/tools/hyphy/hyphy_branch_lengths_wrapper.xml
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1<?xml version="1.2.1"?> 2<tool name="Branch Lengths" id="hyphy_branch_lengths_wrapper1"> 3 4 <description>Estimation</description> 5 6 <command interpreter="python">hyphy_branch_lengths_wrapper.py $input1 $out_file1 "$tree" "$model" "$base_freq" "Global" ${GALAXY_DATA_INDEX_DIR}</command> 7 8 <inputs> 9 <page> 10 <param format="fasta" name="input1" type="data" label="Fasta file"/> 11 <param name="tree" type="text" label="Tree Definition" size="20" help="For example: ((hg17,panTro1),(mm5,rn3),canFam1)"/> 12 <param name="model" type="select" label="Substitution Model"> 13 <option value="000000">F81</option> 14 <option value="010010">HKY85</option> 15 <option value="012345">REV</option> 16 </param> 17<!-- <param name="model_options" type="select" label="Model Options"> 18 <option value="Local">All model parameters are estimated independently for each branch</option> 19 <option value="Global">Model parameters are shared by all branches, branch lengths are estimated independently</option> 20 <option value="Global w/variation">Model parameters are shared by all branches, branch lengths come from a user-chosen distribution, whose parameters are estimated</option> 21 <option value="Global w/variation+HM">Model parameters are shared by all branches, branch lengths come from a user-chosen distribution, whose parameters is estimated; rates at adjacent sites are correlated via a simple Hidden Markov model with an autocorrelation parameter lambda</option> 22 </param> --> 23 <param name="base_freq" type="select" label="Base Frequencies"> 24 <option value="Observed">Nucleotide frequencies collected from the data file will be used as equilibrium frequencies</option> 25 <option value="Equal">Equal (.25) frequencies are used as equilibrium frequencies</option> 26 </param> 27 </page> 28 </inputs> 29 <outputs> 30 <data name="out_file1" format="tabular" /> 31 </outputs> 32 <tests> 33 <test> 34 <param name="input1" value="branchlength_in.fasta"/> 35 <param name="tree" value="((hg17,panTro1),(mm5,rn3),canFam1)"/> 36 <param name="model" value="012345"/> 37 <param name="base_freq" value="Observed"/> 38 <output name="out_file1" file="branchlength_out.tabular"/> 39 </test> 40 </tests> 41 <help> 42This tool takes a single or multiple FASTA alignment file and estimates branch lengths using HYPHY_, a maximum likelihood analyses package. 