Mercurial > repos > devteam > data_manager_fetch_ncbi_taxonomy
diff data_manager/ncbi_taxonomy_fetcher.xml @ 5:eaca3e270bf6 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 3d78021971b83d585c432830cee0488ada7bd257"
author | iuc |
---|---|
date | Fri, 19 Mar 2021 21:43:14 +0000 |
parents | cef5c909ccb8 |
children |
line wrap: on
line diff
--- a/data_manager/ncbi_taxonomy_fetcher.xml Tue Jul 07 00:05:59 2020 +0000 +++ b/data_manager/ncbi_taxonomy_fetcher.xml Fri Mar 19 21:43:14 2021 +0000 @@ -1,6 +1,9 @@ <?xml version="1.0"?> -<tool id="ncbi_taxonomy_fetcher" name="NCBI" tool_type="manage_data" version="1.0.1"> +<tool id="ncbi_taxonomy_fetcher" name="NCBI" tool_type="manage_data" version="1.0.3"> <description>taxonomy downloader</description> + <requirements> + <requirement type="package" version="3.7">python</requirement> + </requirements> <command detect_errors="exit_code"> <![CDATA[ python '$__tool_directory__/data_manager.py' --out '${out_file}' @@ -10,13 +13,36 @@ #if $database_name: --name '${database_name}' #end if + $name_maps + $partial_data ]]> </command> <inputs> <param name="database_name" type="text" optional="true" label="Name for this database" help="Enter a unique identifier, or leave blank for today's date" /> <param name="taxonomy_url" type="text" value='ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz' label="Enter URL for taxonomy files" /> + <param name="name_maps" type="boolean" truevalue="--name-maps" falsevalue="" label="Also download accession2taxid data" checked="false" /> + <param name="partial_data" type="hidden" value="" help="Used for testing"/> </inputs> <outputs> <data name="out_file" format="data_manager_json" /> </outputs> + <tests> + <test> + <param name="database_name" value="tax_name"/> + <param name="database_id" value="tax_id"/> + <output name="out_file" value="taxonomy.json"/> + </test> + <test> + <param name="database_name" value="tax_name"/> + <param name="database_id" value="tax_id"/> + <param name="name_maps" value="true"/> + <param name="partial_data" value="--partial"/> + <output name="out_file" value="taxonomy_with_accession2taxid.json"/> + </test> + </tests> + <help> + Download a taxonomy dump from a provided URL. + The default URL is the latest dump from NCBI taxonomy. + The accession2taxid data comes from ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/ and can be used by the Diamond data_manager (uses ~20Gb as of 2021). + </help> </tool>