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comparison snpSift_annotate.xml @ 1:98708b88af9f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
author iuc
date Tue, 07 Jun 2016 10:04:09 -0400
parents 9e8280e19338
children bf8c1526871b
comparison
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0:9e8280e19338 1:98708b88af9f
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