[2] | 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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