diff snpEff_macros.xml @ 10:5b4ac70948d2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef

--- a/snpEff_macros.xml	Tue Nov 14 05:42:51 2017 -0500
+++ b/snpEff_macros.xml	Tue Mar 27 09:44:18 2018 -0400
@@ -1,8 +1,6 @@
 <macros>
-    <xml name="requirements">
-        <requirements>
-            <requirement type="package" version="4.3.1r">snpeff</requirement>
-        </requirements>
+    <xml name="requirement">
+        <requirement type="package" version="4.3.1t">snpeff</requirement>
     </xml>
   <xml name="stdio">
     <stdio>
@@ -15,16 +13,61 @@
 snpEff -version
     ]]></version_command>
   </xml>
-  <token name="@WRAPPER_VERSION@">4.3r</token>
-  <token name="@SNPEFF_VERSION@">SnpEff4.3</token>
-  <token name="@SNPEFF_DATABASE_URL@">https://sourceforge.net/projects/snpeff/files/databases/v4_3/</token>
-  <token name="@EXTERNAL_DOCUMENTATION@">
-For details about this tool, please go to: http://snpeff.sourceforge.net/SnpEff_manual.html
+  <token name="@wrapper_version@">4.3.1t</token>
+  <token name="@snpeff_version@">SnpEff4.3</token>
+  <token name="@snpeff_database_url@">https://sourceforge.net/projects/snpeff/files/databases/v4_3/</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
+
+**Using SnpEff in Galaxy: A few points to remember**
+
+SnpEff relies on specially formatted databases to generate annotations. It will not work without them. There are several ways in which these databases can be obtained.
+
+**Pre-cached databases**
+
+Many standard (e.g., human, mouse, *Drosophila*) databases are likely pre-cached within a given Galaxy instance. You should be able to see them listed in **Genome** drop-down of **SbpEff eff** tool. 
+
+In you *do not see them* keep reading...
+
+**Download pre-built databases**
+
+SnpEff project generates large numbers of pre-build databases. These are available at @SNPEFF_DATABASE_URL@ and can downloaded. Follow these steps:
+
+  #. Use **SnpEff databases** tool to generate a list of existing databases. Note the name of the database you need.
+  #. Use **SnpEff download** tool to download the database.
+  #. Finally, use **SnpEff eff** by choosing the downloaded database from the history using *Downloaded snpEff database in your history* option of the **Genome source** parameter.
+
+Alternatively, you can specify the name of the database directly in **SnpEff eff** using the *Download on demand* option (again, **Genome source** parameter). In this case snpEff will download the database before performing annotation. 
+
+**Create your own database**
+
+In cases when you are dealing with bacterial or viral (or, frankly, any other) genomes it may be easier to create database yourself. For this you need:
+
+ #. Download Genbank record corresponding to your genome of interest from from NCBI. 
+ #. Use **SnpEff build** to create the database. 
+ #. Use the database in **SnpEff eff** (using *Custom* option for **Genome source** parameter).
+
+Creating custom database has one benefit. The **SnpEff build** tool normally produces two outputs: (1) a SnpEff database and (2) FASTA file containing sequences from the Genbank file. If you are performing your experiment from the beginning by mapping reads against a genome and finding variants before annotating them with SnpEff you can use **this FASTA file** as a reference to map your reads against. This will guarantee that you will not have any issues related to reference sequence naming -- the most common source of SnpEff errors. 
+
+</token>
+
+
+
   <xml name="citations">
       <citations>
         <citation type="doi">10.4161/fly.19695</citation>
         <yield />
       </citations>
   </xml>
-</macros>
+</macros>
\ No newline at end of file