Mercurial > repos > devteam > data_manager_fetch_genome_dbkeys_all_fasta
changeset 10:4a82d1157b14 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 57d05675396f0b44265fb4dbc8f9f891c6073219
| author | iuc |
|---|---|
| date | Thu, 05 Dec 2024 06:49:22 +0000 |
| parents | 4d3eff1bc421 |
| children | |
| files | data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml data_manager_conf.xml test-data/fetch_data_manager.1.data_manager_json test-data/fetch_data_manager.2.data_manager_json test-data/phiX174.data_manager_json |
| diffstat | 6 files changed, 27 insertions(+), 13 deletions(-) [+] |
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--- a/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py Thu Dec 05 17:10:39 2019 -0500 +++ b/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py Thu Dec 05 06:49:22 2024 +0000 @@ -279,6 +279,8 @@ target_directory=target_directory, dbkey=dbkey, dbkey_name=dbkey_name, + sequence_id=sequence_id, + sequence_name=sequence_name, fasta_filename=fasta_filename) _add_data_table_entry(data_manager_dict, data_table_entry=dict(value=sequence_id, dbkey=dbkey, name=sequence_name, path=os.path.basename(fasta_filename)), @@ -286,11 +288,11 @@ return fasta_filename -def add_dbkey_to_table(data_manager_dict, target_directory, dbkey, dbkey_name, fasta_filename): +def add_dbkey_to_table(data_manager_dict, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, fasta_filename): # do len calc here - len_base_name = "%s.len" % (dbkey) + len_base_name = f"{sequence_id}.len" compute_fasta_length(fasta_filename, os.path.join(target_directory, len_base_name), keep_first_word=True) - dbkey_dict = dict(value=dbkey, name=dbkey_name, len_path=len_base_name) + dbkey_dict = dict(dbkey=dbkey, value=sequence_id, name=sequence_name, len_path=len_base_name) _add_data_table_entry(data_manager_dict, data_table_entry=dbkey_dict, data_table_name='__dbkeys__') @@ -345,7 +347,7 @@ if isinstance(input_filename, list): fasta_readers = [get_stream_reader(open(filename, 'rb'), tmp_dir) for filename in input_filename] else: - fasta_readers = get_stream_reader(open(input_filename), tmp_dir) + fasta_readers = get_stream_reader(open(input_filename, 'rb'), tmp_dir) return fasta_readers for data_table_name, data_table_entry in data_table_entries: if data_table_entry:
--- a/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml Thu Dec 05 17:10:39 2019 -0500 +++ b/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml Thu Dec 05 06:49:22 2024 +0000 @@ -1,7 +1,7 @@ -<tool id="data_manager_fetch_genome_all_fasta_dbkey" name="Create DBKey and Reference Genome" version="0.0.4" tool_type="manage_data" profile="19.01"> +<tool id="data_manager_fetch_genome_all_fasta_dbkey" name="Create DBKey and Reference Genome" version="0.0.5" tool_type="manage_data" profile="23.0"> <description>fetching</description> <requirements> - <requirement type="package" version="3.7">python</requirement> + <requirement type="package" version="3.11">python</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ python '$__tool_directory__/data_manager_fetch_genome_all_fasta_dbkeys.py' @@ -83,12 +83,23 @@ <test> <param name="dbkey" value="phiX174"/> <param name="dbkey_source|dbkey_source_selector" value="new"/> + <param name="dbkey_source|dbkey_name" value="phiX174 dbkey name"/> <param name="sequence_name" value="phiX174 sequence name"/> - <param name="sequence_id" value="phix174"/> <param name="reference_source_selector" value="history"/> <param name="input_fasta" value="phiX174.fasta"/> <param name="sort_selector" value="as_is"/> - <output name="out_file" file="phiX174.data_manager_json"/> + <output name="out_file" file="fetch_data_manager.1.data_manager_json"/> + </test> + <test> + <param name="dbkey" value="phiX174"/> + <param name="dbkey_source|dbkey_source_selector" value="new"/> + <param name="dbkey_source|dbkey_name" value="phiX174 dbkey name"/> + <param name="sequence_name" value="phiX174 Variant 1 sequence name"/> + <param name="sequence_id" value="phiX174Variant1"/> + <param name="reference_source_selector" value="history"/> + <param name="input_fasta" value="phiX174.fasta"/> + <param name="sort_selector" value="as_is"/> + <output name="out_file" file="fetch_data_manager.2.data_manager_json"/> </test> </tests> <help>
--- a/data_manager_conf.xml Thu Dec 05 17:10:39 2019 -0500 +++ b/data_manager_conf.xml Thu Dec 05 06:49:22 2024 +0000 @@ -10,9 +10,9 @@ <column name="path" output_ref="out_file" > <move type="file"> <source>${path}</source> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/seq/${path}</target> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">genomes/${dbkey}/seq/${path}</target> </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/seq/${path}</value_translation> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/genomes/${dbkey}/seq/${path}</value_translation> <value_translation type="function">abspath</value_translation> </column> </output> @@ -24,9 +24,9 @@ <column name="len_path" output_ref="out_file" > <move type="file"> <source>${len_path}</source> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${value}/len/${len_path}</target> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">genomes/${dbkey}/len/${len_path}</target> </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${value}/len/${len_path}</value_translation> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/genomes/${dbkey}/len/${len_path}</value_translation> <value_translation type="function">abspath</value_translation> </column> </output>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fetch_data_manager.1.data_manager_json Thu Dec 05 06:49:22 2024 +0000 @@ -0,0 +1,1 @@ +{"data_tables": {"__dbkeys__": [{"dbkey": "phiX174", "len_path": "phiX174.len", "name": "phiX174 sequence name", "value": "phiX174"}], "all_fasta": [{"dbkey": "phiX174", "name": "phiX174 sequence name", "path": "phiX174.fa", "value": "phiX174"}]}} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fetch_data_manager.2.data_manager_json Thu Dec 05 06:49:22 2024 +0000 @@ -0,0 +1,1 @@ +{"data_tables": {"__dbkeys__": [{"dbkey": "phiX174", "len_path": "phiX174Variant1.len", "name": "phiX174 Variant 1 sequence name", "value": "phiX174Variant1"}], "all_fasta": [{"dbkey": "phiX174", "name": "phiX174 Variant 1 sequence name", "path": "phiX174Variant1.fa", "value": "phiX174Variant1"}]}} \ No newline at end of file
--- a/test-data/phiX174.data_manager_json Thu Dec 05 17:10:39 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -{"data_tables": {"__dbkeys__": [{"len_path": "phiX174.len", "name": "phiX174", "value": "phiX174"}], "all_fasta": [{"dbkey": "phiX174", "name": "phiX174 sequence name", "path": "phix174.fa", "value": "phix174"}]}} \ No newline at end of file