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comparison snpSift_annotate.xml @ 14:80da7fae14b8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
author iuc
date Mon, 05 Dec 2016 12:10:54 -0500
parents ed810da439cc
children 8bd645802765
comparison
equal deleted inserted replaced
13:ed810da439cc 14:80da7fae14b8
1 <tool id="snpSift_annotate" name="SnpSift Annotate" version="@WRAPPER_VERSION@.0"> 1 <tool id="snpSift_annotate" name="SnpSift Annotate" version="@WRAPPER_VERSION@.1">
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>
7 <import>snpSift_macros.xml</import> 7 <import>snpSift_macros.xml</import>
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 java -Xmx6G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" $annotate_cmd 13 @CONDA_SNPSIFT_JAR_PATH@ &&
14 java -Xmx6G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" $annotate_cmd
14 #if $annotate.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" > "$output"
20 ]]> 21 ]]>
21 </command> 22 </command>
22 <inputs> 23 <inputs>
23 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> 24 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
24 <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" 25 <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)"
25 help="The ID field for a variant in input will be assigned from a matching variant in this file."/> 26 help="The ID field for a variant in input will be assigned from a matching variant in this file."/>
26 <conditional name="annotate"> 27 <conditional name="annotate">
27 <param name="id" type="boolean" truevalue="id" falsevalue="info" checked="True" label="Only annotate ID field (do not add INFO field)" help=""/> 28 <param name="id" type="boolean" truevalue="id" falsevalue="info" checked="True" label="Only annotate ID field (do not add INFO field)" help=""/>
28 <when value="id"/> 29 <when value="id"/>
29 <when value="info"> 30 <when value="info">
30 <param name="info_ids" type="text" value="" optional="true" label="Limit INFO annotation to these INFO IDs" 31 <param name="info_ids" type="text" value="" label="Limit INFO annotation to these INFO IDs" help="List is a comma separated list of fields. When blank, all INFO fields are included">
31 help="list is a comma separated list of fields. When blank, all INFO fields are included">
32 <validator type="regex" message="IDs separted by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</validator> 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 </param> 33 </param>
34 </when> 34 </when>
35 </conditional> 35 </conditional>
36 <param name="annotate_cmd" type="boolean" truevalue="annMem" falsevalue="annotate" checked="false" label="Allow unsorted VCF files"> 36 <param name="annotate_cmd" type="boolean" truevalue="annMem" falsevalue="annotate" checked="false" label="Allow unsorted VCF files">
37 <help> 37 <help>
38 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).
39 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).
40 </help> 40 </help>
41 </param> 41 </param>
42 </inputs> 42 </inputs>
43 <outputs> 43 <outputs>
44 <data format="vcf" name="output" /> 44 <data format="vcf" name="output" />