Mercurial > repos > iuc > snpsift_dbnsfp_generic

diff snpSift_macros.xml @ 0:6e5ba121e250 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp_generic/ commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
author iuc
date Mon, 05 Dec 2016 12:05:54 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snpSift_macros.xml	Mon Dec 05 12:05:54 2016 -0500
@@ -0,0 +1,33 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="4.1">snpsift</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_SNPSIFT_JAR_PATH@">if [ -z "\$SNPSIFT_JAR_PATH" ]; then export SNPSIFT_JAR_PATH=\$(dirname \$(readlink -e \$(which SnpSift))); fi</token>
+  <xml name="version_command">
+    <version_command><![CDATA[
+    if [ -z "$SNPSIFT_JAR_PATH" ]; then export SNPSIFT_JAR_PATH=$(dirname $(readlink -e $(which SnpSift))); fi &&
+    java -jar "$SNPSIFT_JAR_PATH/SnpSift.jar" dbnsfp 2>&1|head -n 1
+    ]]></version_command>
+  </xml>
+  <token name="@WRAPPER_VERSION@">4.1</token>
+  <token name="@EXTERNAL_DOCUMENTATION@">
+
+For details about this tool, please go to:
+	http://snpeff.sourceforge.net/SnpEff_manual.html
+
+  </token>
+  <xml name="citations">
+      <citations>
+        <citation type="doi">10.3389/fgene.2012.00035</citation>
+        <yield />
+      </citations>
+  </xml>
+</macros>