Mercurial > repos > jjohnson > snpeff

annotate data_manager/data_manager_snpEff_databases.xml @ 0:e1d9f6a0ad53

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author jjohnson
date Thu, 04 Jul 2013 10:43:55 -0400
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1 <tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="3.2" tool_type="manage_data">
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2 <description>Read the list of available snpEff databases</description>
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3 <requirements>
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4 <requirement type="package" version="3.2">snpEff</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 data_manager_snpEff_databases.py --jar_path \$JAVA_JAR_PATH/snpEff.jar "$out_file"
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8 </command>
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9 <inputs>
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10 </inputs>
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11 <outputs>
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12 <data name="out_file" format="data_manager_json"/>
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13 </outputs>
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14 <stdio>
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15 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
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16 <exit_code range="1:" level="fatal" description="Error" />
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17 </stdio>
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18
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19 <help>
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20
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21 This tool updatess the list of SnpEff databases for the SnpEff Download data manager.
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22 It should only need to be run once for a snpEff version,
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23 since it populates the SnpEff Download data manager from the snpEff config file.
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24
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25 For information about snpEff: http://snpEff.sourceforge.net
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26
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27 </help>
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28 </tool>
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