root/galaxy-central/tools/human_genome_variation/snpFreq.xml

リビジョン 2, 4.5 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="hgv_snpFreq" name="snpFreq" version="1.0.0">
2  <description>significant SNPs in case-control data</description>
3
4  <command interpreter="perl">
5    snpFreq2.pl $input $group1_1 $group1_2 $group1_3 $group2_1 $group2_2 $group2_3 0.05 $output
6  </command>
7
8  <inputs>
9    <param format="tabular" name="input" type="data" label="Dataset" />
10    <param name="group1_1" label="Column with genotype 1 count for group 1" type="data_column" data_ref="input" />
11    <param name="group1_2" label="Column with genotype 2 count for group 1" type="data_column" data_ref="input" />
12    <param name="group1_3" label="Column with genotype 3 count for group 1" type="data_column" data_ref="input" />
13    <param name="group2_1" label="Column with genotype 1 count for group 2" type="data_column" data_ref="input" />
14    <param name="group2_2" label="Column with genotype 2 count for group 2" type="data_column" data_ref="input" />
15    <param name="group2_3" label="Column with genotype 3 count for group 2" type="data_column" data_ref="input" />
16  </inputs>
17
18  <outputs>
19    <data format="tabular" name="output" />
20  </outputs>
21
22  <requirements>
23    <requirement type="binary">R</requirement>
24  </requirements>
25
26  <tests>
27    <test>
28      <param name="input" ftype="tabular" value="snpFreqInput.txt" dbkey="hg18" />
29      <param name="group1_1" value="4" />
30      <param name="group1_2" value="5" />
31      <param name="group1_3" value="6" />
32      <param name="group2_1" value="7" />
33      <param name="group2_2" value="8" />
34      <param name="group2_3" value="9" />
35      <output name="output" file="snpFreqTestOut.txt" />
36    </test>
37  </tests>
38
39  <help>
40
41**Dataset formats**
42
43The input is tabular_, with six columns of allele counts.  The output is also tabular,
44and includes all of the input data plus the additional columns described below.
45(`Dataset missing?`_)
46
47.. _tabular: ./static/formatHelp.html#tab
48.. _Dataset missing?: ./static/formatHelp.html
49
50-----
51
52**What it does**
53
54This tool performs a basic analysis of bi-allelic SNPs in case-control
55data, using the R statistical environment and Fisher's exact test to
56identify SNPs with a significant difference in the allele frequencies
57between the two groups.  R's "qvalue" package is used to correct for
58multiple testing.
59
60The input file includes counts for each allele combination (AA aa Aa)
61for each group at each SNP position.  The assignment of codes (1 2 3)
62to these genotypes is arbitrary, as long as it is consistent for both
63groups.  Any other input columns are ignored in the computation, but
64are copied to the output.  The output appends eight additional columns,
65namely the minimum expected counts of the three genotypes for each
66group, the p-value, and the q-value.
67
68-----
69
70**Example**
71
72- input file::
73
74    chr1  210  211  38  4  15  56  0   1   x
75    chr1  228  229  55  0  2   56  0   1   x
76    chr1  230  231  46  0  11  55  0   2   x
77    chr1  234  235  43  0  14  55  0   2   x
78    chr1  236  237  55  0  2   13  10  34  x
79    chr1  437  438  55  0  2   46  0   11  x
80    chr1  439  440  56  0  1   55  0   2   x
81    chr1  449  450  56  0  1   13  20  24  x
82    chr1  518  519  56  0  1   38  4   15  x
83
84Here the group 1 genotype counts are in columns 4 - 6, while those
85for group 2 are in columns 7 - 9.
86
87Note that the "x" column has no meaning.  It was added to this example
88to show that extra columns can be included, and to make it easier
89to see where the new columns are appended in the output.
90
91- output file::
92
93    chr1  210  211  38  4  15  56  0   1   x  47    2   8     47    2   8     1.50219088598917e-05  6.32501425679652e-06
94    chr1  228  229  55  0  2   56  0   1   x  55.5  0   1.5   55.5  0   1.5   1                     0.210526315789474
95    chr1  230  231  46  0  11  55  0   2   x  50.5  0   6.5   50.5  0   6.5   0.0155644201009862    0.00409590002657532
96    chr1  234  235  43  0  14  55  0   2   x  49    0   8     49    0   8     0.00210854461554067   0.000739840215979182
97    chr1  236  237  55  0  2   13  10  34  x  34    5   18    34    5   18    6.14613878554783e-17  4.31307984950725e-17
98    chr1  437  438  55  0  2   46  0   11  x  50.5  0   6.5   50.5  0   6.5   0.0155644201009862    0.00409590002657532
99    chr1  439  440  56  0  1   55  0   2   x  55.5  0   1.5   55.5  0   1.5   1                     0.210526315789474
100    chr1  449  450  56  0  1   13  20  24  x  34.5  10  12.5  34.5  10  12.5  2.25757007974134e-18  2.37638955762246e-18
101    chr1  518  519  56  0  1   38  4   15  x  47    2   8     47    2   8     1.50219088598917e-05  6.32501425679652e-06
102
103  </help>
104</tool>
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