Mercurial > repos > jjohnson > snpeff
annotate data_manager/data_manager_snpEff_databases.xml @ 8:aecbd8878923
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| author | bgruening |
|---|---|
| date | Fri, 29 Nov 2013 09:29:05 -0500 |
| parents | 8952990fcab9 |
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| rev | line source |
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8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
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1 <tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="3.4" tool_type="manage_data"> |
| 0 | 2 <description>Read the list of available snpEff databases</description> |
| 3 <requirements> | |
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8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
4
diff
changeset
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4 <requirement type="package" version="3.4">snpEff</requirement> |
| 0 | 5 </requirements> |
| 6 <command interpreter="python"> | |
| 2 | 7 data_manager_snpEff_databases.py --jar_path \$SNPEFF_JAR_PATH/snpEff.jar "$out_file" |
| 0 | 8 </command> |
| 9 <inputs> | |
| 10 </inputs> | |
| 11 <outputs> | |
| 12 <data name="out_file" format="data_manager_json"/> | |
| 13 </outputs> | |
| 14 <stdio> | |
| 15 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> | |
| 16 <exit_code range="1:" level="fatal" description="Error" /> | |
| 17 </stdio> | |
| 4 | 18 <tests> |
| 19 <test> | |
| 20 <output name="out_file"> | |
| 21 <assert_contents> | |
| 22 <!-- Check that a genome was added --> | |
| 23 <has_text text="GRCh37.72" /> | |
| 24 </assert_contents> | |
| 25 </output> | |
| 26 </test> | |
| 27 </tests> | |
| 0 | 28 <help> |
| 29 | |
| 30 This tool updatess the list of SnpEff databases for the SnpEff Download data manager. | |
| 31 It should only need to be run once for a snpEff version, | |
| 32 since it populates the SnpEff Download data manager from the snpEff config file. | |
| 33 | |
| 34 For information about snpEff: http://snpEff.sourceforge.net | |
| 35 | |
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5
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
4
diff
changeset
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36 Please cite: |
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8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
4
diff
changeset
|
37 "A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process] |
|
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
4
diff
changeset
|
38 |
| 0 | 39 </help> |
| 40 </tool> | |
| 41 |