Mercurial > repos > bebatut > data_manager_sortmerna_database_downloader
changeset 9:afe988ad1e1d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sortmerna_database_downloader commit d10a3522c8a776162c5f3936c5e820bb3fa5c3ca-dirty
| author | bebatut |
|---|---|
| date | Mon, 12 Jun 2017 10:05:24 -0400 |
| parents | 240907f60646 |
| children | d2a91cfb9eef |
| files | data_manager/data_manager_sortmerna_download.py data_manager/data_manager_sortmerna_download.xml data_manager_conf.xml |
| diffstat | 3 files changed, 12 insertions(+), 26 deletions(-) [+] |
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--- a/data_manager/data_manager_sortmerna_download.py Mon Jun 12 09:35:57 2017 -0400 +++ b/data_manager/data_manager_sortmerna_download.py Mon Jun 12 10:05:24 2017 -0400 @@ -126,17 +126,19 @@ if not filename.endswith("fasta"): continue input_filepath = os.path.join(file_dir, filename) - output_filepath = os.path.join(target_dir, filename) + output_dir = os.path.join(target_dir, filename) + os.makedir(output_dir) + db_name = os.path.splitext(filename)[0] + fasta_filepath = os.path.join(output_dir, "%s.fasta" % db_name) + indexed_filepath = os.path.join(output_dir, db_name) # Move file - os.rename(input_filepath, output_filepath) + os.rename(input_filepath, fasta_filepath) # Index the file with indexdb_rna - indexed_filepath = os.path.splitext(output_filepath)[0] command = "indexdb_rna --ref %s,%s" % ( - output_filepath, + fasta_filepath, indexed_filepath) process = subprocess.call(command, shell=True ) # Add entry in the data table - db_name = os.path.splitext(filename)[0] add_data_table_entry( data_tables, "rRNA_databases",
--- a/data_manager/data_manager_sortmerna_download.xml Mon Jun 12 09:35:57 2017 -0400 +++ b/data_manager/data_manager_sortmerna_download.xml Mon Jun 12 10:05:24 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="data_manager_sortmerna_download" name="Download SortMeRNA" version="@VERSION@.1" tool_type="manage_data"> +<tool id="data_manager_sortmerna_download" name="Download SortMeRNA" version="@VERSION@.2" tool_type="manage_data"> <description>reference databases</description> <macros> <import>macros.xml</import>
--- a/data_manager_conf.xml Mon Jun 12 09:35:57 2017 -0400 +++ b/data_manager_conf.xml Mon Jun 12 10:05:24 2017 -0400 @@ -6,27 +6,11 @@ <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool --> <column name="name" /> <!-- columns that are going to be specified by the Data Manager Tool --> <column name="path" output_ref="out_file" > - <move type="file"> - <source>${path}.fasta</source> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">rRNA_databases/${name}.fasta</target> - </move> - <move type="file"> - <source>${path}.stats</source> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">rRNA_databases/${name}.stats</target> + <move type="directory"> + <source>${path}</source> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">rRNA_databases/${name}</target> </move> - <move type="file"> - <source>${path}.pos_0.dat</source> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">rRNA_databases/${name}.pos_0.dat</target> - </move> - <move type="file"> - <source>${path}.kmer_0.dat</source> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">rRNA_databases/${name}.kmer_0.dat</target> - </move> - <move type="file"> - <source>${path}.bursttrie_0.dat</source> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">rRNA_databases/${name}.bursttrie_0.dat</target> - </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/rRNA_databases/${name}.fasta</value_translation> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/rRNA_databases/${name}/${name}.fasta</value_translation> <value_translation type="function">abspath</value_translation> </column> </output>