Mercurial > repos > iuc > gemini_dump
diff gemini_dump.xml @ 0:187b57debbba draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
| author | iuc |
|---|---|
| date | Thu, 18 Feb 2016 08:56:38 -0500 |
| parents | |
| children | a32c298053e4 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gemini_dump.xml Thu Feb 18 08:56:38 2016 -0500 @@ -0,0 +1,109 @@ +<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> + <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="" selected="False" /> + <param argument="--tfam" type="boolean" label="Output sample information to TFAM information" truevalue="--tfam" falsevalue="" selected="False" /> + </inputs> + <outputs> + <data name="outfile" format="tabular" /> + </outputs> + <tests> + <test> + <param name="infile" value="gemini_comphets_input.db" ftype="gemini.sqlite" /> + <param name="header" value="True" /> + <param name="report" value="--genotypes" /> + <output name="outfile" file="gemini_dump_result.tabular" /> + </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>