Mercurial > repos > iuc > gemini_qc
view gemini_qc.xml @ 2:9872131c2377 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
author | iuc |
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date | Thu, 09 Nov 2017 13:17:27 -0500 |
parents | a875f940d8fd |
children | 246ad1a7ff20 |
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<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> <description>Quality control tool</description> <macros> <import>gemini_macros.xml</import> <token name="@BINARY@">qc</token> </macros> <expand macro="requirements" /> <expand macro="stdio" /> <expand macro="version_command" /> <command> <![CDATA[ gemini @BINARY@ --mode sex --chrom "$chrom" "${ infile }" > "${ outfile }" ]]> </command> <inputs> <expand macro="infile" /> <param name="chrom" type="text" value="chrX" label="Which chromosome should the sex test be applied to?" help="(--chrom)"/> </inputs> <outputs> <data name="outfile" format="tabular" /> </outputs> <tests> <test> <param name="infile" value="gemini_amend_input.db" ftype="gemini.sqlite" /> <param name="chrom" value="chrX" ftype="gemini.sqlite" /> <output name="outfile" file="gemini_qc_result.tabular" /> </test> </tests> <help> <![CDATA[ **What it does** Checks whether the given sex of the samples are probable. It issues the query:: SELECT gt_types FROM variants WHERE chrom = '$chrom' AND start > 2699520 and start < 154931044 AND call_rate > 0.90 AND depth > 1000 AND filter is NULL ORDER BY random() LIMIT 10000 and returns the called variants on that region of the given chromosome in a table:: sample sex X_homref X_het X_homalt het_homref_ratio SMS173 male 7265 1975 8010 0.271851342051 SMS254 male 5440 1316 3846 0.241911764706 SMS255 female 6275 3188 5423 0.508047808765 SMS253 male 5536 1355 3582 0.244761560694 SMS243 male 6181 1506 4479 0.243649894839 SMS242 male 6365 1437 4200 0.225765907306 SMS193 male 6667 1864 5829 0.279586020699 SMS238 male 6263 1638 4891 0.261536005109 SMS239 female 6755 3669 7618 0.543153219837 SMS244 female 6489 2953 5140 0.45507782401 SMS230 male 7209 1784 7146 0.247468442225 SMS231 female 7306 4659 9332 0.637695045168 ]]> </help> <expand macro="citations"/> </tool>