Mercurial > repos > jjohnson > snpeff
comparison data_manager/data_manager_snpEff_databases.xml @ 0:e1d9f6a0ad53
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| author | jjohnson |
|---|---|
| date | Thu, 04 Jul 2013 10:43:55 -0400 |
| parents | |
| children | 6ad9205c1307 |
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| -1:000000000000 | 0:e1d9f6a0ad53 |
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| 1 <tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="3.2" tool_type="manage_data"> | |
| 2 <description>Read the list of available snpEff databases</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="3.2">snpEff</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> | |
| 7 data_manager_snpEff_databases.py --jar_path \$JAVA_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 | |
| 19 <help> | |
| 20 | |
| 21 This tool updatess the list of SnpEff databases for the SnpEff Download data manager. | |
| 22 It should only need to be run once for a snpEff version, | |
| 23 since it populates the SnpEff Download data manager from the snpEff config file. | |
| 24 | |
| 25 For information about snpEff: http://snpEff.sourceforge.net | |
| 26 | |
| 27 </help> | |
| 28 </tool> | |
| 29 |