Mercurial > repos > iuc > gemini_annotate

comparison gemini_annotate.xml @ 3:f052e48b4783 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
author iuc
date Fri, 07 Dec 2018 12:51:48 -0500
parents 54f607ff195b
children 80024600788f
comparison
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2:54f607ff195b 3:f052e48b4783
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> 1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.2">
2 <description>adding your own custom annotations</description> 2 <description>adding your own custom annotations</description>
3 <macros> 3 <macros>
4 <import>gemini_macros.xml</import> 4 <import>gemini_macros.xml</import>
5 <token name="@BINARY@">annotate</token> 5 <token name="@BINARY@">annotate</token>
6 </macros> 6 </macros>
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 ## For GEMINI to work correctly, tabixed file must have form [name].[bed|vcf].gz
14 tabix -p bed tabixed.gz && 14 #set $tabixed_file = "tabixed.%s.gz" % $annotate_source.ext
15 bgzip -c "$annotate_source" > $tabixed_file &&
16 tabix -p "$annotate_source.ext" $tabixed_file &&
17
18 @PROVIDE_ANNO_DATA@
15 19
16 gemini @BINARY@ 20 gemini @BINARY@
17 -f tabixed.gz 21 -f $tabixed_file
18 -c $column_name 22 -c $column_name
19 -a $a.a_selector 23 -a $a.a_selector
20 #if $a.a_selector == 'extract': 24 #if $a.a_selector == 'extract':
21 -t $a.column_type 25 -t $a.column_type
22 -e $a.column_extracts 26 -e $a.column_extracts
28 ]]> 32 ]]>
29 33
30 </command> 34 </command>
31 <inputs> 35 <inputs>
32 <expand macro="infile" /> 36 <expand macro="infile" />
33 <param name="annotate_source" type="data" format="bed" label="File containing the annotations in BED format" help="(-f)"/> 37 <param name="annotate_source" type="data" format="vcf,bed" label="File containing the annotations in BED/VCF format" help="(-f)"/>
34 38
35 <param name="column_name" type="text" value="" 39 <param name="column_name" type="text" value=""
36 label="The name of the column to be added to the variant table" 40 label="The name of the column to be added to the variant table"
37 help=" If the input file is a VCF, then this is the name of the info field to pull. (-c)"> 41 help=" If the input file is a VCF, then this is the name of the info field to pull. (-c)">
38 <sanitizer invalid_char=" "> 42 <sanitizer invalid_char=" ">
43 </param> 47 </param>
44 <conditional name="a"> 48 <conditional name="a">
45 <param name="a_selector" type="select" label="How should the annotation file be used?" help="(-a)"> 49 <param name="a_selector" type="select" label="How should the annotation file be used?" help="(-a)">
46 <option value="boolean">Did a variant overlap a region or not? (boolean)</option> 50 <option value="boolean">Did a variant overlap a region or not? (boolean)</option>
47 <option value="count">How many regions did a variant overlap? (count)</option> 51 <option value="count">How many regions did a variant overlap? (count)</option>
48 <option value="extract" selected="True">Extract specific values from a BED file. (extract)</option> 52 <option value="extract" selected="True">Extract specific values from a BED/VCF file. (extract)</option>
49 </param> 53 </param>
50 <when value="extract"> 54 <when value="extract">
51 55
52 <param name="column_extracts" label="Column to extract information from for list annotations" 56 <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."
53 type="data_column" data_ref="annotate_source" force_select="true" help="(-e)"/> 57 type="text" force_select="true" help="(-e)"/>
54 58
55 59
56 <param name="column_type" type="select" label="What data type(s) should be used to represent the new values in the database?" 60 <param name="column_type" type="select" label="What data type(s) should be used to represent the new values in the database?"
57 help="(-t)"> 61 help="(-t)">
58 <option value="float">Decimal precision number (float)</option> 62 <option value="float">Decimal precision number (float)</option>