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comparison hyphy_fade.xml @ 0:bcd72352534f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
author rdvelazquez
date Fri, 16 Nov 2018 15:41:48 -0500
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children 9e5fa270a08a
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-1:000000000000 0:bcd72352534f
1 <?xml version="1.0"?>
2 <tool id="hyphy_fade" name="HyPhy-FADE" version="@VERSION@+galaxy0">
3 <description>: FUBAR* Approach to Directional Selection (*Fast
4 Unconstrained Bayesian Approximation)</description>
5 <macros>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="requirements"/>
9 <version_command>HYPHYMP --version | tail -n 1 | awk '{print
10 $1}'</version_command>
11 <command detect_errors="exit_code"><![CDATA[
12 ln -s '$input_file' fade_input.fa &&
13 ln -s '$input_nhx' fade_input.nhx &&
14 echo $substitutionmodel > tool_params &&
15 echo `pwd`/fade_input.fa >> tool_params &&
16 echo `pwd`/fade_input.nhx >> tool_params &&
17 echo '$grid_points' >> tool_params &&
18 echo '$mcmc' >> tool_params &&
19 echo '$chain_length' >> tool_params &&
20 echo '$samples' >> tool_params &&
21 echo '$samples_per_chain' >> tool_params &&
22 echo '$concentration' >> tool_params &&
23 echo '$branches' >> tool_params &&
24 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FADE.bf > '$fade_log'
25 ]]></command>
26 <inputs>
27 <param name="input_file" type="data" format="fasta" label="Input FASTA file"/>
28 <param name="input_nhx" type="data" format="nhx" label="Input newick file"/>
29 <param name="substitutionmodel" type="select" label="Substitution Model">
30 <option value="1">LG (Generalist empirical model from Le and
31 Gascuel 2008)</option>
32 <option value="2">WAG (Generalist empirical model from Whelon
33 and Goldman 2001)</option>
34 <option value="3">JTT (Generalist empirical model from Jones,
35 Taylor and Thornton 1996)</option>
36 <option value="4">JC69 (Generalist empirical model with equal
37 exhangeability rates among all amino acids)</option>
38 <option value="5">mtMet (Specialist empirical model for
39 metazoan mitochondrial genomes from Le, Dang and Le
40 2007)</option>
41 <option value="6">mtVer (Specialist empirical model for
42 vertebrate mitochondrial gemones from Le, Dang and Le
43 2007)</option>
44 <option value="7">mtInv (Specialist empirical model for
45 invertebrate mitochondrial genomes from Le, Dang and Le
46 2007)</option>
47 <option value="8">gcpREV (Specialist empirical model for
48 green plant chloroplast genomes from Cox and Foster
49 20013)</option>
50 <option value="9">HIVBm (Specialist empirical model for
51 between-host HIV sequences from Nickle et al. 2007)</option>
52 <option value="10">HIVWm (Specialist empirical model for
53 within-host HIV sequences from Nickle et al. 2007)</option>
54 <option value="11">GTR (General time reversible model; 189
55 estimated parameters)</option>
56 </param>
57 <param name="grid_points" type="integer" value="20" min="5" max="50" label="Grid points"/>
58 <param name="mcmc" type="integer" value="5" min="2" max="20" label="Number of MCMC chains"/>
59 <param name="chain_length" type="integer" value="2000000" min="500000" max="50000000" label="Length of each chain"/>
60 <param name="samples" type="integer" value="1000000" min="100000" max="1900000" label="Samples to use for burn-in"/>
61 <param name="samples_per_chain" type="integer" value="100" min="50" max="1000000" label="Samples to draw from each chain"/>
62 <param name="concentration" type="float" value="0.5" min="0.001" max="1" label="Concentration parameter of the Dirichlet prior"/>
63 <param name="branches" type="select" label="Set of branches to test">
64 <option value="1">All branches</option>
65 <option value="2">Internal branches</option>
66 <option value="3">Leaf branches</option>
67 <option value="4">Unlabeled branches</option>
68 </param>
69 </inputs>
70 <outputs>
71 <data name="fade_log" format="txt"/>
72 <data name="fade_output" format="json" from_work_dir="fade_input.fa.FADE.json"/>
73 </outputs>
74 <tests>
75 <test>
76 <param name="input_file" ftype="fasta" value="fade-in1.fa"/>
77 <param name="input_nhx" ftype="nhx" value="fade-in1.nhx"/>
78 <output name="fade_output" file="fade-out1.json" compare="sim_size"/>
79 </test>
80 </tests>
81 <help><![CDATA[
82 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 site evolving under directional evolution in protien alignments.
83 ]]></help>
84 <expand macro="citations">
85 <citation type="doi">10.1093/molbev/msv022</citation>
86 </expand>
87 </tool>