Mercurial > repos > jjohnson > snpeff_with_dep
annotate snpEff_download.xml @ 25:7c1c337fb21c default tip
Update tool_dependencies.xml for testtoolshed
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Tue, 07 May 2013 15:05:54 -0500 |
| parents | f22f28cd881e |
| children |
| rev | line source |
|---|---|
| 24 | 1 <tool id="snpEff_download" name="SnpEff Download" version="3.2"> |
| 0 | 2 <description>Download a new database</description> |
| 3 <requirements> | |
| 24 | 4 <requirement type="package" version="3.2">snpEff</requirement> |
| 0 | 5 </requirements> |
| 14 | 6 <command>java -jar \$JAVA_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile </command> |
| 0 | 7 <inputs> |
| 8 <param name="genomeVersion" type="select" label="Genome"> | |
|
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4430626bd994
Use snpeffect_genomedb.loc for genomeVersions, have snpEff attempt to download genomeVersions that are not already locally cached
Jim Johnson <jj@umn.edu>
parents:
20
diff
changeset
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9 <options from_file="snpeffect_genomedb.loc"> |
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4430626bd994
Use snpeffect_genomedb.loc for genomeVersions, have snpEff attempt to download genomeVersions that are not already locally cached
Jim Johnson <jj@umn.edu>
parents:
20
diff
changeset
|
10 <column name="name" index="1"/> |
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4430626bd994
Use snpeffect_genomedb.loc for genomeVersions, have snpEff attempt to download genomeVersions that are not already locally cached
Jim Johnson <jj@umn.edu>
parents:
20
diff
changeset
|
11 <column name="value" index="0"/> |
|
4430626bd994
Use snpeffect_genomedb.loc for genomeVersions, have snpEff attempt to download genomeVersions that are not already locally cached
Jim Johnson <jj@umn.edu>
parents:
20
diff
changeset
|
12 </options> |
| 0 | 13 </param> |
| 14 </inputs> | |
| 15 | |
| 16 <outputs> | |
| 17 <data format="txt" name="logfile" /> | |
| 18 </outputs> | |
| 5 | 19 <stdio> |
| 20 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> | |
| 21 <exit_code range="1:" level="fatal" description="Error" /> | |
| 22 </stdio> | |
| 0 | 23 |
| 24 <help> | |
| 25 | |
| 26 This tool downloads a SnpEff database. | |
| 27 | |
| 28 For details about this tool, please go to http://snpEff.sourceforge.net | |
| 29 | |
| 30 </help> | |
| 31 </tool> | |
| 32 |