43 44For the tree definition, you only need to specify the species build names. For example, you could use the tree *((hg17,panTro1),(mm5,rn3),canFam1)*, if your FASTA file looks like this:: 45 46 >hg17.chr7(+):26907301-26907310|hg17_0 47 GTGGGAGGT 48 >panTro1.chr6(+):28037319-28037328|panTro1_0 49 GTGGGAGGT 50 >mm5.chr6(+):52104022-52104031|mm5_0 51 GTGGGAGGT 52 >rn3.chr4(+):80734395-80734404|rn3_0 53 GTGGGAGGT 54 >canFam1.chr14(+):42826409-42826418|canFam1_0 55 GTGGGAGGT 56 57 >hg17.chr7(+):26907310-26907326|hg17_1 58 AGTCAGAGTGTCTGAG 59 >panTro1.chr6(+):28037328-28037344|panTro1_1 60 AGTCAGAGTGTCTGAG 61 >mm5.chr6(+):52104031-52104047|mm5_1 62 AGTCAGAGTGTCTGAG 63 >rn3.chr4(+):80734404-80734420|rn3_1 64 AGTCAGAGTATCTGAG 65 >canFam1.chr14(+):42826418-42826434|canFam1_1 66 AGTCAGAGTGTCTGAG 67 68 >hg17.chr7(+):26907326-26907338|hg17_2 69 GTAGAAGACCCC 70 >panTro1.chr6(+):28037344-28037356|panTro1_2 71 GTAGAAGACCCC 72 >mm5.chr6(+):52104047-52104059|mm5_2 73 GTAGACGATGCC 74 >rn3.chr4(+):80734420-80734432|rn3_2 75 GTAGATGATGCG 76 >canFam1.chr14(+):42826434-42826446|canFam1_2 77 GTAGAAGACCCC 78 79 >hg17.chr7(+):26907338-26907654|hg17_3 80 GGGGAAGGAACGCAGGGCGAAGAGCTGGACTTCTCTGAGGAT---TCCTCGGCCTTCTCGT-----CGTTTCCTGG----CGGGGTGGCCGGAGAGATGGGCAAGAGACCCTCCTTCTCACGTTTCTTTTGCTTCATTCGGCGGTTCTGGAACCAGATCTTCACTTGGGTCTCGTTGAGCTGCAGGGATGCAGCGATCTCCACCCTGCGGGCGCGCGTCAGGTACTTGTTGAAGTGGAACTCCTTCTCCAGTTCCGTGAGCTGCTTGGTAGTGAAGTTGGTGCGCACCGCGTTGGGTTGACCCAGGTAGCCGTACTCTCCAACTTTCC 81 >panTro1.chr6(+):28037356-28037672|panTro1_3 82 GGGGAAGGAACGCAGGGCGAAGAGCTGGACTTCTCTGAGGAT---TCCTCGGCCTTCTCGT-----CGTTTCCTGG----CGGGGTGGCCGGAGAGATGGGCAAGAGACCCTCCTTCTCACGTTTCTTTTGCTTCATTCGGCGGTTCTGGAACCAGATCTTCACTTGGGTCTCGTTGAGCTGCAGGGATGCAGCGATCTCCACCCTGCGGGCGCGCGTCAGGTACTTGTTGAAGTGGAACTCCTTCTCCAGTTCCGTGAGCTGCTTGGTAGTGAAGTTGGTGCGCACCGCGTTGGGTTGACCCAGGTAGCCGTACTCTCCAACTTTCC 83 >mm5.chr6(+):52104059-52104375|mm5_3 84 GGAGAAGGGGCACTGGGCGAGGGGCTAGATTTCTCAGATGAT---TCTTCCGTTTTCTCAT-----CGCTGCCAGG----AGGAGTGGCAGGGGAGATGGGCAGGAGCCCCTCCTTCTCACGCTTCTTCTGCTTCATGCGGCGATTCTGGAACCAGATCTTCACCTGGGTCTCATTGAGCTGTAGGGACGCGGCAATCTCCACCCTGCGCGCTCGTGTAAGGTACTTGTTGAAGTGGAACTCCTTCTCCAGCTCTGTGAGCTGCTTGGTGGTGAAATTGGTGCGCACTGCGTTGGGTTGACCCACGTAGCCGTACTCTCCAACTTTCC 85 >rn3.chr4(+):80734432-80734748|rn3_3 86 GGAGAAGGGGCGCTGGGCGAGGAGCTGGATTTCTCAGATGAT---TCTTCAGTTTTCTCAT-----CGCTTCCAGG----AGGGGTGGCGGGTGAAATGGGCAAGAGCCCCTCTTTCTCGCGCTTCTTCTGCTTCATGCGGCGATTCTGGAACCAGATCTTCACCTGGGTCTCATTGAGTTGCAGGGACGCGGCTATCTCCACCCTGCGGGCTCTTGTTAGGTACTTGTTGAAGTGGAACTCCTTCTCCAGCTCTGTGAGCTGCTTGGTGGTGAAGTTGGTGCGCACTGCGTTGGGTTGACCCACGTAGCCATACTCTCCAACTTTCC 87 >canFam1.chr14(+):42826446-42826762|canFam1_3 88 GGAGACGGAATGCAGGGCGAGGAGCTGGATTTCTCTGAAGAT---TCCTCCGCCTTCTCCT-----CACTTCCTGG----CGGGGTGGCAGGGGAGATGGGCAAAAGGCCCTCTTTCTCTCGTTTCTTCTGCTTCATCCGGCGGTTCTGGAACCAGATCTTCACCTGGGTCTCGTTGAGCTGCAGGGATGCTGCGATCTCCACCCTGCGGGCGCGGGTCAGATACTTATTGAAGTGGAACTCCTTTTCCAGCTCGGTGAGCTGCTTGGTGGTGAAGTTGGTACGCACTGCATTCGGTTGACCCACGTAGCCGTACTCTCCAACTTTCC 89 90 91 92.. _HYPHY: http://www.hyphy.org 93 </help> 94</tool> 95