Mercurial > repos > iuc > snpeff
diff snpEff_download.xml @ 17:65ae79bddc69 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102
author | iuc |
---|---|
date | Thu, 06 Sep 2018 13:23:57 -0400 |
parents | 5a29ab10dba6 |
children |
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--- 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>