Mercurial > repos > iuc > snpeff_sars_cov_2

diff snpEff_macros.xml @ 0:2a3a00c1fa0a draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e6d1b32be9df14beb1e2859a0d2fa29a2d09227e"
author: iuc
date: Thu, 18 Jun 2020 16:11:49 -0400
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snpEff_macros.xml	Thu Jun 18 16:11:49 2020 -0400
@@ -0,0 +1,51 @@
+<macros>
+    <xml name="requirement">
+        <requirement type="package" version="4.5covid19">snpeff</requirement>
+        <yield/>
+    </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>
+  <xml name="version_command">
+    <version_command><![CDATA[
+snpEff -version
+    ]]></version_command>
+  </xml>
+  <token name="@WRAPPER_VERSION@">4.5covid19</token>
+  <token name="@SNPEFF_VERSION@">SnpEff4.5</token>
+  <token name="@JAVA_OPTIONS@">-Xmx\${GALAXY_MEMORY_MB:-8192}m</token>
+  <token name="@EXTERNAL_DOCUMENTATION@">
+
+
+-------
+
+To learn more about SnpEff read its manual at http://snpeff.sourceforge.net/SnpEff_manual.html
+  </token>
+  <token name="@SNPEFF_IN_GALAXY_INFO@">
+
+-------
+
+.. class:: warningmark
+
+**Databases in the SnpEff Covid-19 edition**
+
+This special version of SnpEff provides only a fixed number of
+SARS-CoV-2-related genome databases.
+
+Unlike with regular SnpEff releases, it is not possible to extend this set,
+*i.e*, you cannot download additional databases or build custom databases for
+this edition.
+</token>
+
+
+
+  <xml name="citations">
+      <citations>
+        <citation type="doi">10.4161/fly.19695</citation>
+        <yield />
+      </citations>
+  </xml>
+</macros>