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1 <tool id="hgv_add_scores" name="phyloP" version="1.0.0">
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2 <description>interspecies conservation scores</description>
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3
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4 <command>
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5 add_scores $input1 ${input1.metadata.dbkey} ${input1.metadata.chromCol} ${input1.metadata.startCol} ${GALAXY_DATA_INDEX_DIR}/add_scores.loc $out_file1
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6 </command>
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7
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8 <inputs>
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9 <param format="interval" name="input1" type="data" label="Dataset">
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10 <validator type="unspecified_build"/>
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11 <validator type="dataset_metadata_in_file" filename="add_scores.loc" metadata_name="dbkey" metadata_column="0" message="Data is currently not available for the specified build."/>
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12 </param>
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13 </inputs>
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14
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15 <outputs>
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16 <data format="input" name="out_file1" />
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17 </outputs>
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18
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19 <requirements>
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20 <requirement type="package">add_scores</requirement>
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21 </requirements>
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22
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23 <tests>
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24 <test>
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25 <param name="input1" value="add_scores_input1.interval" ftype="interval" dbkey="hg18" />
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26 <output name="output" file="add_scores_output1.interval" />
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27 </test>
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28 <test>
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29 <param name="input1" value="add_scores_input2.bed" ftype="interval" dbkey="hg18" />
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30 <output name="output" file="add_scores_output2.interval" />
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31 </test>
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32 </tests>
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33
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34 <help>
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35 .. class:: warningmark
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36
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37 This currently works only for build hg18.
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38
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39 -----
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40
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41 **Dataset formats**
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42
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43 The input can be any interval_ format dataset. The output is also in interval format.
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44 (`Dataset missing?`_)
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45
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46 .. _interval: ./static/formatHelp.html#interval
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47 .. _Dataset missing?: ./static/formatHelp.html
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48
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49 -----
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50
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51 **What it does**
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52
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53 This tool adds a column that measures interspecies conservation at each SNP
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54 position, using conservation scores for primates pre-computed by the
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55 phyloP program. PhyloP performs an exact P-value computation under a
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56 continuous Markov substitution model.
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57
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58 The chromosome and start position
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59 are used to look up the scores, so if a larger interval is in the input,
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60 only the score for the first nucleotide is returned.
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61
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62 -----
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63
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64 **Example**
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65
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66 - input file, with SNPs::
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67
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68 chr22 16440426 14440427 C/T
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69 chr22 15494851 14494852 A/G
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70 chr22 14494911 14494912 A/T
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71 chr22 14550435 14550436 A/G
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72 chr22 14611956 14611957 G/T
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73 chr22 14612076 14612077 A/G
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74 chr22 14668537 14668538 C
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75 chr22 14668703 14668704 A/T
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76 chr22 14668775 14668776 G
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77 chr22 14680074 14680075 A/T
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78 etc.
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79
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80 - output file, showing conservation scores for primates::
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81
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82 chr22 16440426 14440427 C/T 0.509
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83 chr22 15494851 14494852 A/G 0.427
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84 chr22 14494911 14494912 A/T NA
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85 chr22 14550435 14550436 A/G NA
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86 chr22 14611956 14611957 G/T -2.142
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87 chr22 14612076 14612077 A/G 0.369
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88 chr22 14668537 14668538 C 0.419
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89 chr22 14668703 14668704 A/T -1.462
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90 chr22 14668775 14668776 G 0.470
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91 chr22 14680074 14680075 A/T 0.303
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92 etc.
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93
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94 "NA" means that the phyloP score was not available.
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95
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96 -----
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97
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98 **Reference**
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99
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100 Siepel A, Pollard KS, Haussler D. (2006)
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101 New methods for detecting lineage-specific selection.
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102 In Proceedings of the 10th International Conference on Research in Computational
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103 Molecular Biology (RECOMB 2006), pp. 190-205.
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104
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105 </help>
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106 </tool>
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