annotate snpEff_download.xml @ 0:c07c403fc470

Uploaded
author jjohnson
date Thu, 17 Jan 2013 16:31:12 -0500
parents
children 13b6ad2ddace
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c07c403fc470 Uploaded
jjohnson
parents:
diff changeset
1 <tool id="snpEff_download" name="SnpEff Download" version="3.1">
c07c403fc470 Uploaded
jjohnson
parents:
diff changeset
2 <description>Download a new database</description>
c07c403fc470 Uploaded
jjohnson
parents:
diff changeset
3 <requirements>
c07c403fc470 Uploaded
jjohnson
parents:
diff changeset
4 <requirement type="package" version="3.1">snpEff</requirement>
c07c403fc470 Uploaded
jjohnson
parents:
diff changeset
5 </requirements>
c07c403fc470 Uploaded
jjohnson
parents:
diff changeset
6 <command>java -jar \$JAVA_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile </command>
c07c403fc470 Uploaded
jjohnson
parents:
diff changeset
7 <inputs>
c07c403fc470 Uploaded
jjohnson
parents:
diff changeset
8 <param name="genomeVersion" type="select" label="Genome">
c07c403fc470 Uploaded
jjohnson
parents:
diff changeset
9 <options from_file="snpeffect_genomedb.loc">
c07c403fc470 Uploaded
jjohnson
parents:
diff changeset
10 <column name="name" index="1"/>
c07c403fc470 Uploaded
jjohnson
parents:
diff changeset
11 <column name="value" index="0"/>
c07c403fc470 Uploaded
jjohnson
parents:
diff changeset
12 </options>
c07c403fc470 Uploaded
jjohnson
parents:
diff changeset
13 </param>
c07c403fc470 Uploaded
jjohnson
parents:
diff changeset
14 </inputs>
c07c403fc470 Uploaded
jjohnson
parents:
diff changeset
15
c07c403fc470 Uploaded
jjohnson
parents:
diff changeset
16 <outputs>
c07c403fc470 Uploaded
jjohnson
parents:
diff changeset
17 <data format="txt" name="logfile" />
c07c403fc470 Uploaded
jjohnson
parents:
diff changeset
18 </outputs>
c07c403fc470 Uploaded
jjohnson
parents:
diff changeset
19 <stdio>
c07c403fc470 Uploaded
jjohnson
parents:
diff changeset
20 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
c07c403fc470 Uploaded
jjohnson
parents:
diff changeset
21 <exit_code range="1:" level="fatal" description="Error" />
c07c403fc470 Uploaded
jjohnson
parents:
diff changeset
22 </stdio>
c07c403fc470 Uploaded
jjohnson
parents:
diff changeset
23
c07c403fc470 Uploaded
jjohnson
parents:
diff changeset
24 <help>
c07c403fc470 Uploaded
jjohnson
parents:
diff changeset
25
c07c403fc470 Uploaded
jjohnson
parents:
diff changeset
26 This tool downloads a SnpEff database.
c07c403fc470 Uploaded
jjohnson
parents:
diff changeset
27
c07c403fc470 Uploaded
jjohnson
parents:
diff changeset
28 For details about this tool, please go to http://snpEff.sourceforge.net
c07c403fc470 Uploaded
jjohnson
parents:
diff changeset
29
c07c403fc470 Uploaded
jjohnson
parents:
diff changeset
30 </help>
c07c403fc470 Uploaded
jjohnson
parents:
diff changeset
31 </tool>
c07c403fc470 Uploaded
jjohnson
parents:
diff changeset
32