root/galaxy-central/tools/evolution/add_scores.xml

リビジョン 2, 3.1 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
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
37This currently works only for build hg18.
38
39-----
40
41**Dataset formats**
42
43The 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
53This tool adds a column that measures interspecies conservation at each SNP
54position, using conservation scores for primates pre-computed by the
55phyloP program.  PhyloP performs an exact P-value computation under a
56continuous Markov substitution model.
57
58The chromosome and start position
59are used to look up the scores, so if a larger interval is in the input,
60only 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
100Siepel A, Pollard KS, Haussler D. (2006)
101New methods for detecting lineage-specific selection.
102In Proceedings of the 10th International Conference on Research in Computational
103Molecular Biology (RECOMB 2006), pp. 190-205.
104
105  </help>
106</tool>
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