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comparison gemini_annotate.xml @ 0:14caa57eca63 draft

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author iuc
date Mon, 11 Aug 2014 07:44:30 -0400
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
2 <description>adding your own custom annotations</description>
3 <expand macro="requirements" />
4 <expand macro="version_command" />
5 <macros>
6 <import>gemini_macros.xml</import>
7 <token name="@BINARY@">annotate</token>
8 </macros>
9 <command>
10 <![CDATA[
11
12 bgzip -c $annotate_source > tabixed.gz;
13 tabix -p bed tabixed.gz;
14
15 gemini @BINARY@
16 -f tabixed.gz
17 -c $column_name
18 -a $a.a_selector
19 #if $a.a_selector == 'extract':
20 -t $a.column_type
21 -e $a.column_extracts
22 -o $a.operation
23 #end if
24
25 "${ infile }"
26 > "${ outfile }"
27 ]]>
28
29 </command>
30 <expand macro="stdio" />
31 <inputs>
32 <param name="infile" type="data" format="sqlite" label="GEMINI database" />
33 <param name="annotate_source" type="data" format="bed" label="File containing the annotations in BED format" help="(-f)"/>
34
35 <param name="column_name" size="20" type="text" value=""
36 label="The name of the column to be added to the variant table" help="(-c)">
37 <sanitizer invalid_char=" ">
38 <valid initial="string.letters,string.digits">
39 <add value="_" />
40 </valid>
41 </sanitizer>
42 </param>
43 <conditional name="a">
44 <param name="a_selector" type="select" label="How should the annotation file be used?" help="(-a)">
45 <option value="boolean">Did a variant overlap a region or not? (boolean)</option>
46 <option value="count">How many regions did a variant overlap? (count)</option>
47 <option value="extract" selected="True">Extract specific values from a BED file. (extract)</option>
48 </param>
49 <when value="extract">
50
51 <param name="column_extracts" label="Column to extract information from for list annotations"
52 type="data_column" data_ref="annotate_source" force_select="true" help="(-e)"/>
53
54
55 <param name="column_type" type="select" label="What data type(s) should be used to represent the new values in the database?"
56 help="(-t)">
57 <option value="float">Decimal precision number (float)</option>
58 <option value="integer">Integer number (integer)</option>
59 <option value="text">Text columns such as “valid”, “yes” (text)</option>
60 </param>
61
62 <param name="operation" type="select" label="Operation to apply to the extract column values ..."
63 help="in the event that a variant overlaps multiple annotations in your annotation file. (-o)">
64 <option value="mean">Compute the average of the (numeric) values</option>
65 <option value="median">Compute the median of the (numeric) values</option>
66 <option value="mix">Compute the minimum of the (numeric) values</option>
67 <option value="max">Compute the maximum of the (numeric) values</option>
68 <option value="mode">Compute the maximum of the (numeric) values</option>
69 <option value="first">Use the value from the first record in the annotation file</option>
70 <option value="last">Use the value from the last record in the annotation file</option>
71 <option value="list">Create a comma-separated list of the observed (text) values</option>
72 <option value="uniq_list">Create a comma-separated list of non-redundant observed (text) values</option>
73 </param>
74
75 </when>
76 <when value="boolean"/>
77 <when value="count"/>
78 </conditional>
79
80 </inputs>
81 <outputs>
82 <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
83 </outputs>
84 <tests>
85 <test>
86 </test>
87 </tests>
88 <help>
89 **What it does**
90
91 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.
92
93 @CITATION@
94 </help>
95 <expand macro="citations"/>
96 </tool>