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comparison gemini_annotate.xml @ 4:5bcaca8085bd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
author iuc
date Fri, 14 Dec 2018 12:44:52 -0500
parents 8da05bf2b1d1
children 08f57a8502e4
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3:8f53b238a360 4:5bcaca8085bd
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1"> 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>
10 <command> 10 <command>
11 <![CDATA[ 11 <![CDATA[
12 12
13 ## For GEMINI to work correctly, tabixed file must have form [name].[bed|vcf].gz 13 ## For GEMINI to work correctly, tabixed file must have form [name].[bed|vcf].gz
14 #set $tabixed_file = "tabixed.%s.gz" % $annotate_source.ext 14 #set $tabixed_file = "tabixed.%s.gz" % $annotate_source.ext
15 bgzip -c "$annotate_source" > $tabixed_file && 15 bgzip -c '$annotate_source' > '$tabixed_file' &&
16 tabix -p "$annotate_source.ext" $tabixed_file && 16 tabix -p '$annotate_source.ext' '$tabixed_file' &&
17 17 cp '$infile' '$outfile' &&
18 gemini @BINARY@ 18
19 -f $tabixed_file 19 gemini @BINARY@
20 -c $column_name 20 -f '$tabixed_file'
21 -a $a.a_selector 21 -c '$column_name'
22 #if $a.a_selector == 'extract': 22 -a $a.a_selector
23 -t $a.column_type 23 #if $a.a_selector == 'extract':
24 -e $a.column_extracts 24 -t $a.column_type
25 -o $a.operation 25 -e '$a.column_extracts'
26 #end if 26 -o $a.operation
27 $region_only 27 #end if
28 "${ infile }" 28 $region_only
29 > "${ outfile }" 29 '$outfile'
30 ]]> 30 ]]>
31 31
32 </command> 32 </command>
33 <inputs> 33 <inputs>
34 <expand macro="infile" /> 34 <expand macro="infile" />
35 <param name="annotate_source" type="data" format="vcf,bed" label="File containing the annotations in BED/VCF format" help="(-f)"/> 35 <param name="annotate_source" type="data" format="vcf,bed" label="File containing the annotations in BED/VCF format" help="(-f)"/>
36 36
37 <param name="column_name" type="text" value="" 37 <param name="column_name" type="text" value=""
38 label="The name of the column to be added to the variant table" 38 label="The name of the column to be added to the variant table"
39 help=" If the input file is a VCF, then this is the name of the info field to pull. (-c)"> 39 help="If the input file is a VCF, then this is the name of the info field to pull. (-c)">
40 <sanitizer invalid_char=" "> 40 <sanitizer invalid_char=" ">
41 <valid initial="string.letters,string.digits"> 41 <valid initial="string.letters,string.digits">
42 <add value="_" /> 42 <add value="_" />
43 </valid> 43 </valid>
44 </sanitizer> 44 </sanitizer>
85 label="If set, only region coordinates will be considered when annotating variants." 85 label="If set, only region coordinates will be considered when annotating variants."
86 help="The default is to annotate using region coordinates as well as REF and ALT 86 help="The default is to annotate using region coordinates as well as REF and ALT
87 variant values. This option is only valid if annotation is a VCF file"/> 87 variant values. This option is only valid if annotation is a VCF file"/>
88 </inputs> 88 </inputs>
89 <outputs> 89 <outputs>
90 <data name="outfile" format="tabular" /> 90 <data name="outfile" format="gemini.sqlite" />
91 </outputs> 91 </outputs>
92 <tests> 92 <tests>
93 <test> 93 <test>
94 <param name="infile" value="gemini_annotate_input.db" ftype="gemini.sqlite" /> 94 <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
95 <param name="annotate_source" value="anno.bed" /> 95 <param name="annotate_source" value="anno.bed" />
96 <param name="a_selector" value="count" /> 96 <param name="a_selector" value="count" />
97 <param name="column_name" value="anno5" /> 97 <param name="column_name" value="anno5" />
98 <output name="outfile" file="gemini_annotate_result.tabular" /> 98 <output name="outfile" file="gemini_annotate_result.db" ftype="gemini.sqlite" compare="sim_size" delta="1000"/>
99 </test> 99 </test>
100 </tests> 100 </tests>
101 <help><![CDATA[ 101 <help><![CDATA[
102 **What it does** 102 **What it does**
103 103