Mercurial > repos > iuc > gemini_dump
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
| author | iuc |
|---|---|
| date | Fri, 14 Dec 2018 12:58:00 -0500 |
| parents | a32c298053e4 |
| children |
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<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1"> <description>Extract data from the Gemini DB</description> <macros> <import>gemini_macros.xml</import> <token name="@BINARY@">dump</token> </macros> <expand macro="requirements" /> <expand macro="stdio" /> <expand macro="version_command" /> <command> <![CDATA[ gemini @BINARY@ $report $header $tfam "${ infile }" > "${ outfile }" ]]> </command> <inputs> <expand macro="infile" /> <param name="report" type="select" label="The information to be reported" help="(-t)"> <option value="--variants">All rows/columns from the variants table (--variants)</option> <option value="--genotypes">All rows/columns from the variants table with one line per sample/genotype (--genotypes)</option> <option value="--samples">All rows/columns from the samples table (--samples)</option> </param> <param argument="--header" type="boolean" label="Include a header of column names" truevalue="--header" falsevalue="" checked="False" /> <param argument="--tfam" type="boolean" label="Output sample information to TFAM information" truevalue="--tfam" falsevalue="" checked="False" /> </inputs> <outputs> <data name="outfile" format="tabular" /> </outputs> <tests> <test> <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" /> <param name="header" value="True" /> <param name="report" value="--genotypes" /> <output name="outfile"> <assert_contents> <has_line_matching expression="chrom	start	end	.*sample	.*genotype.*" /> </assert_contents> </output> </test> </tests> <help><![CDATA[ **What it does** Reports information in a Gemini database. **Setting examples** **--samples** GEMINI output with setting --samples (and --header):: sample_id family_id name paternal_id maternal_id sex phenotype 1 1 1_dad 0 0 -1 1 2 1 1_mom 0 0 -1 1 3 1 1_kid 1_dad 1_mom -1 2 4 2 2_dad 0 0 -1 1 5 2 2_mom 0 0 -1 2 6 2 2_kid 2_dad 2_mom -1 2 7 3 3_dad 0 0 -1 2 8 3 3_mom 0 0 -1 -9 9 3 3_kid 3_dad 3_mom -1 2 **--variants** GEMINI output with setting --variants (and --header):: chrom start end vcf_id variant_id anno_id ref alt qual filter type sub_type ... chr10 1142207 1142208 . 1 4 T C 3404.30004883 . snp ts ... chr10 48003991 48003992 . 3 1 C T 1047.86999512 . snp ts ... **--genotypes** GEMINI output with setting --genotypes (and --header):: chrom start end ref alt type sub_type aaf in_dbsnp gene sample genotype chr10 1142207 1142208 T C snp ts 0.277777777778 1 WDR37 1_dad T/T chr10 1142207 1142208 T C snp ts 0.277777777778 1 WDR37 1_mom T/T chr10 1142207 1142208 T C snp ts 0.277777777778 1 WDR37 1_kid T/C chr10 1142207 1142208 T C snp ts 0.277777777778 1 WDR37 2_dad T/T chr10 1142207 1142208 T C snp ts 0.277777777778 1 WDR37 2_mom T/C chr10 1142207 1142208 T C snp ts 0.277777777778 1 WDR37 2_kid T/C chr10 1142207 1142208 T C snp ts 0.277777777778 1 WDR37 3_dad T/C chr10 1142207 1142208 T C snp ts 0.277777777778 1 WDR37 3_mom T/T chr10 1142207 1142208 T C snp ts 0.277777777778 1 WDR37 3_kid T/C chr10 48003991 48003992 C T snp ts 0.277777777778 1 ASAH2C 1_dad C/C chr10 48003991 48003992 C T snp ts 0.277777777778 1 ASAH2C 1_mom C/C chr10 48003991 48003992 C T snp ts 0.277777777778 1 ASAH2C 1_kid C/T chr10 48003991 48003992 C T snp ts 0.277777777778 1 ASAH2C 2_dad C/C chr10 48003991 48003992 C T snp ts 0.277777777778 1 ASAH2C 2_mom C/T chr10 48003991 48003992 C T snp ts 0.277777777778 1 ASAH2C 2_kid C/T chr10 48003991 48003992 C T snp ts 0.277777777778 1 ASAH2C 3_dad C/T chr10 48003991 48003992 C T snp ts 0.277777777778 1 ASAH2C 3_mom C/C chr10 48003991 48003992 C T snp ts 0.277777777778 1 ASAH2C 3_kid C/T chr10 48004991 48004992 C T snp ts 0.277777777778 0 ASAH2C 1_dad C/C chr10 48004991 48004992 C T snp ts 0.277777777778 0 ASAH2C 1_mom C/C chr10 48004991 48004992 C T snp ts 0.277777777778 0 ASAH2C 1_kid C/T chr10 48004991 48004992 C T snp ts 0.277777777778 0 ASAH2C 2_dad C/C chr10 48004991 48004992 C T snp ts 0.277777777778 0 ASAH2C 2_mom C/T chr10 48004991 48004992 C T snp ts 0.277777777778 0 ASAH2C 2_kid C/T ]]></help> <expand macro="citations"/> </tool>