root/galaxy-central/tools/hyphy/hyphy_dnds_wrapper.xml

リビジョン 2, 4.9 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<?xml version="1.1.1"?>
2<tool name="dN/dS Ratio" id="hyphy_dnds_wrapper1">
3       
4        <description>Estimation</description>
5       
6        <command interpreter="python">hyphy_dnds_wrapper.py $input1 $out_file1 "$tree" "$model" $analysis ${GALAXY_DATA_INDEX_DIR}</command>
7       
8    <inputs>
9        <page>
10            <param format="fasta" name="input1" type="data" label="Fasta file"/>
11            <param name="analysis" type="select" label="Analysis to run on every gene">
12                <option value="global">Global</option>
13                <option value="local">Local</option>
14            </param>
15            <param name="tree" type="text" label="Tree Definition in Newick format" size="20" help="For example: ((hg17,panTro1),(mm5,rn3),canFam1)"/>
16            <param name="model" type="select" label="Substitution Model">
17                <option value="000000">F81</option>
18                <option value="010010">HKY85</option>
19                <option value="012345">REV</option>
20            </param>
21        </page>
22    </inputs>
23        <outputs>
24                <data name="out_file1" format="tabular" />
25        </outputs>
26    <tests>
27      <test>
28        <param name="input1" value="dnds_inp.fasta"/>
29        <param name="tree" value="((human, chimp), mouse)"/>
30        <param name="model" value="000000"/>
31        <param name="analysis" value="global"/>
32        <output name="out_file1" file="dnds_out.tabular"/>
33      </test>
34    </tests>
35        <help>
36
37.. class:: infomark
38
39This tool takes a FASTA alignment file and estimates dN/dS ratio using HYPHY_, a maximum likelihood analyses package.
40
41-----
42
43.. class:: warningmark
44
45The tool returns an error message if no tree definition or an invalid tree definition is supplied.
46Any block/s not containing as many species as mentioned in the tree definition will be omitted from the output.
47
48-----
49
50For 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 the example below. You may also use **Neighbor Joining Tree Builder** tool to obtain the tree definition::
51
52    &gt;hg17.chr7(+):26907301-26907310|hg17_0
53    GTGGGAGGT
54    &gt;panTro1.chr6(+):28037319-28037328|panTro1_0
55    GTGGGAGGT
56    &gt;mm5.chr6(+):52104022-52104031|mm5_0
57    GTGGGAGGT
58    &gt;rn3.chr4(+):80734395-80734404|rn3_0
59    GTGGGAGGT
60    &gt;canFam1.chr14(+):42826409-42826418|canFam1_0
61    GTGGGAGGT
62
63    &gt;hg17.chr7(+):26907310-26907326|hg17_1
64    AGTCAGAGTGTCTGAG
