diff snpEff_download.xml @ 0:e8adfc4c0a6b draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snpEff_download.xml	Wed Dec 11 08:53:32 2013 -0500
@@ -0,0 +1,31 @@
+<tool id="snpEff_download" name="SnpEff Download" version="3.4">
+    <description>Download a new database</description>
+    <expand macro="requirements" />
+    <macros>
+        <import>snpEff_macros.xml</import>
+    </macros>
+    <command>
+    echo $genomeVersion > $snpeff_db; 
+    java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $snpeff_db.extra_files_path -v $genomeVersion > $logfile 
+    </command>
+    <inputs>
+        <param name="genomeVersion" type="select" label="Select the genome version you want to download">
+            <options from_data_table="snpeff_databases">
+                <filter type="sort_by" column="0" />
+            </options>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="txt" name="logfile" />
+        <data format="snpeffdb" name="snpeff_db" label="${genomeVersion}" />
+    </outputs>
+    <expand macro="stdio" />
+    <help>
+
+@EXTERNAL_DOCUMENTATION@
+
+@CITATION_SECTION@
+
+    </help>
+</tool>
+