Mercurial > repos > iuc > gemini_annotate

annotate gemini_annotate.xml @ 6:0919c78f7be8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 85a2af25c79df4758afe9f846e11ef0af16b1c1f
author iuc
date Mon, 17 Dec 2018 12:20:06 -0500
parents 1f5421e565d8
children e5eb597e8f80
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
0919c78f7be8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 85a2af25c79df4758afe9f846e11ef0af16b1c1f
iuc
parents: 5
diff changeset
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@">
0
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
2 <description>adding your own custom annotations</description>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
3 <macros>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
4 <import>gemini_macros.xml</import>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
5 <token name="@BINARY@">annotate</token>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
6 </macros>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
7 <expand macro="requirements" />
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
8 <expand macro="stdio" />
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
9 <expand macro="version_command" />
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
10 <command>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
11 <![CDATA[
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
12
3
f052e48b4783 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
13 ## For GEMINI to work correctly, tabixed file must have form [name].[bed|vcf].gz
f052e48b4783 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
14 #set $tabixed_file = "tabixed.%s.gz" % $annotate_source.ext
5
1f5421e565d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 4
diff changeset
15 bgzip -c '$annotate_source' > '$tabixed_file' &&
1f5421e565d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 4
diff changeset
16 tabix -p '$annotate_source.ext' '$tabixed_file' &&
1f5421e565d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 4
diff changeset
17 cp '$infile' '$outfile' &&
3
f052e48b4783 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
18
5
1f5421e565d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 4
diff changeset
19 gemini @BINARY@
1f5421e565d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 4
diff changeset
20 -f '$tabixed_file'
1f5421e565d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 4
diff changeset
21 -c '$column_name'
1f5421e565d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 4
diff changeset
22 -a $a.a_selector
1f5421e565d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 4
diff changeset
23 #if $a.a_selector == 'extract':
1f5421e565d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 4
diff changeset
24 -t $a.column_type
1f5421e565d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 4
diff changeset
25 -e '$a.column_extracts'
1f5421e565d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 4
diff changeset
26 -o $a.operation
1f5421e565d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 4
diff changeset
27 #end if
1f5421e565d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 4
diff changeset
28 $region_only
1f5421e565d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 4
diff changeset
29 '$outfile'
0
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
30 ]]>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
31
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
32 </command>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
33 <inputs>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
34 <expand macro="infile" />
3
f052e48b4783 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
35 <param name="annotate_source" type="data" format="vcf,bed" label="File containing the annotations in BED/VCF format" help="(-f)"/>
0
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
36
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
37 <param name="column_name" type="text" value=""
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
38 label="The name of the column to be added to the variant table"
5
1f5421e565d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 4
diff changeset
39 help="If the input file is a VCF, then this is the name of the info field to pull. (-c)">
0
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
40 <sanitizer invalid_char=" ">
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
41 <valid initial="string.letters,string.digits">
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
42 <add value="_" />
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
43 </valid>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
44 </sanitizer>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
45 </param>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
46 <conditional name="a">
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
47 <param name="a_selector" type="select" label="How should the annotation file be used?" help="(-a)">
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
48 <option value="boolean">Did a variant overlap a region or not? (boolean)</option>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
49 <option value="count">How many regions did a variant overlap? (count)</option>
3
f052e48b4783 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
50 <option value="extract" selected="True">Extract specific values from a BED/VCF file. (extract)</option>
0
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
51 </param>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
52 <when value="extract">
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
53
3
f052e48b4783 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
54 <param name="column_extracts" label="Column to extract information from for list annotations. For BED files, this is the column number. For VCF files, this is the name of the INFO field."
f052e48b4783 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
55 type="text" force_select="true" help="(-e)"/>
0
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
56
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
57
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
58 <param name="column_type" type="select" label="What data type(s) should be used to represent the new values in the database?"
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
59 help="(-t)">
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
60 <option value="float">Decimal precision number (float)</option>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
61 <option value="integer">Integer number (integer)</option>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
62 <option value="text">Text columns such as “valid”, “yes” (text)</option>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
63 </param>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
64
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
65 <param name="operation" type="select" label="Operation to apply to the extract column values ..."
