Mercurial > repos > jjohnson > snpeff

annotate data_manager/data_manager_snpEff_databases.xml @ 3:a8f4ebfb8253

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Update tool_dependencies.xml for package_snpeff_3_3
author Jim Johnson <jj@umn.edu>
date Fri, 04 Oct 2013 09:31:27 -0500
parents 6ad9205c1307
children 47ddc9f4d0b6
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
6ad9205c1307 Update to SnpEff version 3.3
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
1 <tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="3.3" tool_type="manage_data">
0
e1d9f6a0ad53 Uploaded
jjohnson
parents:
diff changeset
2 <description>Read the list of available snpEff databases</description>
e1d9f6a0ad53 Uploaded
jjohnson
parents:
diff changeset
3 <requirements>
2
6ad9205c1307 Update to SnpEff version 3.3
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
4 <requirement type="package" version="3.3">snpEff</requirement>
0
e1d9f6a0ad53 Uploaded
jjohnson
parents:
diff changeset
5 </requirements>
e1d9f6a0ad53 Uploaded
jjohnson
parents:
diff changeset
6 <command interpreter="python">
2
6ad9205c1307 Update to SnpEff version 3.3
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
7 data_manager_snpEff_databases.py --jar_path \$SNPEFF_JAR_PATH/snpEff.jar "$out_file"
0
e1d9f6a0ad53 Uploaded
jjohnson
parents:
diff changeset
8 </command>
e1d9f6a0ad53 Uploaded
jjohnson
parents:
diff changeset
9 <inputs>
e1d9f6a0ad53 Uploaded
jjohnson
parents:
diff changeset
10 </inputs>
e1d9f6a0ad53 Uploaded
jjohnson
parents:
diff changeset
11 <outputs>
e1d9f6a0ad53 Uploaded
jjohnson
parents:
diff changeset
12 <data name="out_file" format="data_manager_json"/>
e1d9f6a0ad53 Uploaded
jjohnson
parents:
diff changeset
13 </outputs>
e1d9f6a0ad53 Uploaded
jjohnson
parents:
diff changeset
14 <stdio>
e1d9f6a0ad53 Uploaded
jjohnson
parents:
diff changeset
15 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
e1d9f6a0ad53 Uploaded
jjohnson
parents:
diff changeset
16 <exit_code range="1:" level="fatal" description="Error" />
e1d9f6a0ad53 Uploaded
jjohnson
parents:
diff changeset
17 </stdio>
e1d9f6a0ad53 Uploaded
jjohnson
parents:
diff changeset
18
e1d9f6a0ad53 Uploaded
jjohnson
parents:
diff changeset
19 <help>
e1d9f6a0ad53 Uploaded
jjohnson
parents:
diff changeset
20
e1d9f6a0ad53 Uploaded
jjohnson
parents:
diff changeset
21 This tool updatess the list of SnpEff databases for the SnpEff Download data manager.
e1d9f6a0ad53 Uploaded
jjohnson
parents:
diff changeset
22 It should only need to be run once for a snpEff version,
e1d9f6a0ad53 Uploaded
jjohnson
parents:
diff changeset
23 since it populates the SnpEff Download data manager from the snpEff config file.
e1d9f6a0ad53 Uploaded
jjohnson
parents:
diff changeset
24
e1d9f6a0ad53 Uploaded
jjohnson
parents:
diff changeset
25 For information about snpEff: http://snpEff.sourceforge.net
e1d9f6a0ad53 Uploaded
jjohnson
parents:
diff changeset
26
e1d9f6a0ad53 Uploaded
jjohnson
parents:
diff changeset
27 </help>
e1d9f6a0ad53 Uploaded
jjohnson
parents:
diff changeset
28 </tool>
e1d9f6a0ad53 Uploaded
jjohnson
parents:
diff changeset
29