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comparison gemini_db_info.xml @ 0:dc56b2d9d27c draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
author iuc
date Thu, 18 Feb 2016 08:56:51 -0500
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-1:000000000000 0:dc56b2d9d27c
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
2 <description>List the gemini database tables and columns</description>
3 <macros>
4 <import>gemini_macros.xml</import>
5 <token name="@BINARY@">db_info</token>
6 </macros>
7 <expand macro="requirements" />
8 <expand macro="stdio" />
9 <expand macro="version_command" />
10 <command>
11 <![CDATA[
12 gemini @BINARY@
13 "${ infile }" | tr -s ' ' '\t'
14 > "${ outfile }"
15 ]]>
16 </command>
17 <inputs>
18 <expand macro="infile" />
19 </inputs>
20 <outputs>
21 <data name="outfile" format="tabular" />
22 </outputs>
23 <tests>
24 <test>
25 <param name="infile" value="gemini_comphets_input.db" ftype="gemini.sqlite" />
26 <output name="outfile" file="gemini_dbinfo_result.tabular" />
27 </test>
28 </tests>
29 <help><![CDATA[
30 **What it does**
31
32 Because of the sheer number of annotations that are stored in gemini, there are admittedly too many columns to remember by rote.
33 If you can’t recall the name of particular column, just use the db_info tool.
34 It will report all of the tables and all of the columns / types in each table::
35
36 table_name column_name type
37 variants chrom text
38 variants start integer
39 variants end integer
40 variants variant_id integer
41 variants anno_id integer
42 variants ref text
43 variants alt text
44 variants qual float
45 variants filter text
46 variants type text
47 variants sub_type text
48 variants gts blob
49 variants gt_types blob
50 variants gt_phases blob
51 variants gt_depths blob
52 variants call_rate float
53 variants in_dbsnp bool
54 variants rs_ids text
55 variants in_omim bool
56 variants clin_sigs text
57 variants cyto_band text
58 variants rmsk text
59 variants in_cpg_island bool
60 variants in_segdup bool
61 variants is_conserved bool
62 variants num_hom_ref integer
63 variants num_het integer
64 variants num_hom_alt integer
65 variants num_unknown integer
66 variants aaf float
67 variants hwe float
68 variants inbreeding_coeff float
69 variants pi float
70 variants recomb_rate float
71 variants gene text
72 variants transcript text
73 variants is_exonic bool
74 variants is_coding bool
75 variants is_lof bool
76 variants exon text
77 variants codon_change text
78 variants aa_change text
79 ... ... ...
80
81 For more columns see https://gemini.readthedocs.org/en/latest/content/tools.html#db-info-list-the-gemini-database-tables-and-columns
82
83 ]]></help>
84 <expand macro="citations"/>
85 </tool>