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