Mercurial > repos > iuc > gemini_dump
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 85a2af25c79df4758afe9f846e11ef0af16b1c1f
| author | iuc |
|---|---|
| date | Mon, 17 Dec 2018 12:21:48 -0500 |
| parents | a48f00c341dc |
| children |
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<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@"> <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> <!-- The genotypes option is broken in gemini v0.20.1. Add this option back in once there is an upstream fix! Remember then to replace all underscores with dashes on the following line. They are only there to not break this comment! <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_de_novo_input.db" ftype="gemini.sqlite" /> <param name="header" value="True" /> <param name="report" value="--samples" /> <output name="outfile"> <assert_contents> <has_line_matching expression="sample_id	family_id	name	paternal_id	maternal_id	sex	phenotype" /> </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>