Mercurial > repos > iuc > snpsift
comparison snpSift_annotate.xml @ 1:98708b88af9f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
author | iuc |
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date | Tue, 07 Jun 2016 10:04:09 -0400 |
parents | 9e8280e19338 |
children | bf8c1526871b |
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0:9e8280e19338 | 1:98708b88af9f |
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1 <tool id="snpSift_annotate" name="SnpSift Annotate" version="4.0.0"> | 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 <expand macro="requirements" /> | |
7 <macros> | 6 <macros> |
8 <import>snpSift_macros.xml</import> | 7 <import>snpSift_macros.xml</import> |
9 </macros> | 8 </macros> |
10 <command> | 9 <expand macro="requirements" /> |
11 java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar $annotate_cmd | 10 <expand macro="stdio" /> |
11 <expand macro="version_command" /> | |
12 <command><![CDATA[ | |
13 java -Xmx6G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" $annotate_cmd | |
12 #if $annotate.id : | 14 #if $annotate.id : |
13 -id | 15 -id |
14 #elif $annotate.info_ids.__str__.strip() != '' : | 16 #elif str($annotate.info_ids).strip() != '' : |
15 -info "$annotate.info_ids" | 17 -info "$annotate.info_ids" |
16 #end if | 18 #end if |
17 -q $dbSnp $input > $output | 19 -q "$dbSnp" "$input" > "$output" |
20 ]]> | |
18 </command> | 21 </command> |
19 <inputs> | 22 <inputs> |
20 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> | 23 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> |
21 <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" | 24 <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" |
22 help="The ID field for a variant in input will be assigned from a matching variant in this file."/> | 25 help="The ID field for a variant in input will be assigned from a matching variant in this file."/> |
23 <conditional name="annotate"> | 26 <conditional name="annotate"> |
24 <param name="id" type="boolean" truevalue="id" falsevalue="info" checked="True" label="Only annotate ID field (do not add INFO field)" help=""/> | 27 <param name="id" type="boolean" truevalue="id" falsevalue="info" checked="True" label="Only annotate ID field (do not add INFO field)" help=""/> |
25 <when value="id"/> | 28 <when value="id"/> |
26 <when value="info"> | 29 <when value="info"> |
27 <param name="info_ids" type="text" value="" size="60" optional="true" label="Limit INFO annotation to these INFO IDs" | 30 <param name="info_ids" type="text" value="" optional="true" label="Limit INFO annotation to these INFO IDs" |
28 help="list is a comma separated list of fields. When blank, all INFO fields are included"> | 31 help="list is a comma separated list of fields. When blank, all INFO fields are included"> |
29 <validator type="regex" message="IDs separted by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</validator> | 32 <validator type="regex" message="IDs separted by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</validator> |
30 </param> | 33 </param> |
31 </when> | 34 </when> |
32 </conditional> | 35 </conditional> |
35 This option will load the entire 'database' VCF file into memory (which may not be practical for large 'database' VCF files). | 38 This option will load the entire 'database' VCF file into memory (which may not be practical for large 'database' VCF files). |
36 Otherwise, both the database and the input VCF files should be sorted by position (Chromosome sort order can differ between files). | 39 Otherwise, both the database and the input VCF files should be sorted by position (Chromosome sort order can differ between files). |
37 </help> | 40 </help> |
38 </param> | 41 </param> |
39 </inputs> | 42 </inputs> |
40 <expand macro="stdio" /> | |
41 <outputs> | 43 <outputs> |
42 <data format="vcf" name="output" /> | 44 <data format="vcf" name="output" /> |
43 </outputs> | 45 </outputs> |
44 <tests> | 46 <tests> |
45 <test> | 47 <test> |
52 <has_text text="rs76166080" /> | 54 <has_text text="rs76166080" /> |
53 </assert_contents> | 55 </assert_contents> |
54 </output> | 56 </output> |
55 </test> | 57 </test> |
56 </tests> | 58 </tests> |
57 <help> | 59 <help><![CDATA[ |
58 | 60 |
59 This is typically used to annotate IDs from dbSnp. | 61 This is typically used to annotate IDs from dbSnp. |
60 | 62 |
61 Annotatating only the ID field from dbSnp137.vcf :: | 63 Annotatating only the ID field from dbSnp137.vcf :: |
62 | 64 |
90 | 92 |
91 | 93 |
92 @EXTERNAL_DOCUMENTATION@ | 94 @EXTERNAL_DOCUMENTATION@ |
93 http://snpeff.sourceforge.net/SnpSift.html#annotate | 95 http://snpeff.sourceforge.net/SnpSift.html#annotate |
94 | 96 |
95 @CITATION_SECTION@ | 97 ]]> |
96 | |
97 | |
98 </help> | 98 </help> |
99 <expand macro="citations" /> | |
99 </tool> | 100 </tool> |
100 | 101 |