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comparison snpSift_annotate.xml @ 3:20c7d583fec1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
author iuc
date Mon, 12 Jun 2017 10:25:32 -0400
parents bf8c1526871b
children b04635ebfab0
comparison
equal deleted inserted replaced
2:bf8c1526871b 3:20c7d583fec1
1 <tool id="snpSift_annotate" name="SnpSift Annotate" version="@WRAPPER_VERSION@.1"> 1 <tool id="snpSift_annotate" name="SnpSift Annotate" version="@WRAPPER_VERSION@.0">
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>
8 </macros> 8 </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 @CONDA_SNPSIFT_JAR_PATH@ && 13 SnpSift annotate
14 java -Xmx6G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" $annotate_cmd 14 #if $annotate.id == 'id':
15 #if $annotate.id : 15 -id
16 -id 16 #elif str($annotate.info_ids).strip() != '':
17 #elif str($annotate.info_ids).strip() != '' : 17 -info "$annotate.info_ids"
18 -info "$annotate.info_ids" 18 #end if
19 #end if 19 -q '$dbSnp' '$input' > '$output'
20 -q "$dbSnp" "$input" > "$output" 20 ]]></command>
21 ]]>
22 </command>
23 <inputs> 21 <inputs>
24 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> 22 <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/>
25 <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" 23 <param name="dbSnp" type="data" format="vcf" label="VCF File with ID field annotated (e.g. dnSNP.vcf)"
26 help="The ID field for a variant in input will be assigned from a matching variant in this file."/> 24 help="The ID field for a variant in input will be assigned from a matching variant in this file."/>
27 <conditional name="annotate"> 25 <conditional name="annotate">
28 <param name="id" type="boolean" truevalue="id" falsevalue="info" checked="True" label="Only annotate ID field (do not add INFO field)" help=""/> 26 <param name="id" type="select" label="Fields to annotate">
27 <option value="id">Only annotate ID field (no INFO fields will be added)</option>
28 <option value="info">Add also INFO fields</option>
29 </param>
29 <when value="id"/> 30 <when value="id"/>
30 <when value="info"> 31 <when value="info">
31 <param name="info_ids" type="text" value="" label="Limit INFO annotation to these INFO IDs" help="List is a comma separated list of fields. When blank, all INFO fields are included"> 32 <param name="info_ids" type="text" value="" label="Limit INFO annotation to these INFO IDs" help="List is a comma separated list of fields. When blank, all INFO fields are included">
32 <validator type="regex" message="IDs separted by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</validator> 33 <validator type="regex" message="IDs separted by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</validator>
33 </param> 34 </param>
34 </when> 35 </when>
35 </conditional> 36 </conditional>
36 <param name="annotate_cmd" type="boolean" truevalue="annMem" falsevalue="annotate" checked="false" label="Allow unsorted VCF files">
37 <help>
38 This option will load the entire 'database' VCF file into memory (which may not be practical for large 'database' VCF files).
39 Otherwise, both the database and the input VCF files should be sorted by position (Chromosome sort order can differ between files).
40 </help>
41 </param>
42 </inputs> 37 </inputs>
43 <outputs> 38 <outputs>
44 <data format="vcf" name="output" /> 39 <data name="output" format="vcf" />
45 </outputs> 40 </outputs>
46 <tests> 41 <tests>
47 <test> 42 <test>
48 <param name="input" ftype="vcf" value="annotate_1.vcf"/> 43 <param name="input" ftype="vcf" value="annotate_1.vcf"/>
49 <param name="dbSnp" ftype="vcf" value="db_test_1.vcf"/> 44 <param name="dbSnp" ftype="vcf" value="db_test_1.vcf"/>
50 <param name="annotate_cmd" value="False"/> 45 <param name="id" value="id"/>
51 <param name="id" value="True"/>
52 <output name="output"> 46 <output name="output">
53 <assert_contents> 47 <assert_contents>
54 <has_text text="rs76166080" /> 48 <has_text text="rs76166080" />
55 </assert_contents> 49 </assert_contents>
56 </output> 50 </output>
57 </test> 51 </test>
58 </tests> 52 </tests>
59 <help><![CDATA[ 53 <help><![CDATA[
60
61 This is typically used to annotate IDs from dbSnp. 54 This is typically used to annotate IDs from dbSnp.
62 55
63 Annotatating only the ID field from dbSnp137.vcf :: 56 Annotatating only the ID field from dbSnp137.vcf ::
64 57
65 Input VCF: 58 Input VCF:
72 #CHROM POS ID REF ALT QUAL FILTER INFO 65 #CHROM POS ID REF ALT QUAL FILTER INFO
73 22 16157571 . T G 0.0 FAIL NS=53 66 22 16157571 . T G 0.0 FAIL NS=53
74 22 16346045 rs56234788 T C 0.0 FAIL NS=244 67 22 16346045 rs56234788 T C 0.0 FAIL NS=244
75 22 16350245 rs2905295 C A 0.0 FAIL NS=192 68 22 16350245 rs2905295 C A 0.0 FAIL NS=192
76 69
77
78
79 Annotatating both the ID and INFO fields from dbSnp137.vcf :: 70 Annotatating both the ID and INFO fields from dbSnp137.vcf ::
80 71
81 Input VCF: 72 Input VCF:
82 #CHROM POS ID REF ALT QUAL FILTER INFO 73 #CHROM POS ID REF ALT QUAL FILTER INFO
83 22 16157571 . T G 0.0 FAIL NS=53 74 22 16157571 . T G 0.0 FAIL NS=53
88 #CHROM POS ID REF ALT QUAL FILTER INFO 79 #CHROM POS ID REF ALT QUAL FILTER INFO
89 22 16157571 . T G 0.0 FAIL NS=53 80 22 16157571 . T G 0.0 FAIL NS=53
90 22 16346045 rs56234788 T C 0.0 FAIL NS=244;RSPOS=16346045;GMAF=0.162248628884826;dbSNPBuildID=129;SSR=0;SAO=0;VP=050100000000000100000100;WGT=0;VC=SNV;SLO;GNO 81 22 16346045 rs56234788 T C 0.0 FAIL NS=244;RSPOS=16346045;GMAF=0.162248628884826;dbSNPBuildID=129;SSR=0;SAO=0;VP=050100000000000100000100;WGT=0;VC=SNV;SLO;GNO
91 22 16350245 rs2905295 C A 0.0 FAIL NS=192;RSPOS=16350245;GMAF=0.230804387568556;dbSNPBuildID=101;SSR=1;SAO=0;VP=050000000000000100000140;WGT=0;VC=SNV;GNO 82 22 16350245 rs2905295 C A 0.0 FAIL NS=192;RSPOS=16350245;GMAF=0.230804387568556;dbSNPBuildID=101;SSR=1;SAO=0;VP=050000000000000100000140;WGT=0;VC=SNV;GNO
92 83
93
94 @EXTERNAL_DOCUMENTATION@ 84 @EXTERNAL_DOCUMENTATION@
95 http://snpeff.sourceforge.net/SnpSift.html#annotate 85 - http://snpeff.sourceforge.net/SnpSift.html#annotate
96 86 ]]></help>
97 ]]>
98 </help>
99 <expand macro="citations" /> 87 <expand macro="citations" />
100 </tool> 88 </tool>
101