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
66 help="in the event that a variant overlaps multiple annotations in your annotation file. (-o)">
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
67 <option value="mean">Compute the average of the (numeric) values</option>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
68 <option value="sum">Compute the sum of the (numeric) values</option>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
69 <option value="median">Compute the median of the (numeric) values</option>
2
54f607ff195b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents: 0
diff changeset
70 <option value="min">Compute the minimum of the (numeric) values</option>
0
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
71 <option value="max">Compute the maximum of the (numeric) values</option>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
72 <option value="mode">Compute the maximum of the (numeric) values</option>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
73 <option value="first">Use the value from the first record in the annotation file</option>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
74 <option value="last">Use the value from the last record in the annotation file</option>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
75 <option value="list">Create a comma-separated list of the observed (text) values</option>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
76 <option value="uniq_list">Create a comma-separated list of non-redundant observed (text) values</option>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
77 </param>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
78
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
79 </when>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
80 <when value="boolean"/>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
81 <when value="count"/>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
82 </conditional>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
83 <param name="region_only" argument="--region-only" type="boolean" checked="false"
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
84 truevalue="--region-only" falsevalue=""
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
85 label="If set, only region coordinates will be considered when annotating variants."
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
86 help="The default is to annotate using region coordinates as well as REF and ALT
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
87 variant values. This option is only valid if annotation is a VCF file"/>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
88 </inputs>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
89 <outputs>
5
1f5421e565d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 4
diff changeset
90 <data name="outfile" format="gemini.sqlite" />
0
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
91 </outputs>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
92 <tests>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
93 <test>
5
1f5421e565d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 4
diff changeset
94 <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
0
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
95 <param name="annotate_source" value="anno.bed" />
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
96 <param name="a_selector" value="count" />
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
97 <param name="column_name" value="anno5" />
5
1f5421e565d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 4
diff changeset
98 <output name="outfile" file="gemini_annotate_result.db" ftype="gemini.sqlite" compare="sim_size" delta="1000"/>
0
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
99 </test>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
100 </tests>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
101 <help><![CDATA[
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
102 **What it does**
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
103
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
104 It is inevitable that researchers will want to enhance the GEMINI framework with their own, custom annotations. GEMINI provides a sub-command called annotate for exactly this purpose.
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
105
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
106 **Details**
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
107
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
108 It is inevitable that researchers will want to enhance the GEMINI framework with their own, custom annotations. GEMINI provides a sub-command called annotate for exactly this purpose. As long as you provide a tabix‘ed annotation file in BED or VCF format, the annotate tool will, for each variant in the variants table, screen for overlaps in your annotation file and update a one or more new column in the variants table that you may specify on the command line. This is best illustrated by a following **example**.
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
109
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
110 **Input files**
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
111
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
112 Let’s assume you have already created a GEMINI database of a **VCF file** using the *load module*.
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
113
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
114 Now, let’s imagine you have an annotated file in **BED format** (important.bed) that describes regions of the genome that are particularly relevant to your lab’s research. You would like to annotate in the GEMINI database which variants overlap these crucial regions. We want to store this knowledge in a new column in the variants table called important_variant that tracks whether a given variant overlapped (1) or did not overlap (0) intervals in your annotation file.
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
115
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
116 *To do this, you must first TABIX your BED file*
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
117
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
118 **-a boolean - Did a variant overlap a region or not?**
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
119
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
120 Now, you can use this *TABIX*’ed file to annotate which variants overlap your important regions. In the example below, the results will be stored in a new column called “important”. The **-t boolean** option says that you just want to track whether (1) or not (0) the variant overlapped one or more of your regions.
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
121
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
122 Since a new columns has been created in the database, we can now directly query the new column. In the example results below, the first and third variants overlapped a crucial region while the second did not::
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
123
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
124 chr22 100 101 1 1
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
125 chr22 200 201 2 0
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
126 chr22 300 500 3 1
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
127
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
128 **-a count - How many regions did a variant overlap?**
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
129
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
130 Instead of a simple yes or no, we can use the **-t count** option to count how many important regions a variant overlapped. It turns out that the 3rd variant actually overlapped two important regions::
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
131
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
132 chr22 100 101 1 1
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
133 chr22 200 201 2 0
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
134 chr22 300 500 3 2
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
135
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
136 **-a extract - Extract specific values from a BED file**
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
137
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
138 Lastly, we may also extract values from specific fields in a BED file (or from the INFO field in a VCF) and populate one or more new columns in the database based on overlaps with the annotation file and the values of the fields therein. To do this, we use the **-a extract** option.
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
139
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
140 This is best described with an example. To set this up, let’s imagine that we have a VCF file from a different experiment and we want to annotate the variants in our GEMINI database with the allele frequency and depth tags from the INFO fields for the same variants in this other VCF file.
