diff snpEff_download.xml @ 10:5b4ac70948d2 draft

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

--- a/snpEff_download.xml	Tue Nov 14 05:42:51 2017 -0500
+++ b/snpEff_download.xml	Tue Mar 27 09:44:18 2018 -0400
@@ -1,22 +1,24 @@
-<tool id="snpEff_download" name="SnpEff Download" version="@WRAPPER_VERSION@.1">
-    <description>Download a new database</description>
+<tool id="snpEff_download" name="SnpEff download:" version="@wrapper_version@.1">
+    <description> download a pre-built database</description>
     <macros>
         <import>snpEff_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
+    <requirements>
+        <expand macro="requirement" />
+    </requirements>
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command><![CDATA[
 snpEff download -dataDir '$snpeff_db.files_path' -v '$genome_version'
     ]]></command>
     <inputs>
-        <param name="genome_version" type="text" value="" label="Select the genome version you want to download (e.g. GRCh38.86, GRCh37.75, hg38, or GRCm38.86)">
-            <help>@SNPEFF_DATABASE_URL@</help>
+        <param name="genome_version" type="text" value="" label="Select the annotation database you want to download (e.g. GRCh38.86, mm10 etc.)" help="The list of available databases can be obtained with 'SnpEff databases' tool">
+            <help>@snpeff_database_url@</help>
             <validator type="regex" message="A genome version name is required">\S+</validator>
         </param>
     </inputs>
     <outputs>
-        <data format="snpeffdb" name="snpeff_db" label="${tool.name} @SNPEFF_VERSION@ ${genome_version}" />
+        <data format="snpeffdb" name="snpeff_db" label="${tool.name} @snpeff_version@ ${genome_version}"/>
     </outputs>
     <tests>
         <test>
@@ -29,7 +31,24 @@
         </test>
     </tests>
     <help><![CDATA[
-@EXTERNAL_DOCUMENTATION@
+
+**What it does**
+
+This tool downloads a specified database from @snpeff_database_url@. It deposits it into the history. 
+
+-------
+
+.. class:: infomark
+
+**The usage scenario**
+
+Suppose you want to annoate a VCF file containing variants within mm10 version of the Mouse genome. To do this you can:
+
+    #. Download mm10 snpEff database by typing *mm10* into **Select the annotation database...** text box.
+    #. Use **SnpEff eff** by choosing the downloaded database from the history using *Downloaded snpEff database in your history* option of the **Genome source** parameter.
+    
+@snpeff_in_galaxy_info@
+@external_documentation@
     ]]></help>
     <expand macro="citations" />
 </tool>