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