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
141
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
142 Now that we have a proper *TABIX*’ed VCF file, we can use the **-a extract** option to populate new columns in the GEMINI database. In order to do so, we must specify:
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
143
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
144 1) its type (e.g., text, int, float,) (**-t**)
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
145 2) the field in the INFO column of the VCF file that we should use to extract data with which to populate the new column (**-e**)
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
146 3) what operation should be used to summarize the data in the event of multiple overlaps in the annotation file (**-o**)
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
147 4) (optionally) the name of the column we want to add (**-c**), if this is not specified, it will use the value from **-e**.
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
148
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
149 For example, let’s imagine we want to create a new column called “other_allele_freq” (**-c**) using the AF field in our VCF file to populate it.
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
150
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
151 This create a new column in my.db called other_allele_freq and this new column will be a FLOAT (**-t float**). In the event of multiple records in the VCF file overlapping a variant in the database, the average (**-o mean**) of the allele frequencies values from the VCF file will be used.
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
152
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
153 At this point, one can query the database based on the values of the new other_allele_freq column (using **GEMINI query**).
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
154
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
155 **-t TYPE - Specifying the column type(s) when using -a extract**
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
156
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
157 The annotate tool will create three different types of columns via the **-t** option:
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
158
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
159 1) Floating point columns for annotations with decimal precision as above (-t float)
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
160 2) Integer columns for integral annotations (-t integer)
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
161 3) Text columns for string columns such as “valid”, “yes”, etc. (-t text)
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
162
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
163 *The -t option is only valid when using the -a extract option.*
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
164
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
165 **-o OPERATION - Specifying the summary operations when using -a extract**
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
166
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
167 In the event of multiple overlaps between a variant and records in the annotation file, the annotate tool can summarize the values observed with multiple options:
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
168
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
169 - -o mean Compute the average of the values. They must be numeric.
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
170 - -o median Compute the median of the values. They must be numeric.
2
54f607ff195b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents: 0
diff changeset
171 - -o min Compute the minimum of the values. They must be numeric.
0
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
172 - -o max Compute the maximum of the values. They must be numeric.
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
173 - -o mode Compute the maximum of the values. They must be numeric.
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
174 - -o first Use the value from the first record in the annotation file.
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
175 - -o last Use the value from the last record in the annotation file.
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
176 - -o list Create a comma-separated list of the observed values.
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
177 - -o uniq_list Create a comma-separated list of the distinct observed values.
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
178 - -o sum Compute the sum of the values. They must be numeric.
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
179
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
180 The -o option is only valid when using the -a extract option.
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
181
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
182 **Annotating with VCF**
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
183
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
184 Most of the examples to this point have pulled a column from a tabix indexed bed file. It is likewise possible to pull from the INFO field of a tabix index VCF. The syntax is identical but the **-e** operation will specify the names of fields in the INFO column to pull. By default, those names will be used, but that can still be specified with the **-c column**.
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
185
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
186 To put a DP column in the db, set:
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
187
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
188 -o list, -e DP, -t integer
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
189
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
190 ... and name it 'depth', set:
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
191
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
192 -o list, -e DP, -c depth, -t integer
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
193
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
194
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
195 Missing values are allowed since we expect that in some cases an annotation VCF will not have all INFO fields specified for all variants.
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
196
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
197 *We recommend decomposing and normalizing variants before annotating. See Step 1. split, left-align, and trim variants for a detailed explanation of how to do this. To do that see the GEMINI* preprocessing_ *website.*
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
198
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
199 **Extracting and populating multiple columns at once**
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
200
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
201 One can also extract and populate multiple columns at once by providing comma-separated lists (no spaces) of column names (**-c**), types (**-t**), numbers (**-e**), and summary operations (**-o**). For example, recall that in the VCF example above, we created a *TABIX*’ed BED file containg the allele frequency and depth values from the INFO field as the 4th and 5th columns in the BED, respectively.
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
202
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
203 Instead of running the annotate tool twice (once for each column), we can run the tool once and load both columns in the same run. For example with settings:
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
204
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
205 - -a extract
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
206 - -c other_allele_freq,other_depth
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
207 - -t float,integer
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
208 - -e 4,5
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
209 - -o mean,max
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
210
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
211 We can then use each of the new columns to filter variants with a *GEMINI query*:
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
212
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
213 .. _preprocessing: https://gemini.readthedocs.org/en/latest/content/preprocessing.html#preprocess
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
214
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
215 ]]></help>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
216 <expand macro="citations"/>
c30f03974122 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
217 </tool>