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/tools/hyphy/hyphy_branch_lengths_wrapper.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 95 lines | 77 code | 12 blank | 6 comment | 0 complexity | 9ef7c03b3585b8745355a9bcf48f3ad4 MD5 | raw file
 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    &gt;hg17.chr7(+):26907301-26907310|hg17_0
47    GTGGGAGGT
48    &gt;panTro1.chr6(+):28037319-28037328|panTro1_0
49    GTGGGAGGT
50    &gt;mm5.chr6(+):52104022-52104031|mm5_0
51    GTGGGAGGT
52    &gt;rn3.chr4(+):80734395-80734404|rn3_0
53    GTGGGAGGT
54    &gt;canFam1.chr14(+):42826409-42826418|canFam1_0
55    GTGGGAGGT
56
57    &gt;hg17.chr7(+):26907310-26907326|hg17_1
58    AGTCAGAGTGTCTGAG
59    &gt;panTro1.chr6(+):28037328-28037344|panTro1_1
60    AGTCAGAGTGTCTGAG
61    &gt;mm5.chr6(+):52104031-52104047|mm5_1
62    AGTCAGAGTGTCTGAG
63    &gt;rn3.chr4(+):80734404-80734420|rn3_1
64    AGTCAGAGTATCTGAG
65    &gt;canFam1.chr14(+):42826418-42826434|canFam1_1
66    AGTCAGAGTGTCTGAG
67
68    &gt;hg17.chr7(+):26907326-26907338|hg17_2
69    GTAGAAGACCCC
70    &gt;panTro1.chr6(+):28037344-28037356|panTro1_2
71    GTAGAAGACCCC
72    &gt;mm5.chr6(+):52104047-52104059|mm5_2
73    GTAGACGATGCC
74    &gt;rn3.chr4(+):80734420-80734432|rn3_2
75    GTAGATGATGCG
76    &gt;canFam1.chr14(+):42826434-42826446|canFam1_2
77    GTAGAAGACCCC
78
79    &gt;hg17.chr7(+):26907338-26907654|hg17_3
80    GGGGAAGGAACGCAGGGCGAAGAGCTGGACTTCTCTGAGGAT---TCCTCGGCCTTCTCGT-----CGTTTCCTGG----CGGGGTGGCCGGAGAGATGGGCAAGAGACCCTCCTTCTCACGTTTCTTTTGCTTCATTCGGCGGTTCTGGAACCAGATCTTCACTTGGGTCTCGTTGAGCTGCAGGGATGCAGCGATCTCCACCCTGCGGGCGCGCGTCAGGTACTTGTTGAAGTGGAACTCCTTCTCCAGTTCCGTGAGCTGCTTGGTAGTGAAGTTGGTGCGCACCGCGTTGGGTTGACCCAGGTAGCCGTACTCTCCAACTTTCC
81    &gt;panTro1.chr6(+):28037356-28037672|panTro1_3
82    GGGGAAGGAACGCAGGGCGAAGAGCTGGACTTCTCTGAGGAT---TCCTCGGCCTTCTCGT-----CGTTTCCTGG----CGGGGTGGCCGGAGAGATGGGCAAGAGACCCTCCTTCTCACGTTTCTTTTGCTTCATTCGGCGGTTCTGGAACCAGATCTTCACTTGGGTCTCGTTGAGCTGCAGGGATGCAGCGATCTCCACCCTGCGGGCGCGCGTCAGGTACTTGTTGAAGTGGAACTCCTTCTCCAGTTCCGTGAGCTGCTTGGTAGTGAAGTTGGTGCGCACCGCGTTGGGTTGACCCAGGTAGCCGTACTCTCCAACTTTCC
83    &gt;mm5.chr6(+):52104059-52104375|mm5_3
84    GGAGAAGGGGCACTGGGCGAGGGGCTAGATTTCTCAGATGAT---TCTTCCGTTTTCTCAT-----CGCTGCCAGG----AGGAGTGGCAGGGGAGATGGGCAGGAGCCCCTCCTTCTCACGCTTCTTCTGCTTCATGCGGCGATTCTGGAACCAGATCTTCACCTGGGTCTCATTGAGCTGTAGGGACGCGGCAATCTCCACCCTGCGCGCTCGTGTAAGGTACTTGTTGAAGTGGAACTCCTTCTCCAGCTCTGTGAGCTGCTTGGTGGTGAAATTGGTGCGCACTGCGTTGGGTTGACCCACGTAGCCGTACTCTCCAACTTTCC
85    &gt;rn3.chr4(+):80734432-80734748|rn3_3
86    GGAGAAGGGGCGCTGGGCGAGGAGCTGGATTTCTCAGATGAT---TCTTCAGTTTTCTCAT-----CGCTTCCAGG----AGGGGTGGCGGGTGAAATGGGCAAGAGCCCCTCTTTCTCGCGCTTCTTCTGCTTCATGCGGCGATTCTGGAACCAGATCTTCACCTGGGTCTCATTGAGTTGCAGGGACGCGGCTATCTCCACCCTGCGGGCTCTTGTTAGGTACTTGTTGAAGTGGAACTCCTTCTCCAGCTCTGTGAGCTGCTTGGTGGTGAAGTTGGTGCGCACTGCGTTGGGTTGACCCACGTAGCCATACTCTCCAACTTTCC
87    &gt;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