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

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584

--- a/data_manager/data_manager_snpEff_download.xml	Thu Jan 22 09:14:50 2015 -0500
+++ b/data_manager/data_manager_snpEff_download.xml	Tue Jun 07 10:11:50 2016 -0400
@@ -1,14 +1,18 @@
-<tool id="data_manager_snpeff_download" name="SnpEff Download" version="4.0.0" tool_type="manage_data">
+<tool id="data_manager_snpeff_download" name="SnpEff Download" version="4.1.0" tool_type="manage_data">
     <description>Download a new database</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_download.py --jar_path \$SNPEFF_JAR_PATH/snpEff.jar --config \$SNPEFF_JAR_PATH/snpEff.config 
+        data_manager_snpEff_download.py --jar_path "\$SNPEFF_JAR_PATH/snpEff.jar" --config "\$SNPEFF_JAR_PATH/snpEff.config"
           --genome_version "$genome_version" "$out_file"
         </command>
     <inputs>
-        <param name="genome_version" type="text" size="40" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)">
+        <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)">
             <help>https://snpeff-data.galaxyproject.org/databases/</help>
             <validator type="regex" message="A genome version name is required">\S+</validator>
         </param>
@@ -17,10 +21,6 @@
     <outputs>
            <data name="out_file" format="data_manager_json" label="${tool.name}"/>
     </outputs>
-    <stdio>
-        <exit_code range=":-1"  level="fatal"   description="Error: Cannot open file" />
-        <exit_code range="1:"  level="fatal"   description="Error" />
-    </stdio>
     <tests>
         <test>
             <param name="genome_version" value="GRCh38.76"/>
@@ -38,7 +38,7 @@
 
 This tool downloads a SnpEff database and populates data tables: snpeffv_genomedb, snpeffv_regulationdb, and snpeffv_annotations.
 
-To see the list of available SnpEff genomes run the "SnpEff Databases" data manager which records the available genome databases in data table: snpeff4_databases 
+To see the list of available SnpEff genomes run the "SnpEff Databases" data manager which records the available genome databases in data table: snpeff4_databases
 
 The SnpEff genome databases are at: http://sourceforge.net/projects/snpeff/files/databases/
 
@@ -49,5 +49,8 @@
 "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>