Mercurial > repos > iuc > snpsift
annotate snpSift_vartype.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 |
rev | line source |
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1
98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
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changeset
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1 <tool id="snpsift_vartype" name="SnpSift Variant Type" version="@WRAPPER_VERSION@.0"> |
0 | 2 <description>Annotate with variant type</description> |
3 <macros> | |
4 <import>snpSift_macros.xml</import> | |
5 </macros> | |
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98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
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6 <expand macro="requirements" /> |
98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
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7 <expand macro="stdio" /> |
98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
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changeset
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8 <expand macro="version_command" /> |
98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
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9 <command><![CDATA[ |
98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
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10 java -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" varType "$input" 2> "$log" > "$output" |
98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
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changeset
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11 ]]> |
0 | 12 </command> |
13 <inputs> | |
14 <param format="vcf" name="input" type="data" label="Variant file (VCF)"/> | |
15 </inputs> | |
16 <outputs> | |
17 <data format="vcf" name="output" label="${tool.name} on ${on_string}: VCF" /> | |
18 <data format="txt" name="log" label="${tool.name} on ${on_string}: log" /> | |
19 </outputs> | |
20 <tests> | |
21 </tests> | |
1
98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
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0
diff
changeset
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22 <help><![CDATA[ |
0 | 23 **What it does** |
24 | |
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). | |
26 | |
27 .. _SnpSift Variant type: http://snpeff.sourceforge.net/SnpSift.html#VariantType | |
28 | |
29 ------ | |
30 | |
31 **License** | |
32 | |
33 This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_ and is released under the `MIT license`_. | |
34 | |
35 .. _CRS4 Srl.: http://www.crs4.it/ | |
36 .. _MIT license: http://opensource.org/licenses/MIT | |
37 | |
38 @CITATION_SECTION@ | |
1
98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
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39 |
98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
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0
diff
changeset
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40 ]]> |
0 | 41 </help> |
42 <expand macro="citations" /> | |
43 </tool> |