Mercurial > repos > jjohnson > snpsift
annotate snpSift_vartype.xml @ 9:88f4997ccb02 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 93465571cf180554c3548338a68fa0f1604985dc-dirty
| author | jjohnson |
|---|---|
| date | Mon, 11 Apr 2016 09:31:49 -0400 |
| parents | 2f40467536cf |
| children |
| rev | line source |
|---|---|
| 4 | 1 <tool id="snpsift_vartype" name="SnpSift Variant Type" version="@WRAPPER_VERSION@.0"> |
| 2 <description>Annotate with variant type</description> | |
| 3 <macros> | |
| 4 <import>snpSift_macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <expand macro="version_command" /> | |
| 9 <command><![CDATA[ | |
|
8
2f40467536cf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 93465571cf180554c3548338a68fa0f1604985dc-dirty
jjohnson
parents:
4
diff
changeset
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10 java -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" varType "$input" 2> "$log" > "$output" |
| 4 | 11 ]]> |
| 12 </command> | |
| 13 <inputs> | |
| 14 <param format="vcf" name="input" type="data" label="Variant file (VCF)"/> | |
| 15 </inputs> | |
| 16 <outputs> | |
| 17 <data format="vcf" name="output" label="${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> | |
| 22 <help><![CDATA[ | |
| 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@ | |
| 39 | |
| 40 ]]> | |
| 41 </help> | |
| 42 <expand macro="citations" /> | |
| 43 </tool> |