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comparison snpSift_vartype.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_vartype" name="SnpSift Variant Type" version="4.0.0"> 1 <tool id="snpsift_vartype" name="SnpSift Variant Type" version="@WRAPPER_VERSION@.0">
2 <description>Annotate with variant type</description> 2 <description>Annotate with variant type</description>
3 <expand macro="requirements" />
4 <macros> 3 <macros>
5 <import>snpSift_macros.xml</import> 4 <import>snpSift_macros.xml</import>
6 </macros> 5 </macros>
7 <command> 6 <expand macro="requirements" />
8 java -jar \$SNPEFF_JAR_PATH/SnpSift.jar varType $input 2&gt; $log &gt; $output 7 <expand macro="stdio" />
8 <expand macro="version_command" />
9 <command><![CDATA[
10 java -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" varType "$input" 2> "$log" > "$output"
11 ]]>
9 </command> 12 </command>
10 <inputs> 13 <inputs>
11 <param format="vcf" name="input" type="data" label="Variant file (VCF)"/> 14 <param format="vcf" name="input" type="data" label="Variant file (VCF)"/>
12 </inputs> 15 </inputs>
13 <outputs> 16 <outputs>
14 <data format="vcf" name="output" label="${tool.name} on ${on_string}: VCF" /> 17 <data format="vcf" name="output" label="${tool.name} on ${on_string}: VCF" />
15 <data format="txt" name="log" label="${tool.name} on ${on_string}: log" /> 18 <data format="txt" name="log" label="${tool.name} on ${on_string}: log" />
16 </outputs> 19 </outputs>
17 <expand macro="stdio" />
18 <tests> 20 <tests>
19 </tests> 21 </tests>
20 <help> 22 <help><![CDATA[
21 **What it does** 23 **What it does**
22 24
23 This tool uses `SnpSift Variant type`_ to add the variant type (SNP/MNP/INS/DEL/MIXED) in the INFO field. It also adds "HOM/HET", but this last one works if there is only one sample (otherwise it doesn't make any sense). 25 This tool uses `SnpSift Variant type`_ to add the variant type (SNP/MNP/INS/DEL/MIXED) in the INFO field. It also adds "HOM/HET", but this last one works if there is only one sample (otherwise it doesn't make any sense).
24 26
25 .. _SnpSift Variant type: http://snpeff.sourceforge.net/SnpSift.html#VariantType 27 .. _SnpSift Variant type: http://snpeff.sourceforge.net/SnpSift.html#VariantType
32 34
33 .. _CRS4 Srl.: http://www.crs4.it/ 35 .. _CRS4 Srl.: http://www.crs4.it/
34 .. _MIT license: http://opensource.org/licenses/MIT 36 .. _MIT license: http://opensource.org/licenses/MIT
35 37
36 @CITATION_SECTION@ 38 @CITATION_SECTION@
39
40 ]]>
37 </help> 41 </help>
38 <expand macro="citations" /> 42 <expand macro="citations" />
39 </tool> 43 </tool>