65    &gt;panTro1.chr6(+):28037328-28037344|panTro1_1
66    AGTCAGAGTGTCTGAG
67    &gt;mm5.chr6(+):52104031-52104047|mm5_1
68    AGTCAGAGTGTCTGAG
69    &gt;rn3.chr4(+):80734404-80734420|rn3_1
70    AGTCAGAGTATCTGAG
71    &gt;canFam1.chr14(+):42826418-42826434|canFam1_1
72    AGTCAGAGTGTCTGAG
73
74    &gt;hg17.chr7(+):26907326-26907338|hg17_2
75    GTAGAAGACCCC
76    &gt;panTro1.chr6(+):28037344-28037356|panTro1_2
77    GTAGAAGACCCC
78    &gt;mm5.chr6(+):52104047-52104059|mm5_2
79    GTAGACGATGCC
80    &gt;rn3.chr4(+):80734420-80734432|rn3_2
81    GTAGATGATGCG
82    &gt;canFam1.chr14(+):42826434-42826446|canFam1_2
83    GTAGAAGACCCC
84
85    &gt;hg17.chr7(+):26907338-26907654|hg17_3
86    GGGGAAGGAACGCAGGGCGAAGAGCTGGACTTCTCTGAGGAT---TCCTCGGCCTTCTCGT-----CGTTTCCTGG----CGGGGTGGCCGGAGAGATGGGCAAGAGACCCTCCTTCTCACGTTTCTTTTGCTTCATTCGGCGGTTCTGGAACCAGATCTTCACTTGGGTCTCGTTGAGCTGCAGGGATGCAGCGATCTCCACCCTGCGGGCGCGCGTCAGGTACTTGTTGAAGTGGAACTCCTTCTCCAGTTCCGTGAGCTGCTTGGTAGTGAAGTTGGTGCGCACCGCGTTGGGTTGACCCAGGTAGCCGTACTCTCCAACTTTCC
87    &gt;panTro1.chr6(+):28037356-28037672|panTro1_3
88    GGGGAAGGAACGCAGGGCGAAGAGCTGGACTTCTCTGAGGAT---TCCTCGGCCTTCTCGT-----CGTTTCCTGG----CGGGGTGGCCGGAGAGATGGGCAAGAGACCCTCCTTCTCACGTTTCTTTTGCTTCATTCGGCGGTTCTGGAACCAGATCTTCACTTGGGTCTCGTTGAGCTGCAGGGATGCAGCGATCTCCACCCTGCGGGCGCGCGTCAGGTACTTGTTGAAGTGGAACTCCTTCTCCAGTTCCGTGAGCTGCTTGGTAGTGAAGTTGGTGCGCACCGCGTTGGGTTGACCCAGGTAGCCGTACTCTCCAACTTTCC
89    &gt;mm5.chr6(+):52104059-52104375|mm5_3
90    GGAGAAGGGGCACTGGGCGAGGGGCTAGATTTCTCAGATGAT---TCTTCCGTTTTCTCAT-----CGCTGCCAGG----AGGAGTGGCAGGGGAGATGGGCAGGAGCCCCTCCTTCTCACGCTTCTTCTGCTTCATGCGGCGATTCTGGAACCAGATCTTCACCTGGGTCTCATTGAGCTGTAGGGACGCGGCAATCTCCACCCTGCGCGCTCGTGTAAGGTACTTGTTGAAGTGGAACTCCTTCTCCAGCTCTGTGAGCTGCTTGGTGGTGAAATTGGTGCGCACTGCGTTGGGTTGACCCACGTAGCCGTACTCTCCAACTTTCC
91    &gt;rn3.chr4(+):80734432-80734748|rn3_3
92    GGAGAAGGGGCGCTGGGCGAGGAGCTGGATTTCTCAGATGAT---TCTTCAGTTTTCTCAT-----CGCTTCCAGG----AGGGGTGGCGGGTGAAATGGGCAAGAGCCCCTCTTTCTCGCGCTTCTTCTGCTTCATGCGGCGATTCTGGAACCAGATCTTCACCTGGGTCTCATTGAGTTGCAGGGACGCGGCTATCTCCACCCTGCGGGCTCTTGTTAGGTACTTGTTGAAGTGGAACTCCTTCTCCAGCTCTGTGAGCTGCTTGGTGGTGAAGTTGGTGCGCACTGCGTTGGGTTGACCCACGTAGCCATACTCTCCAACTTTCC
93    &gt;canFam1.chr14(+):42826446-42826762|canFam1_3
94    GGAGACGGAATGCAGGGCGAGGAGCTGGATTTCTCTGAAGAT---TCCTCCGCCTTCTCCT-----CACTTCCTGG----CGGGGTGGCAGGGGAGATGGGCAAAAGGCCCTCTTTCTCTCGTTTCTTCTGCTTCATCCGGCGGTTCTGGAACCAGATCTTCACCTGGGTCTCGTTGAGCTGCAGGGATGCTGCGATCTCCACCCTGCGGGCGCGGGTCAGATACTTATTGAAGTGGAACTCCTTTTCCAGCTCGGTGAGCTGCTTGGTGGTGAAGTTGGTACGCACTGCATTCGGTTGACCCACGTAGCCGTACTCTCCAACTTTCC
95   
96
97
98.. _HYPHY: http://www.hyphy.org
99        </help>
100</tool>
101
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