190802229909,
+           "proportion":0.3253704669723343
+          }
+        }
+      },
+     "display order":3
+    }
+  },
+ "timers":{
+   "Overall":{
+     "timer":313,
+     "order":0
+    },
+   "Preliminary model fitting":{
+     "timer":17,
+     "order":1
+    },
+   "RELAX alternative model fitting":{
+     "timer":190,
+     "order":3
+    },
+   "RELAX null model fitting":{
+     "timer":56,
+     "order":4
+    }
+  },
+ "test results":{
+   "LRT":13.95605272227021,
+   "p-value":0.0001871341719564823,
+   "relaxation or intensification parameter":2.842932101048393
+  },
+ "tested":{
+   "0":{
+     "Pig":"Test",
+     "Cow":"Test",
+     "Node3":"Test",
+     "Horse":"Unclassified",
+     "Cat":"Unclassified",
+     "Node2":"Test",
+     "RhMonkey":"Reference",
+     "Baboon":"Reference",
+     "Node9":"Reference",
+     "Human":"Reference",
+     "Chimp":"Reference",
+     "Node12":"Unclassified",
+     "Node8":"Reference",
+     "Node1":"Reference",
+     "Rat":"Reference",
+     "Mouse":"Reference"
+    }
+  },
+ "data partitions":{
+   "0":{
+     "name":"relax.filter.default",
+     "coverage":[
+      [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186]
+      ]
+    }
+  },
+ "branch attributes":{
+   "0":{
+     "Human":{
+       "original name":"Human",
+       "Nucleotide GTR":0,
+       "MG94xREV with separate rates for branch sets":0,
+       "RELAX alternative":0,
+       "RELAX null":0
+      },
+     "Chimp":{
+       "original name":"Chimp",
+       "Nucleotide GTR":0.001818722292071369,
+       "MG94xREV with separate rates for branch sets":0.001825814939240948,
+       "RELAX alternative":0.001827359202671433,
+       "RELAX null":0.001832714466554264
+      },
+     "Baboon":{
+       "original name":"Baboon",
+       "Nucleotide GTR":0.001682319705247233,
+       "MG94xREV with separate rates for branch sets":0.001766484099039326,
+       "RELAX alternative":0.001861371759740878,
+       "RELAX null":0.001880673658452964
+      },
+     "RhMonkey":{
+       "original name":"RhMonkey",
+       "Nucleotide GTR":0.003776495523121213,
+       "MG94xREV with separate rates for branch sets":0.003723898882047009,
+       "RELAX alternative":0.003639853124053051,
+       "RELAX null":0.003643307484186126
+      },
+     "Cow":{
+       "original name":"Cow",
+       "Nucleotide GTR":0.2483201583381086,
+       "MG94xREV with separate rates for branch sets":0.2498568912791163,
+       "RELAX alternative":0.3277677731077431,
+       "RELAX null":0.2925738796283687
+      },
+     "Pig":{
+       "original name":"Pig",
+       "Nucleotide GTR":0.1871417867164377,
+       "MG94xREV with separate rates for branch sets":0.1928170361685192,
+       "RELAX alternative":0.2277442542245479,
+       "RELAX null":0.2135004206466554
+      },
+     "Horse":{
+       "original name":"Horse",
+       "Nucleotide GTR":0.2091567334932583,
+       "MG94xREV with separate rates for branch sets":0.2104729862905725,
+       "RELAX alternative":0.4059233413351091,
+       "RELAX null":0.3765897594433346
+      },
+     "Cat":{
+       "original name":"Cat",
+       "Nucleotide GTR":0.2660040109418023,
+       "MG94xREV with separate rates for branch sets":0.276682483263765,
+       "RELAX alternative":0.5282692675142623,
+       "RELAX null":0.4799690800516377
+      },
+     "Mouse":{
+       "original name":"Mouse",
+       "Nucleotide GTR":0.1182531454610134,
+       "MG94xREV with separate rates for branch sets":0.1195032731554601,
+       "RELAX alternative":0.1308145806782354,
+       "RELAX null":0.1470888073398289
+      },
+     "Rat":{
+       "original name":"Rat",
+       "Nucleotide GTR":0.06669544716210057,
+       "MG94xREV with separate rates for branch sets":0.06802863234285669,
+       "RELAX alternative":0.07245491834414142,
+       "RELAX null":0.07477863103169577
+      },
+     "Node1":{
+       "Nucleotide GTR":0.2771601504028877,
+       "MG94xREV with separate rates for branch sets":0.2884041028198522,
+       "RELAX alternative":0.3730383578090298,
+       "RELAX null":0.451812176248499
+      },
+     "Node12":{
+       "Nucleotide GTR":0.01783222754921504,
+       "MG94xREV with separate rates for branch sets":0.01732908050208956,
+       "RELAX alternative":0.01753088629189957,
+       "RELAX null":0.01907243110988959
+      },
+     "Node2":{
+       "Nucleotide GTR":0.06619118337434968,
+       "MG94xREV with separate rates for branch sets":0.06256202484222494,
+       "RELAX alternative":0.0560159229945103,
+       "RELAX null":0.05930942174393248
+      },
+     "Node3":{
+       "Nucleotide GTR":0.09883746945145887,
+       "MG94xREV with separate rates for branch sets":0.1006688620480881,
+       "RELAX alternative":0.1304440727067901,
+       "RELAX null":0.12356636531614
+      },
+     "Node8":{
+       "Nucleotide GTR":0.106110061225871,
+       "MG94xREV with separate rates for branch sets":0.1136940853020744,
+       "RELAX alternative":0.1350606162092146,
+       "RELAX null":0.1366048365485918
+      },
+     "Node9":{
+       "Nucleotide GTR":0.02567391471029082,
+       "MG94xREV with separate rates for branch sets":0.02652712807205039,
+       "RELAX alternative":0.02969171453244129,
+       "RELAX null":0.02893959719634103
+      }
+    },
+   "attributes":{
+     "original name":{
+       "attribute type":"node label",
+       "display order":-1
+      },
+     "Nucleotide GTR":{
+       "attribute type":"branch length",
+       "display order":0
+      },
+     "MG94xREV with separate rates for branch sets":{
+       "attribute type":"branch length",
+       "display order":1
+      },
+     "RELAX alternative":{
+       "attribute type":"branch length",
+       "display order":2
+      },
+     "RELAX null":{
+       "attribute type":"branch length",
+       "display order":3
+      }
+    }
+  }
+}
\ No newline at end of file