Mercurial > repos > devteam > data_manager_twobit_builder
changeset 8:4a7740ee2892 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
author | iuc |
---|---|
date | Sun, 16 Apr 2023 08:28:51 +0000 |
parents | 94bffa4fdedc |
children | |
files | data_manager/twobit_builder.py data_manager/twobit_builder.xml |
diffstat | 2 files changed, 5 insertions(+), 12 deletions(-) [+] |
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--- a/data_manager/twobit_builder.py Sun Apr 16 08:15:04 2023 +0000 +++ b/data_manager/twobit_builder.py Sun Apr 16 08:28:51 2023 +0000 @@ -26,14 +26,11 @@ return sequence_id, sequence_name -def build_twobit(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, long): +def build_twobit(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name): twobit_base_name = "%s.2bit" % (sequence_id) twobit_filename = os.path.join(target_directory, twobit_base_name) - args = ['faToTwoBit'] - if long: - args.append('-long') - args.extend([fasta_filename, twobit_filename]) + args = ['faToTwoBit', fasta_filename, twobit_filename] tmp_stderr = tempfile.NamedTemporaryFile(prefix="tmp-data-manager-twobit-builder-stderr") proc = subprocess.Popen(args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno()) return_code = proc.wait() @@ -45,7 +42,7 @@ chunk = tmp_stderr.read(CHUNK_SIZE) if not chunk: break - sys.stderr.write(chunk.decode('utf-8')) + sys.stderr.write(chunk) sys.exit(return_code) tmp_stderr.close() # lastz_seqs @@ -74,8 +71,6 @@ parser.add_option('-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename') parser.add_option('-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey') parser.add_option('-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description') - parser.add_option('-l', '--long', dest='long', action="store_true", default=False, help='For big genomes you need to pass the -long option.') - (options, args) = parser.parse_args() filename = args[0] @@ -95,7 +90,7 @@ sequence_id, sequence_name = get_id_name(params, dbkey=dbkey, fasta_description=options.fasta_description) # build the index - build_twobit(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, options.long) + build_twobit(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name) # save info to json file with open(filename, 'w') as fh:
--- a/data_manager/twobit_builder.xml Sun Apr 16 08:15:04 2023 +0000 +++ b/data_manager/twobit_builder.xml Sun Apr 16 08:28:51 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="twobit_builder_data_manager" name="TwoBit" tool_type="manage_data" version="0.0.5" profile="19.05"> +<tool id="twobit_builder_data_manager" name="TwoBit" tool_type="manage_data" version="0.0.4" profile="19.05"> <requirements> <requirement type="package" version="377">ucsc-fatotwobit</requirement> <requirement type="package" version="3.7">python</requirement> @@ -7,7 +7,6 @@ <command detect_errors="exit_code"><![CDATA[ python '$__tool_directory__/twobit_builder.py' '${out_file}' -$long --fasta_filename '${all_fasta_source.fields.path}' --fasta_dbkey '${all_fasta_source.fields.dbkey}' --fasta_description '${all_fasta_source.fields.name}' @@ -18,7 +17,6 @@ </param> <param name="sequence_name" type="text" value="" label="Name of sequence" /> <param name="sequence_id" type="text" value="" label="ID for sequence" /> - <param argument="--long" type="boolean" truevalue="--long" falsevalue="" label="Use the -long option for very big genomes." /> </inputs> <outputs> <data name="out_file" format="data_manager_json"/>