diff snpEff_download.xml @ 17:65ae79bddc69 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102

--- a/snpEff_download.xml	Tue Aug 28 03:03:45 2018 -0400
+++ b/snpEff_download.xml	Thu Sep 06 13:23:57 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="snpEff_download" name="SnpEff download:" version="@wrapper_version@.galaxy1">
+<tool id="snpEff_download" name="SnpEff download:" version="@WRAPPER_VERSION@.galaxy2">
     <description> download a pre-built database</description>
     <macros>
         <import>snpEff_macros.xml</import>
@@ -9,16 +9,17 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command><![CDATA[
-snpEff download -dataDir '$snpeff_db.files_path' -v '$genome_version'
+snpEff download -dataDir "\$PWD/temp" -v '$genome_version' &&
+mkdir -p '$snpeff_db.files_path' &&
+mv temp/'$genome_version' '$snpeff_db.files_path'
     ]]></command>
     <inputs>
         <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>
+            <validator type="empty_field" message="A genome version name is required" />
         </param>
     </inputs>
     <outputs>
-        <data format="snpeffdb" name="snpeff_db" label="${tool.name} @snpeff_version@ ${genome_version}"/>
+        <data name="snpeff_db" format="snpeffdb" label="${tool.name} @SNPEFF_VERSION@ ${genome_version}"/>
     </outputs>
     <tests>
         <test>
@@ -29,12 +30,19 @@
                 </assert_contents>
             </output>
         </test>
+        <test>
+            <param name="genome_version" value="Bdellovibrio_bacteriovorus_hd100"/>
+            <output name="snpeff_db">
+                <assert_contents>
+                    <has_text text="Bdellovibrio_bacteriovorus_hd100" />
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
-
 **What it does**
 
-This tool downloads a specified database from @snpeff_database_url@. It deposits it into the history.
+This tool downloads a specified database from @SNPEFF_DATABASE_URL@. It deposits it into the history.
 
 -------
 
@@ -47,8 +55,8 @@
     #. 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@
+@SNPEFF_IN_GALAXY_INFO@
+@EXTERNAL_DOCUMENTATION@
     ]]></help>
     <expand macro="citations" />
 </tool>