Mercurial > repos > iuc > snpsift_genesets
annotate snpSift_geneSets.xml @ 2:9ba6e2c298ab draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 44b3b8a31f9f912a3b754aef1d467a90a4ed3504
| author | iuc |
|---|---|
| date | Mon, 19 Sep 2016 14:43:55 -0400 |
| parents | 0af41de4eda1 |
| children | 847db7b39bdc |
| rev | line source |
|---|---|
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0af41de4eda1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
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1 <tool id="snpSift_geneSets" name="SnpSift GeneSets" version="@WRAPPER_VERSION@.0"> |
| 0 | 2 <description>Annotating GeneSets, such as Gene Ontology, KEGG, Reactome</description> |
| 3 <!-- | |
| 4 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) | |
| 5 --> | |
| 6 <macros> | |
| 7 <import>snpSift_macros.xml</import> | |
| 8 </macros> | |
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0af41de4eda1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
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9 <expand macro="requirements" /> |
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0af41de4eda1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
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10 <expand macro="stdio" /> |
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0af41de4eda1
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 <expand macro="version_command" /> |
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0af41de4eda1
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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12 <command><![CDATA[ |
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9ba6e2c298ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 44b3b8a31f9f912a3b754aef1d467a90a4ed3504
iuc
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1
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13 @CONDA_SNPEFF_JAR_PATH@ && |
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0af41de4eda1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
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14 java -Xmx2G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" geneSets -v |
| 0 | 15 #if $db_opts.db_opts_selector == "db" |
| 16 "${db_opts.database.fields.path}" | |
| 17 #elif $db_opts.db_opts_selector == "histdb" | |
| 18 "$db_opts.histdb" | |
| 19 #end if | |
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0af41de4eda1
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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20 "$input" 2> "$log" > "$output" |
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0af41de4eda1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
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changeset
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21 ]]> |
| 0 | 22 </command> |
| 23 <inputs> | |
| 24 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> | |
| 25 <conditional name="db_opts"> | |
| 26 <param name="db_opts_selector" type="select" label="Select Annotation database" help=""> | |
| 27 <option value="db" selected="True">Locally installed database</option> | |
| 28 <option value="histdb">database from your history</option> | |
| 29 </param> | |
| 30 <when value="db"> | |
| 31 <param name="database" type="select" label="Molecular Signatures Database (MSigDB)"> | |
| 32 <options from_data_table="snpeff_msigdb_database" /> | |
| 33 </param> | |
| 34 <param name="histdb" type="hidden" value="" /> | |
| 35 </when> | |
| 36 <when value="histdb"> | |
| 37 <param name="histdb" type="data" format="txt" label="Molecular Signatures Database (MSigDB)" /> | |
| 38 </when> | |
| 39 </conditional> | |
| 40 </inputs> | |
| 41 <outputs> | |
| 42 <data format="vcf" name="output" label="${tool.name} on ${on_string}: VCF" /> | |
| 43 <data format="txt" name="log" label="${tool.name} on ${on_string}: log" /> | |
| 44 </outputs> | |
| 45 <tests> | |
| 46 </tests> | |
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0af41de4eda1
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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47 <help><![CDATA[ |
| 0 | 48 This tool uses `SnpSift GeneSets`_ to add annotations from `MSigDB`_, a collection of annotated gene sets from different sources including Gene Ontology (GO), KEGG, Reactome. |
| 49 | |
| 50 .. _SnpSift GeneSets: http://snpeff.sourceforge.net/SnpSift.html#geneSets | |
| 51 | |
| 52 .. class:: warningmark | |
| 53 | |
| 54 The input VCF file must be annotated using SnpEff before performing GeneSets annotations. This is because the tool must know which gene the variant affects. | |
| 55 | |
| 56 @EXTERNAL_DOCUMENTATION@ | |
| 57 | |
| 58 @CITATION_SECTION@ | |
| 59 | |
| 60 For `MSigDB`_, please cite |Subramanian2005|_. | |
| 61 | |
| 62 .. _MSigDB: http://www.broadinstitute.org/gsea/msigdb/ | |
| 63 .. |Subramanian2005| replace:: Subramanian, A., *et al.* (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. *Proc. Natl. Acad. Sci. U.S.A.* 102(43), 15545-15550 | |
| 64 .. _Subramanian2005: http://www.pnas.org/content/102/43/15545 | |
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0af41de4eda1
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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65 |
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0af41de4eda1
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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66 ]]> |
| 0 | 67 </help> |
| 68 <expand macro="citations"> | |
| 69 <citation type="doi">10.1073/pnas.0506580102</citation><!-- MSigDB citation --> | |
| 70 </expand> | |
| 71 </tool> |