Mercurial > repos > iuc > gemini_annotate

comparison gemini_annotate.xml @ 2:54f607ff195b 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 05:56:10 -0500
parents c30f03974122
children f052e48b4783
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1:7a5d387d6e31 2:54f607ff195b
8 <expand macro="stdio" /> 8 <expand macro="stdio" />
9 <expand macro="version_command" /> 9 <expand macro="version_command" />
10 <command> 10 <command>
11 <![CDATA[ 11 <![CDATA[
12 12
13 bgzip -c $annotate_source > tabixed.gz; 13 bgzip -c "$annotate_source" > tabixed.gz &&
14 tabix -p bed tabixed.gz; 14 tabix -p bed tabixed.gz &&
15 15
16 gemini @BINARY@ 16 gemini @BINARY@
17 -f tabixed.gz 17 -f tabixed.gz
18 -c $column_name 18 -c $column_name
19 -a $a.a_selector 19 -a $a.a_selector
63 <param name="operation" type="select" label="Operation to apply to the extract column values ..." 63 <param name="operation" type="select" label="Operation to apply to the extract column values ..."
64 help="in the event that a variant overlaps multiple annotations in your annotation file. (-o)"> 64 help="in the event that a variant overlaps multiple annotations in your annotation file. (-o)">
65 <option value="mean">Compute the average of the (numeric) values</option> 65 <option value="mean">Compute the average of the (numeric) values</option>
66 <option value="sum">Compute the sum of the (numeric) values</option> 66 <option value="sum">Compute the sum of the (numeric) values</option>
67 <option value="median">Compute the median of the (numeric) values</option> 67 <option value="median">Compute the median of the (numeric) values</option>
68 <option value="mix">Compute the minimum of the (numeric) values</option> 68 <option value="min">Compute the minimum of the (numeric) values</option>
69 <option value="max">Compute the maximum of the (numeric) values</option> 69 <option value="max">Compute the maximum of the (numeric) values</option>
70 <option value="mode">Compute the maximum of the (numeric) values</option> 70 <option value="mode">Compute the maximum of the (numeric) values</option>
71 <option value="first">Use the value from the first record in the annotation file</option> 71 <option value="first">Use the value from the first record in the annotation file</option>
72 <option value="last">Use the value from the last record in the annotation file</option> 72 <option value="last">Use the value from the last record in the annotation file</option>
73 <option value="list">Create a comma-separated list of the observed (text) values</option> 73 <option value="list">Create a comma-separated list of the observed (text) values</option>
164 164
165 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: 165 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:
166 166
167 - -o mean Compute the average of the values. They must be numeric. 167 - -o mean Compute the average of the values. They must be numeric.
168 - -o median Compute the median of the values. They must be numeric. 168 - -o median Compute the median of the values. They must be numeric.
169 - -o mix Compute the minimum of the values. They must be numeric. 169 - -o min Compute the minimum of the values. They must be numeric.
170 - -o max Compute the maximum of the values. They must be numeric. 170 - -o max Compute the maximum of the values. They must be numeric.
171 - -o mode Compute the maximum of the values. They must be numeric. 171 - -o mode Compute the maximum of the values. They must be numeric.
172 - -o first Use the value from the first record in the annotation file. 172 - -o first Use the value from the first record in the annotation file.
173 - -o last Use the value from the last record in the annotation file. 173 - -o last Use the value from the last record in the annotation file.
174 - -o list Create a comma-separated list of the observed values. 174 - -o list Create a comma-separated list of the observed values.