Mercurial > repos > jjohnson > snpeff

diff snpEff_databases.xml @ 16:3790e16a0be0

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Add datatype: snpeffdbv4
author Jim Johnson <jj@umn.edu>
date Thu, 23 Oct 2014 05:09:26 -0500
parents
children 36f3c82323e6
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snpEff_databases.xml	Thu Oct 23 05:09:26 2014 -0500
@@ -0,0 +1,24 @@
+<tool id="snpEff_databases" name="SnpEff Available Databases" version="4.0.0">
+    <description></description>
+    <expand macro="requirements" />
+    <macros>
+        <import>snpEff_macros.xml</import>
+    </macros>
+    <command>
+    java -jar \$SNPEFF_JAR_PATH/snpEff.jar databases |  grep -v '^---' | sed 's/^Genome/#Genome/' | sed  's/  *//g' > $snpeff_dbs 
+    </command>
+    <inputs>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="snpeff_dbs" label="${tool.name} available databases" />
+    </outputs>
+    <expand macro="stdio" />
+    <help>
+
+@EXTERNAL_DOCUMENTATION@
+
+@CITATION_SECTION@
+
+    </help>
+</tool>
+