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comparison gemini_stats.xml @ 0:720cbfb4190d draft

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Imported from capsule None
author iuc
date Mon, 25 Aug 2014 17:15:54 -0400
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children 93bb0cfacefb
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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 > "${ outfile }"
15 ]]>
16 </command>
17 <expand macro="stdio" />
18 <inputs>
19 <param name="infile" type="data" format="sqlite" label="GEMINI database" />
20
21 <param name="stats_type" type="select" label="Studying ..." help="">
22 <option value="--tstv">Compute the transition and transversion ratios for the snps (--tstv)</option>
23 <option value="--tstv-coding">Compute the transition/transversion ratios for the snps in the coding regions (--tstv-coding)</option>
24 <option value="--tstv-noncoding">Compute the transition/transversion ratios for the snps in the non-coding regions (--tstv-noncoding)</option>
25 <option value="--snp-counts">Compute the type and count of the snps (--snp-counts)</option>
26 <option value="--sfs">Calculate the site frequency spectrum of the variants (--sfs)</option>
27 <option value="--mds">Compute the pair-wise genetic distance between each sample (--mds)</option>
28 <option value="--vars_by_sample">Return the total variants per sample, sum of homozygous and heterozygous variants (--vars-by-sample)</option>
29 </param>
30
31 </inputs>
32 <outputs>
33 <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
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>