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comparison snpSift_annotate.xml @ 18:0b0035e38abe draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 693e1a3641c776965f68d688c8e1409adba7da1e
author iuc
date Wed, 16 Jan 2019 15:35:02 -0500
parents ede8954f5c82
children f90f08ed9810
comparison
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17:ede8954f5c82 18:0b0035e38abe
1 <tool id="snpSift_annotate" name="SnpSift Annotate" version="@WRAPPER_VERSION@.galaxy0"> 1 <tool id="snpSift_annotate" name="SnpSift Annotate" version="@WRAPPER_VERSION@.galaxy1">
2 <description>SNPs from dbSnp</description> 2 <description>SNPs from dbSnp</description>
3 <!-- 3 <!--
4 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) 4 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
5 --> 5 -->
6 <macros> 6 <macros>
9 <expand macro="requirements" /> 9 <expand macro="requirements" />
10 <expand macro="stdio" /> 10 <expand macro="stdio" />
11 <expand macro="version_command" /> 11 <expand macro="version_command" />
12 <command><![CDATA[ 12 <command><![CDATA[
13 SnpSift -Xmx8G annotate 13 SnpSift -Xmx8G annotate
14 #if $annotate.id == 'id': 14 ${annotate.no_info}
15 -id 15 #if str($annotate.info_ids).strip():
16 #elif str($annotate.info_ids).strip() != '': 16 -info '$annotate.info_ids'
17 -info "$annotate.info_ids"
18 #end if 17 #end if
19 -q '$dbSnp' '$input' > '$output' 18 -q '$dbSnp' '$input' > '$output'
20 ]]></command> 19 ]]></command>
21 <inputs> 20 <inputs>
22 <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/> 21 <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/>
23 <param name="dbSnp" type="data" format="vcf" label="VCF File with ID field annotated (e.g. dbSNP.vcf)" 22 <param name="dbSnp" type="data" format="vcf" label="VCF File with ID field annotated (e.g. dbSNP.vcf)"
24 help="The ID field for a variant in input will be assigned from a matching variant in this file."/> 23 help="The ID field for a variant in input will be assigned from a matching variant in this file."/>
25 <conditional name="annotate"> 24 <conditional name="annotate">
26 <param name="id" type="select" label="Fields to annotate"> 25 <param name="no_info" type="select" label="Fields to annotate">
27 <option value="id">Only annotate ID field (no INFO fields will be added)</option> 26 <option value="-noInfo">Only annotate ID field (no INFO fields will be added)</option>
28 <option value="info">Add also INFO fields</option> 27 <option value="">Add also INFO fields</option>
29 </param> 28 </param>
30 <when value="id"/> 29 <when value="-noInfo">
31 <when value="info"> 30 <param name="info_ids" type="hidden" value="" />
31 </when>
32 <when value="">
32 <param name="info_ids" type="text" value="" label="Limit INFO annotation to these INFO IDs" help="List is a comma separated list of fields. When blank, all INFO fields are included"> 33 <param name="info_ids" type="text" value="" label="Limit INFO annotation to these INFO IDs" help="List is a comma separated list of fields. When blank, all INFO fields are included">
33 <validator type="regex" message="IDs separted by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</validator> 34 <validator type="regex" message="IDs separated by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</validator>
34 </param> 35 </param>
35 </when> 36 </when>
36 </conditional> 37 </conditional>
37 </inputs> 38 </inputs>
38 <outputs> 39 <outputs>
40 </outputs> 41 </outputs>
41 <tests> 42 <tests>
42 <test> 43 <test>
43 <param name="input" ftype="vcf" value="annotate_1.vcf"/> 44 <param name="input" ftype="vcf" value="annotate_1.vcf"/>
44 <param name="dbSnp" ftype="vcf" value="db_test_1.vcf"/> 45 <param name="dbSnp" ftype="vcf" value="db_test_1.vcf"/>
45 <param name="id" value="id"/> 46 <conditional name="annotate">
47 <param name="no_info" value=""/>
48 </conditional>
46 <output name="output"> 49 <output name="output">
47 <assert_contents> 50 <assert_contents>
48 <has_text text="rs76166080" /> 51 <has_line_matching expression="1&#009;872687&#009;rs76166080&#009;C&#009;G&#009;.&#009;.&#009;.+;.+" />
52 </assert_contents>
53 </output>
54 </test>
55 <test>
56 <param name="input" ftype="vcf" value="annotate_1.vcf"/>
57 <param name="dbSnp" ftype="vcf" value="db_test_1.vcf"/>
58 <conditional name="annotate">
59 <param name="no_info" value=""/>
60 <param name="info_ids" value="dbSNPBuildID" />
61 </conditional>
62 <output name="output">
63 <assert_contents>
64 <has_line_matching expression="1&#009;872687&#009;rs76166080&#009;C&#009;G&#009;.&#009;.&#009;dbSNPBuildID=137" />
65 </assert_contents>
66 </output>
67 </test>
68 <test>
69 <param name="input" ftype="vcf" value="annotate_1.vcf"/>
70 <param name="dbSnp" ftype="vcf" value="db_test_1.vcf"/>
71 <conditional name="annotate">
72 <param name="no_info" value="-noInfo"/>
73 </conditional>
74 <output name="output">
75 <assert_contents>
76 <has_line line="1&#009;872687&#009;rs76166080&#009;C&#009;G&#009;.&#009;.&#009;." />
49 </assert_contents> 77 </assert_contents>
50 </output> 78 </output>
51 </test> 79 </test>
52 </tests> 80 </tests>
53 <help><![CDATA[ 81 <help><![CDATA[
54 This is typically used to annotate IDs from dbSnp. 82 This is typically used to annotate IDs from dbSnp.
55 83
56 Annotatating only the ID field from dbSnp137.vcf :: 84 Annotating only the ID field from dbSnp137.vcf ::
57 85
58 Input VCF: 86 Input VCF:
59 CHROM POS ID REF ALT QUAL FILTER INFO 87 CHROM POS ID REF ALT QUAL FILTER INFO
60 22 16157571 . T G 0.0 FAIL NS=53 88 22 16157571 . T G 0.0 FAIL NS=53
61 22 16346045 . T C 0.0 FAIL NS=244 89 22 16346045 . T C 0.0 FAIL NS=244
65 #CHROM POS ID REF ALT QUAL FILTER INFO 93 #CHROM POS ID REF ALT QUAL FILTER INFO
66 22 16157571 . T G 0.0 FAIL NS=53 94 22 16157571 . T G 0.0 FAIL NS=53
67 22 16346045 rs56234788 T C 0.0 FAIL NS=244 95 22 16346045 rs56234788 T C 0.0 FAIL NS=244
68 22 16350245 rs2905295 C A 0.0 FAIL NS=192 96 22 16350245 rs2905295 C A 0.0 FAIL NS=192
69 97
70 Annotatating both the ID and INFO fields from dbSnp137.vcf :: 98 Annotating both the ID and INFO fields from dbSnp137.vcf ::
71 99
72 Input VCF: 100 Input VCF:
73 #CHROM POS ID REF ALT QUAL FILTER INFO 101 #CHROM POS ID REF ALT QUAL FILTER INFO
74 22 16157571 . T G 0.0 FAIL NS=53 102 22 16157571 . T G 0.0 FAIL NS=53
75 22 16346045 . T C 0.0 FAIL NS=244 103 22 16346045 . T C 0.0 FAIL NS=244