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annotate snpEff_databases.xml @ 17:13d81e5226cd

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Put gene info in Summary Report extra_files_path
author Jim Johnson <jj@umn.edu>
date Mon, 10 Nov 2014 09:33:36 -0600
parents 3790e16a0be0
children 36f3c82323e6
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1 <tool id="snpEff_databases" name="SnpEff Available Databases" version="4.0.0">
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2 <description></description>
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3 <expand macro="requirements" />
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4 <macros>
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5 <import>snpEff_macros.xml</import>
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6 </macros>
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7 <command>
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8 java -jar \$SNPEFF_JAR_PATH/snpEff.jar databases | grep -v '^---' | sed 's/^Genome/#Genome/' | sed 's/ *//g' > $snpeff_dbs
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9 </command>
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10 <inputs>
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11 </inputs>
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12 <outputs>
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13 <data format="tabular" name="snpeff_dbs" label="${tool.name} available databases" />
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14 </outputs>
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15 <expand macro="stdio" />
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16 <help>
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18 @EXTERNAL_DOCUMENTATION@
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19
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20 @CITATION_SECTION@
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21
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22 </help>
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23 </tool>
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