|
0
|
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
|
|
|
2 <description>Compute useful variant statistics</description>
|
|
|
3 <expand macro="requirements" />
|
|
|
4 <expand macro="version_command" />
|
|
|
5 <macros>
|
|
|
6 <import>gemini_macros.xml</import>
|
|
|
7 <token name="@BINARY@">stats</token>
|
|
|
8 </macros>
|
|
|
9 <command>
|
|
|
10 <![CDATA[
|
|
|
11 gemini @BINARY@
|
|
|
12 $stats_type
|
|
|
13 "${ infile }"
|
|
|
14 > "${ outfile }"
|
|
|
15 ]]>
|
|
|
16 </command>
|
|
|
17 <expand macro="stdio" />
|
|
|
18 <inputs>
|
|
2
|
19 <expand macro="infile" />
|
|
0
|
20
|
|
|
21 <param name="stats_type" type="select" label="Studying ..." help="">
|
|
|
22 <option value="--tstv">Compute the transition and transversion ratios for the snps (--tstv)</option>
|
|
|
23 <option value="--tstv-coding">Compute the transition/transversion ratios for the snps in the coding regions (--tstv-coding)</option>
|
|
|
24 <option value="--tstv-noncoding">Compute the transition/transversion ratios for the snps in the non-coding regions (--tstv-noncoding)</option>
|
|
|
25 <option value="--snp-counts">Compute the type and count of the snps (--snp-counts)</option>
|
|
|
26 <option value="--sfs">Calculate the site frequency spectrum of the variants (--sfs)</option>
|
|
|
27 <option value="--mds">Compute the pair-wise genetic distance between each sample (--mds)</option>
|
|
|
28 <option value="--vars_by_sample">Return the total variants per sample, sum of homozygous and heterozygous variants (--vars-by-sample)</option>
|
|
|
29 </param>
|
|
|
30
|
|
|
31 </inputs>
|
|
|
32 <outputs>
|
|
2
|
33 <data name="outfile" format="tabular" />
|
|
0
|
34 </outputs>
|
|
|
35 <tests>
|
|
|
36 <test>
|
|
|
37 </test>
|
|
|
38 </tests>
|
|
|
39 <help>
|
|
|
40 **What it does**
|
|
|
41
|
|
|
42 The stats tool computes some useful variant statistics for a GEMINI database.
|
|
|
43
|
|
|
44
|
|
|
45 $ gemini stats --summarize "select * from variants where in_dbsnp=1 and chrom='chr1'" my.db
|
|
|
46 sample total num_het num_hom_alt
|
|
|
47 M10475 1 1 0
|
|
|
48 M128215 1 1 0
|
|
|
49 M10478 2 2 0
|
|
|
50 M10500 2 1 1
|
|
|
51
|
|
|
52
|
|
|
53
|
|
|
54 @CITATION@
|
|
|
55 </help>
|
|
|
56 <expand macro="citations"/>
|
|
|
57 </tool>
|
