--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_snpEff_download.xml	Thu Jun 26 09:13:02 2014 -0400
@@ -0,0 +1,71 @@
+<tool id="data_manager_snpeff_download" name="SnpEff Download" version="3.6" tool_type="manage_data">
+    <description>Download a new database</description>
+    <requirements>
+        <requirement type="package" version="3.6">snpEff</requirement>
+    </requirements>
+    <command interpreter="python">
+        data_manager_snpEff_download.py --jar_path \$SNPEFF_JAR_PATH/snpEff.jar --config \$SNPEFF_JAR_PATH/snpEff.config 
+        #if $snpDb.genomeSrc == "named":
+          --genome_version "${snpDb.genome_version}"
+        #else
+          --genome_version "${snpDb.genome_databases.fields.value}"
+          --organism "${snpDb.genome_databases.fields.name}"
+        #end if
+        "$out_file"
+        </command>
+    <inputs>
+        <conditional name="snpDb">
+            <param name="genomeSrc" type="select" label="Select Genome Version">
+                <help>The list is very large and may take some time to display on your browser</help>
+                <option value="named">By Genome Version Name</option>
+                <option value="cached">Select from list</option>
+            </param>
+            <when value="named">
+                <param name="genome_version" type="text" size="40" value="" label="Snpff Genome Version Name (e.g. GRCh37.74)">
+                    <help>http://sourceforge.net/projects/snpeff/files/databases/</help>
+                    <validator type="regex" message="A genome version name is required">\S+</validator>
+                </param>
+            </when>
+            <when value="cached">
+                <param name="genome_databases" type="select" display="checkboxes" multiple="true" label="Genome Version">
+                    <options from_data_table="snpeff_databases">
+                        <filter type="sort_by" column="0" />
+                    </options>
+                </param>
+            </when>
+        </conditional>
+    </inputs>
+
+    <outputs>
+           <data name="out_file" format="data_manager_json" label="${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="genomeSrc"  value="named"/>
+            <param name="genome_version" value="GRCh37.71"/>
+            <output name="out_file">
+                <assert_contents>
+                    <!-- Check that a genome was added -->
+                    <has_text text="GRCh37.71" />
+                    <has_text text="snpeff_regulationdb" />
+                    <has_text text="snpeff_annotations" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+
+This tool downloads a SnpEff database.
+
+For details about this tool, please go to http://snpEff.sourceforge.net
+
+Please cite:
+"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>
+</tool>
+