Mercurial > repos > iuc > gemini
comparison gemini_stats.xml @ 20:b5207530f991 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
| author | iuc |
|---|---|
| date | Tue, 29 Dec 2015 10:19:47 -0500 |
| parents | 27ce3de83007 |
| children |
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| 19:27ce3de83007 | 20:b5207530f991 |
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| 1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> | |
| 2 <description>Compute useful variant statistics</description> | |
| 3 <macros> | |
| 4 <import>gemini_macros.xml</import> | |
| 5 <token name="@BINARY@">stats</token> | |
| 6 </macros> | |
| 7 <expand macro="requirements" /> | |
| 8 <expand macro="stdio" /> | |
| 9 <expand macro="version_command" /> | |
| 10 <command> | |
| 11 <![CDATA[ | |
| 12 gemini @BINARY@ | |
| 13 $stats_type | |
| 14 "${ infile }" | |
| 15 > "${ outfile }" | |
| 16 ]]> | |
| 17 </command> | |
| 18 <inputs> | |
| 19 <expand macro="infile" /> | |
| 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" /> | |
| 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> |