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comparison tools/evolution/add_scores.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="hgv_add_scores" name="phyloP" version="1.0.0">
2 <description>interspecies conservation scores</description>
3
4 <command>
5 add_scores $input1 ${input1.metadata.dbkey} ${input1.metadata.chromCol} ${input1.metadata.startCol} ${GALAXY_DATA_INDEX_DIR}/add_scores.loc $out_file1
6 </command>
7
8 <inputs>
9 <param format="interval" name="input1" type="data" label="Dataset">
10 <validator type="unspecified_build"/>
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."/>
12 </param>
13 </inputs>
14
15 <outputs>
16 <data format="input" name="out_file1" />
17 </outputs>
18
19 <requirements>
20 <requirement type="package">add_scores</requirement>
21 </requirements>
22
23 <tests>
24 <test>
25 <param name="input1" value="add_scores_input1.interval" ftype="interval" dbkey="hg18" />
26 <output name="output" file="add_scores_output1.interval" />
27 </test>
28 <test>
29 <param name="input1" value="add_scores_input2.bed" ftype="interval" dbkey="hg18" />
30 <output name="output" file="add_scores_output2.interval" />
31 </test>
32 </tests>
33
34 <help>
35 .. class:: warningmark
36
37 This currently works only for build hg18.
38
39 -----
40
41 **Dataset formats**
42
43 The input can be any interval_ format dataset. The output is also in interval format.
44 (`Dataset missing?`_)
45
46 .. _interval: ./static/formatHelp.html#interval
47 .. _Dataset missing?: ./static/formatHelp.html
48
49 -----
50
51 **What it does**
52
53 This tool adds a column that measures interspecies conservation at each SNP
54 position, using conservation scores for primates pre-computed by the
55 phyloP program. PhyloP performs an exact P-value computation under a
56 continuous Markov substitution model.
57
58 The chromosome and start position
59 are used to look up the scores, so if a larger interval is in the input,
60 only the score for the first nucleotide is returned.
61
62 -----
63
64 **Example**
65
66 - input file, with SNPs::
67
68 chr22 16440426 14440427 C/T
69 chr22 15494851 14494852 A/G
70 chr22 14494911 14494912 A/T
71 chr22 14550435 14550436 A/G
72 chr22 14611956 14611957 G/T
73 chr22 14612076 14612077 A/G
74 chr22 14668537 14668538 C
75 chr22 14668703 14668704 A/T
76 chr22 14668775 14668776 G
77 chr22 14680074 14680075 A/T
78 etc.
79
80 - output file, showing conservation scores for primates::
81
82 chr22 16440426 14440427 C/T 0.509
83 chr22 15494851 14494852 A/G 0.427
84 chr22 14494911 14494912 A/T NA
85 chr22 14550435 14550436 A/G NA
86 chr22 14611956 14611957 G/T -2.142
87 chr22 14612076 14612077 A/G 0.369
88 chr22 14668537 14668538 C 0.419
89 chr22 14668703 14668704 A/T -1.462
90 chr22 14668775 14668776 G 0.470
91 chr22 14680074 14680075 A/T 0.303
92 etc.
93
94 "NA" means that the phyloP score was not available.
95
96 -----
97
98 **Reference**
99
100 Siepel A, Pollard KS, Haussler D. (2006)
101 New methods for detecting lineage-specific selection.
102 In Proceedings of the 10th International Conference on Research in Computational
103 Molecular Biology (RECOMB 2006), pp. 190-205.
104
105 </help>
106 </tool>