Mercurial > repos > iuc > data_manager_snpeff

diff data_manager/data_manager_snpEff_databases.xml @ 1:85a23e2dd92b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
author iuc
date Tue, 07 Jun 2016 10:11:50 -0400
parents 9ac823a8b328
children e5a471c4630e
line wrap: on
line diff
--- a/data_manager/data_manager_snpEff_databases.xml	Thu Jan 22 09:14:50 2015 -0500
+++ b/data_manager/data_manager_snpEff_databases.xml	Tue Jun 07 10:11:50 2016 -0400
@@ -1,20 +1,20 @@
-<tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="4.0.0" tool_type="manage_data">
+<tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="4.1.0" tool_type="manage_data">
 	<description>Read the list of available snpEff databases</description>
 	<requirements>
-		<requirement type="package" version="4.0">snpEff</requirement>
+		<requirement type="package" version="4.1">snpEff</requirement>
 	</requirements>
+        <stdio>
+          <exit_code range=":-1"  level="fatal"   description="Error: Cannot open file" />
+          <exit_code range="1:"  level="fatal"   description="Error" />
+        </stdio>
 	<command interpreter="python">
-        data_manager_snpEff_databases.py --jar_path \$SNPEFF_JAR_PATH/snpEff.jar "$out_file"
+        data_manager_snpEff_databases.py --jar_path "\$SNPEFF_JAR_PATH/snpEff.jar" "$out_file"
         </command>
 	<inputs>
 	</inputs>
 	<outputs>
            <data name="out_file" format="data_manager_json"/>
 	</outputs>
-        <stdio>
-          <exit_code range=":-1"  level="fatal"   description="Error: Cannot open file" />
-          <exit_code range="1:"  level="fatal"   description="Error" />
-        </stdio>
         <tests>
             <test>
                 <output name="out_file">
@@ -37,5 +37,8 @@
 "A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process]
 
 	</help>
+      <citations>
+        <citation type="doi">10.4161/fly.19695</citation>
+      </citations>
 </tool>