Mercurial > repos > jjohnson > data_manager_snpeff
annotate data_manager/data_manager_snpEff_databases.xml @ 6:a329eda0cdff draft default tip
Uploaded
| author | jjohnson |
|---|---|
| date | Wed, 09 Dec 2015 13:49:55 -0500 |
| parents | 6a378d0f4856 |
| children |
| rev | line source |
|---|---|
| 6 | 1 <tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="4.1.0" tool_type="manage_data"> |
| 0 | 2 <description>Read the list of available snpEff databases</description> |
| 3 <requirements> | |
| 6 | 4 <requirement type="package" version="4.1">snpEff</requirement> |
| 0 | 5 </requirements> |
| 6 <command interpreter="python"> | |
| 7 data_manager_snpEff_databases.py --jar_path \$SNPEFF_JAR_PATH/snpEff.jar "$out_file" | |
| 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> | |
| 18 <tests> | |
| 19 <test> | |
| 20 <output name="out_file"> | |
| 21 <assert_contents> | |
| 22 <!-- Check that a genome was added --> | |
|
4
6a378d0f4856
Only download by name, available genome list now too large to be practical
Jim Johnson <jj@umn.edu>
parents:
1
diff
changeset
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23 <has_text text="GRCh38.76" /> |
| 0 | 24 </assert_contents> |
| 25 </output> | |
| 26 </test> | |
| 27 </tests> | |
| 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 | |
| 36 Please cite: | |
| 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] | |
| 38 | |
| 39 </help> | |
| 40 </tool> | |
| 41 |