Mercurial > repos > iuc > data_manager_snpeff

diff data_manager/snpEff_macros.xml @ 3:e5a471c4630e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit de422632b9310905f8e9d44faee9ff768752968f
author iuc
date Mon, 31 Oct 2016 08:13:11 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/snpEff_macros.xml	Mon Oct 31 08:13:11 2016 -0400
@@ -0,0 +1,28 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="4.1">snpEff</requirement>
+        </requirements>
+    </xml>
+  <xml name="stdio">
+    <stdio>
+        <exit_code range=":-1"  level="fatal" description="Error: Cannot open file" />
+        <exit_code range="1:"  level="fatal" description="Error" />
+    </stdio>
+  </xml>
+  <token name="@CONDA_SNPEFF_JAR_PATH@">if [ -z "\$SNPEFF_JAR_PATH" ]; then export SNPEFF_JAR_PATH=\$(dirname \$(readlink -e \$(which snpEff))); fi</token>
+  <xml name="version_command">
+    <version_command><![CDATA[
+    if [ -z "$SNPEFF_JAR_PATH" ]; then
+        export SNPEFF_JAR_PATH=$(dirname $(readlink -e $(which snpEff)));
+    fi && java -jar "$SNPEFF_JAR_PATH/snpEff.jar" -version
+    ]]></version_command>
+  </xml>
+  <token name="@WRAPPER_VERSION@">4.1</token>
+  <xml name="citations">
+      <citations>
+        <citation type="doi">10.4161/fly.19695</citation>
+        <yield />
+      </citations>
+  </xml>
+</macros>