Mercurial > repos > iuc > data_manager_fetch_busco
changeset 0:53eec20e8fb6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2896dcfd180800d00ea413a59264ef8b11788b8e
| author | iuc |
|---|---|
| date | Thu, 19 Oct 2017 15:56:20 -0400 |
| parents | |
| children | 15b97817550a |
| files | data_manager/busco_fetcher.xml data_manager/data_manager.py data_manager_conf.xml tool-data/busco.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 5 files changed, 169 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/busco_fetcher.xml Thu Oct 19 15:56:20 2017 -0400 @@ -0,0 +1,62 @@ +<?xml version="1.0"?> +<tool id="busco_fetcher" name="Busco" tool_type="manage_data" version="1.0.0"> + <description>dataset dowloader</description> + <command detect_errors="exit_code"> + <![CDATA[ + python '$__tool_directory__/data_manager.py' --out '${out_file}' + --url 'http://busco.ezlab.org/datasets/${dataset}.tar.gz' + --name '${dataset}' + ]]> + </command> + <inputs> + <param name="dataset" type="select" label="Choose dataset to download"> + <option value="eukaryota_odb9">eukaryota</option> + <option value="metazoa_odb9">metazoa</option> + <option value="nematoda_odb9">nematoda</option> + <option value="arthropoda_odb9">arthropoda</option> + <option value="insecta_odb9">insecta</option> + <option value="endopterygota_odb9">endopterygota</option> + <option value="hymenoptera_odb9">hymenoptera</option> + <option value="diptera_odb9">diptera</option> + <option value="vertebrata_odb9">vertebrata</option> + <option value="actinopterygii_odb9">actinopterygii</option> + <option value="tetrapoda_odb9">tetrapoda</option> + <option value="aves_odb9">aves</option> + <option value="mammalia_odb9">mammalia</option> + <option value="euarchontoglires_odb9">euarchontoglires</option> + <option value="laurasiatheria_odb9">laurasiatheria</option> + <option value="embryophyta_odb9">embryophyta</option> + <option value="protists_ensembl">protists</option> + <option value="alveolata_stramenophiles_ensembl">alveolata</option> + <option value="fungi_odb9">fungi</option> + <option value="microsporidia_odb9">microsporidia</option> + <option value="dikarya_odb9">dikarya</option> + <option value="ascomycota_odb9">ascomycota</option> + <option value="pezizomycotina_odb9">pezizomycotina</option> + <option value="eurotiomycetes_odb9">eurotiomycetes</option> + <option value="sordariomyceta_odb9">sordariomyceta</option> + <option value="saccharomyceta_odb9">saccharomyceta</option> + <option value="saccharomycetales_odb9">saccharomycetales</option> + <option value="basidiomycota_odb9">basidiomycota</option> + <option value="bacteria_odb9">bacteria</option> + <option value="proteobacteria_odb9">proteobacteria</option> + <option value="rhizobiales_odb9">rhizobiales</option> + <option value="betaproteobacteria_odb9">betaproteobacteria</option> + <option value="gammaproteobacteria_odb9">gammaproteobacteria</option> + <option value="enterobacteriales_odb9">enterobacteriales</option> + <option value="deltaepsilonsub_odb9">deltaepsilonsub</option> + <option value="actinobacteria_odb9">actinobacteria</option> + <option value="cyanobacteria_odb9">cyanobacteria</option> + <option value="firmicutes_odb9">firmicutes</option> + <option value="clostridia_odb9">clostridia</option> + <option value="lactobacillales_odb9">lactobacillales</option> + <option value="bacillales_odb9">bacillales</option> + <option value="bacteroidetes_odb9">bacteroidetes</option> + <option value="spirochaetes_odb9">spirochaetes</option> + <option value="tenericutes_odb9">tenericutes</option> + </param> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json" /> + </outputs> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager.py Thu Oct 19 15:56:20 2017 -0400 @@ -0,0 +1,69 @@ +import argparse +import datetime +import json +import os +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 + + +def url_download(url, workdir): + file_path = os.path.join(workdir, 'download.dat') + if not os.path.exists(workdir): + os.makedirs(workdir) + src = None + dst = None + try: + req = Request(url) + src = urlopen(req) + with open(file_path, 'wb') as dst: + while True: + chunk = src.read(2**10) + if chunk: + dst.write(chunk) + else: + break + finally: + if src: + src.close() + if tarfile.is_tarfile(file_path): + fh = tarfile.open(file_path, 'r:*') + elif zipfile.is_zipfile(file_path): + fh = zipfile.ZipFile(file_path, 'r') + else: + return + fh.extractall(workdir) + os.remove(file_path) + + +def main(args): + workdir = os.path.join(os.getcwd(), 'busco') + url_download(args.url, workdir) + data_manager_entry = {} + data_manager_entry['value'] = args.name.lower() + data_manager_entry['name'] = args.name + data_manager_entry['path'] = '.' + data_manager_json = dict(data_tables=dict(busco=data_manager_entry)) + params = json.loads(open(args.output).read()) + target_directory = params['output_data'][0]['extra_files_path'] + os.mkdir(target_directory) + output_path = os.path.abspath(os.path.join(os.getcwd(), 'busco')) + for filename in os.listdir(workdir): + shutil.move(os.path.join(output_path, filename), target_directory) + file(args.output, 'w').write(json.dumps(data_manager_json)) + + +if __name__ == '__main__': + parser = argparse.ArgumentParser(description='Create data manager json.') + parser.add_argument('--out', dest='output', action='store', help='JSON filename') + parser.add_argument('--name', dest='name', action='store', default=str(datetime.date.today()), help='Data table entry unique ID') + parser.add_argument('--url', dest='url', action='store', help='Download URL') + args = parser.parse_args() + + main(args)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Thu Oct 19 15:56:20 2017 -0400 @@ -0,0 +1,18 @@ +<?xml version="1.0"?> +<data_managers> + <data_manager tool_file="data_manager/busco_fetcher.xml" id="busco_fetcher" version="1.0.0"> + <data_table name="busco"> + <output> + <column name="value" /> + <column name="name" /> + <column name="path" output_ref="out_file"> + <move type="directory" relativize_symlinks="True"> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">busco/${value}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/busco/${value}</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + </data_manager> +</data_managers>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/busco.loc.sample Thu Oct 19 15:56:20 2017 -0400 @@ -0,0 +1,13 @@ +# This is a sample file distributed with Galaxy that is used to define a +# list of busco datasets, using four columns tab separated: +# +# <unique_build_id> <display_name> <genome_fasta_file_path> +# +# Datasets can be retrieved from http://busco.ezlab.org/frame_wget.html +# +# "/some/path/arthropoda/" would be the last column in the line +# If this were for the mm10 mouse genome, the resulting entry would look like: +# +#arthropoda_2.0 arthropoda_2.0 /some/path/arthropoda/ +# +#
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Oct 19 15:56:20 2017 -0400 @@ -0,0 +1,7 @@ +<?xml version="1.0"?> +<tables> + <table name="busco" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/busco.loc" /> + </table> +</tables>