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comparison gemini_dump.xml @ 0:65845dad49e7 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
author iuc
date Tue, 16 Feb 2016 05:56:28 -0500
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
2 <description>Extract data from the Gemini DB</description>
3 <macros>
4 <import>gemini_macros.xml</import>
5 <token name="@BINARY@">dump</token>
6 </macros>
7 <expand macro="requirements" />
8 <expand macro="stdio" />
9 <expand macro="version_command" />
10 <command>
11 <![CDATA[
12 gemini @BINARY@
13 $report
14 $header
15 $tfam
16
17 "${ infile }"
18 > "${ outfile }"
19 ]]>
20 </command>
21 <inputs>
22 <expand macro="infile" />
23
24 <param name="report" type="select" label="The information to be reported" help="(-t)">
25 <option value="--variants">All rows/columns from the variants table (--variants)</option>
26 <option value="--genotypes">All rows/columns from the variants table with one line per sample/genotype (--genotypes)</option>
27 <option value="--samples">All rows/columns from the samples table (--samples)</option>
28 </param>
29 <param argument="--header" type="boolean" label="Include a header of column names" truevalue="--header" falsevalue="" selected="False" />
30 <param argument="--tfam" type="boolean" label="Output sample information to TFAM information" truevalue="--tfam" falsevalue="" selected="False" />
31 </inputs>
32 <outputs>
33 <data name="outfile" format="tabular" />
34 </outputs>
35 <tests>
36 <test>
37 <param name="infile" value="gemini_comphets_input.db" ftype="gemini.sqlite" />
38 <param name="header" value="True" />
39 <param name="report" value="--genotypes" />
40 <output name="outfile" file="gemini_dump_result.tabular" />
41 </test>
42 </tests>
43 <help><![CDATA[
44 **What it does**
45
46 Reports information in a Gemini database.
47
48 **Setting examples**
49
50
51 **--samples**
52
53 GEMINI output with setting --samples (and --header)::
54
55 sample_id family_id name paternal_id maternal_id sex phenotype
56 1 1 1_dad 0 0 -1 1
57 2 1 1_mom 0 0 -1 1
58 3 1 1_kid 1_dad 1_mom -1 2
59 4 2 2_dad 0 0 -1 1
60 5 2 2_mom 0 0 -1 2
61 6 2 2_kid 2_dad 2_mom -1 2
62 7 3 3_dad 0 0 -1 2
63 8 3 3_mom 0 0 -1 -9
64 9 3 3_kid 3_dad 3_mom -1 2
65
66
67 **--variants**
68
69 GEMINI output with setting --variants (and --header)::
70
71 chrom start end vcf_id variant_id anno_id ref alt qual filter type sub_type ...
72 chr10 1142207 1142208 . 1 4 T C 3404.30004883 . snp ts ...
73 chr10 48003991 48003992 . 3 1 C T 1047.86999512 . snp ts ...
74
75
76 **--genotypes**
77
78 GEMINI output with setting --genotypes (and --header)::
79
80 chrom start end ref alt type sub_type aaf in_dbsnp gene sample genotype
81 chr10 1142207 1142208 T C snp ts 0.277777777778 1 WDR37 1_dad T/T
82 chr10 1142207 1142208 T C snp ts 0.277777777778 1 WDR37 1_mom T/T
83 chr10 1142207 1142208 T C snp ts 0.277777777778 1 WDR37 1_kid T/C
84 chr10 1142207 1142208 T C snp ts 0.277777777778 1 WDR37 2_dad T/T
85 chr10 1142207 1142208 T C snp ts 0.277777777778 1 WDR37 2_mom T/C
86 chr10 1142207 1142208 T C snp ts 0.277777777778 1 WDR37 2_kid T/C
87 chr10 1142207 1142208 T C snp ts 0.277777777778 1 WDR37 3_dad T/C
88 chr10 1142207 1142208 T C snp ts 0.277777777778 1 WDR37 3_mom T/T
89 chr10 1142207 1142208 T C snp ts 0.277777777778 1 WDR37 3_kid T/C
90 chr10 48003991 48003992 C T snp ts 0.277777777778 1 ASAH2C 1_dad C/C
91 chr10 48003991 48003992 C T snp ts 0.277777777778 1 ASAH2C 1_mom C/C
92 chr10 48003991 48003992 C T snp ts 0.277777777778 1 ASAH2C 1_kid C/T
93 chr10 48003991 48003992 C T snp ts 0.277777777778 1 ASAH2C 2_dad C/C
94 chr10 48003991 48003992 C T snp ts 0.277777777778 1 ASAH2C 2_mom C/T
95 chr10 48003991 48003992 C T snp ts 0.277777777778 1 ASAH2C 2_kid C/T
96 chr10 48003991 48003992 C T snp ts 0.277777777778 1 ASAH2C 3_dad C/T
97 chr10 48003991 48003992 C T snp ts 0.277777777778 1 ASAH2C 3_mom C/C
98 chr10 48003991 48003992 C T snp ts 0.277777777778 1 ASAH2C 3_kid C/T
99 chr10 48004991 48004992 C T snp ts 0.277777777778 0 ASAH2C 1_dad C/C
100 chr10 48004991 48004992 C T snp ts 0.277777777778 0 ASAH2C 1_mom C/C
101 chr10 48004991 48004992 C T snp ts 0.277777777778 0 ASAH2C 1_kid C/T
102 chr10 48004991 48004992 C T snp ts 0.277777777778 0 ASAH2C 2_dad C/C
103 chr10 48004991 48004992 C T snp ts 0.277777777778 0 ASAH2C 2_mom C/T
104 chr10 48004991 48004992 C T snp ts 0.277777777778 0 ASAH2C 2_kid C/T
105
106
107 ]]></help>
108 <expand macro="citations"/>
109 </tool>