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