Mercurial > repos > devteam > data_manager_fetch_ncbi_taxonomy
changeset 3:f7b443a73374 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 1bcd553f81064957d5786302361675c29ed58a8d"
| author | iuc |
|---|---|
| date | Mon, 06 Jul 2020 23:29:44 +0000 |
| parents | 3d628f1e1bef |
| children | cef5c909ccb8 |
| files | data_manager/data_manager.py data_manager/ncbi_taxonomy_fetcher.xml test-data/ncbi_taxonomy.loc test-data/taxonomy.json tool-data/ncbi_taxonomy.loc.sample tool_data_table_conf.xml.test |
| diffstat | 6 files changed, 35 insertions(+), 7 deletions(-) [+] |
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--- a/data_manager/data_manager.py Tue Apr 28 07:57:37 2020 +0000 +++ b/data_manager/data_manager.py Mon Jul 06 23:29:44 2020 +0000 @@ -5,12 +5,7 @@ import shutil import tarfile import zipfile -try: - # For Python 3.0 and later - from urllib.request import Request, urlopen -except ImportError: - # Fall back to Python 2 imports - from urllib2 import Request, urlopen +from urllib.request import Request, urlopen def url_download(url, workdir):
--- a/data_manager/ncbi_taxonomy_fetcher.xml Tue Apr 28 07:57:37 2020 +0000 +++ b/data_manager/ncbi_taxonomy_fetcher.xml Mon Jul 06 23:29:44 2020 +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="1.0.2"> <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}' @@ -19,4 +22,15 @@ <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> + </tests> + <help> + Download a taxonomy dump from a provided URL. + The default URL is the latest dump from NCBI taxonomy. + </help> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ncbi_taxonomy.loc Mon Jul 06 23:29:44 2020 +0000 @@ -0,0 +1,5 @@ +# Tab separated fields where +# value is unique key +# name is descriptive name +# path is path to directory containing names.dmp and nodes.dmp files +#value name path
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/taxonomy.json Mon Jul 06 23:29:44 2020 +0000 @@ -0,0 +1,1 @@ +{"data_tables": {"ncbi_taxonomy": {"name": "tax_name", "path": ".", "value": "tax_name"}}} \ No newline at end of file
--- a/tool-data/ncbi_taxonomy.loc.sample Tue Apr 28 07:57:37 2020 +0000 +++ b/tool-data/ncbi_taxonomy.loc.sample Mon Jul 06 23:29:44 2020 +0000 @@ -0,0 +1,5 @@ +# Tab separated fields where +# value is unique key +# name is descriptive name +# path is path to directory containing names.dmp and nodes.dmp files +#value name path
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Mon Jul 06 23:29:44 2020 +0000 @@ -0,0 +1,8 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of taxonomy data downloaded from NCBI --> + <table name="ncbi_taxonomy" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/test-data/ncbi_taxonomy.loc" /> + </table> +</tables>