Mercurial > repos > bebatut > data_manager_metaphlan2_database_downloader
changeset 9:a4b5d0fcd2b2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan2_database_downloader commit b'3deaa3adf381c1f3f6134ef6a36074d443f7e3fc\n'-dirty
| author | bebatut |
|---|---|
| date | Tue, 28 Feb 2017 07:55:10 -0500 |
| parents | dbfade666d42 |
| children | e131ec0db07b |
| files | data_manager/data_manager_metaphlan2_download.py shed.yml tool-data/metaphlan2_database.loc.sample |
| diffstat | 3 files changed, 2 insertions(+), 18 deletions(-) [+] |
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--- a/data_manager/data_manager_metaphlan2_download.py Tue Feb 21 08:49:45 2017 -0500 +++ b/data_manager/data_manager_metaphlan2_download.py Tue Feb 28 07:55:10 2017 -0500 @@ -95,9 +95,7 @@ """ today = datetime.date.today() - db_target_dir = os.path.join(target_dir, build) - os.makedirs(db_target_dir) - cmd = "download_metaphlan2_db.py --output %s" % (db_target_dir) + cmd = "download_metaphlan2_db.py --output %s" % (target_dir) subprocess.check_call(cmd, shell=True) add_data_table_entry( data_tables, @@ -117,7 +115,6 @@ parser.add_option('--database', help="Database name") options, args = parser.parse_args() print("args : %s" % args) - # Check for JSON file if len(args) != 1:
--- a/shed.yml Tue Feb 21 08:49:45 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -name: data_manager_metaphlan2_database_downloader -owner: bebatut -description: "MetaPhlAn for Metagenomic Phylogenetic Analysis" -homepage_url: "https://bitbucket.org/biobakery/metaphlan2/" -long_description: | - MetaPhlAn is a computational tool for profiling the composition of microbial - communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun - sequencing data with species level resolution -remote_repository_url: "https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_metaphlan2_database_downloader" -type: unrestricted -categories: -- Metagenomics -- Data Managers \ No newline at end of file
--- a/tool-data/metaphlan2_database.loc.sample Tue Feb 21 08:49:45 2017 -0500 +++ b/tool-data/metaphlan2_database.loc.sample Tue Feb 28 07:55:10 2017 -0500 @@ -1,4 +1,4 @@ #This is a sample file distributed with Galaxy that enables tools #to use a directory of metagenomics files. #file has this format (white space characters are TAB characters) -#02_16_2014 MetaPhlAn2 clade-specific marker genes db_v20 /path/to/data \ No newline at end of file +#02_16_2014 MetaPhlAn2 clade-specific marker genes db_v20 /path/to/data