Mercurial > repos > iuc > gemini_qc
comparison gemini_qc.xml @ 0:f44bb2b7bfc0 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
| author | iuc |
|---|---|
| date | Tue, 16 Feb 2016 05:53:28 -0500 |
| parents | |
| children | e923a49732d7 |
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| -1:000000000000 | 0:f44bb2b7bfc0 |
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| 1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> | |
| 2 <description>Quality control tool</description> | |
| 3 <macros> | |
| 4 <import>gemini_macros.xml</import> | |
| 5 <token name="@BINARY@">qc</token> | |
| 6 </macros> | |
| 7 <expand macro="requirements" /> | |
| 8 <expand macro="stdio" /> | |
| 9 <expand macro="version_command" /> | |
| 10 <command> | |
| 11 <![CDATA[ | |
| 12 gemini @BINARY@ | |
| 13 --mode sex | |
| 14 --chrom "$chrom" | |
| 15 | |
| 16 "${ infile }" | |
| 17 > "${ outfile }" | |
| 18 ]]> | |
| 19 </command> | |
| 20 <inputs> | |
| 21 <expand macro="infile" /> | |
| 22 <param name="chrom" type="text" value="chrX" label="Which chromosome should the sex test be applied to?" help="(--chrom)"/> | |
| 23 | |
| 24 </inputs> | |
| 25 <outputs> | |
| 26 <data name="outfile" format="tabular" /> | |
| 27 </outputs> | |
| 28 <tests> | |
| 29 <test> | |
| 30 <param name="infile" value="gemini_amend_input.db" ftype="gemini.sqlite" /> | |
| 31 <param name="chrom" value="chrX" ftype="gemini.sqlite" /> | |
| 32 <output name="outfile" file="gemini_qc_result.tabular" /> | |
| 33 </test> | |
| 34 </tests> | |
| 35 <help> | |
| 36 <![CDATA[ | |
| 37 **What it does** | |
| 38 | |
| 39 Checks whether the given sex of the samples are probable. It issues the query:: | |
| 40 | |
| 41 SELECT gt_types | |
| 42 FROM variants | |
| 43 WHERE chrom = '$chrom' | |
| 44 AND start > 2699520 and start < 154931044 | |
| 45 AND call_rate > 0.90 | |
| 46 AND depth > 1000 | |
| 47 AND filter is NULL | |
| 48 ORDER BY random() | |
| 49 LIMIT 10000 | |
| 50 | |
| 51 and returns the called variants on that region of the given chromosome in a table:: | |
| 52 | |
| 53 sample sex X_homref X_het X_homalt het_homref_ratio | |
| 54 SMS173 male 7265 1975 8010 0.271851342051 | |
| 55 SMS254 male 5440 1316 3846 0.241911764706 | |
| 56 SMS255 female 6275 3188 5423 0.508047808765 | |
| 57 SMS253 male 5536 1355 3582 0.244761560694 | |
| 58 SMS243 male 6181 1506 4479 0.243649894839 | |
| 59 SMS242 male 6365 1437 4200 0.225765907306 | |
| 60 SMS193 male 6667 1864 5829 0.279586020699 | |
| 61 SMS238 male 6263 1638 4891 0.261536005109 | |
| 62 SMS239 female 6755 3669 7618 0.543153219837 | |
| 63 SMS244 female 6489 2953 5140 0.45507782401 | |
| 64 SMS230 male 7209 1784 7146 0.247468442225 | |
| 65 SMS231 female 7306 4659 9332 0.637695045168 | |
| 66 ]]> | |
| 67 | |
| 68 </help> | |
| 69 <expand macro="citations"/> | |
| 70 </tool> |