| Next changeset 1:1ff9996995ee (2020-11-22) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" |
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added:
data_manager/data_manager.py data_manager/data_manager_mitos.xml data_manager_conf.xml test-data/mitos.loc test-data/mitos_refseq39.json tool-data/mitos.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r 26a6f95e82c8 data_manager/data_manager.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager.py Fri Mar 27 17:50:23 2020 -0400 |
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| @@ -0,0 +1,91 @@ +import argparse +import json +import os +import shutil +import tarfile +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 + +ZENODO = { + "mitos": "2683856", + "mitos2": "3685310" +} +NAMES = { + "mitos1-refdata": "RefSeq39 + MiTFi tRNA models", + "refseq39": "RefSeq39 (equivalent to MITOS1 data)", + "refseq63m": "RefSeq63 Metazoa", + "refseq63f": "RefSeq63 Fungi", + "refseq63o": "RefSeq63 Opisthokonta", + "refseq89m": "RefSeq89 Metazoa", + "refseq89f": "RefSeq89 Fungi", + "refseq89o": "RefSeq89 Opisthokonta" +} + + +def url_download(tpe, db, workdir): + """ + download http://ab.inf.uni-tuebingen.de/data/software/megan6/download/FNAME + to workdir + and unzip + + return the name of the resulting dir + """ + tarfname = os.path.join(workdir, db + ".tar.bz") + if not os.path.exists(workdir): + os.makedirs(workdir) + src = None + dst = None + try: + req = Request("https://zenodo.org/record/{zenodoid}/files/{db}.tar.bz2?download=1".format(zenodoid=ZENODO[tpe], db=db)) + src = urlopen(req) + with open(tarfname, 'wb') as dst: + while True: + chunk = src.read(2**10) + if chunk: + dst.write(chunk) + else: + break + finally: + if src: + src.close() + with tarfile.open(tarfname, "r:bz2") as tar: + dirname = tar.getnames()[0] + tar.extractall(workdir) + os.remove(tarfname) + return dirname + + +def main(tpe, db, outjson): + workdir = os.getcwd() + + path = url_download(tpe, db, workdir) + + data_manager_entry = {} + data_manager_entry['value'] = db + data_manager_entry['name'] = NAMES[db] + data_manager_entry['type'] = tpe + data_manager_entry['path'] = path + data_manager_json = dict(data_tables=dict(mitos=data_manager_entry)) + + with open(outjson) as f: + params = json.loads(f.read()) + target_directory = params['output_data'][0]['extra_files_path'] + os.mkdir(target_directory) + # output_path = os.path.abspath(os.path.join(os.getcwd(), 'mitos')) + shutil.move(os.path.join(workdir, path), target_directory) + with open(outjson, 'w') as fh: + fh.write(json.dumps(data_manager_json, sort_keys=True)) + + +if __name__ == '__main__': + parser = argparse.ArgumentParser(description='Create data manager json.') + parser.add_argument('--out', action='store', help='JSON filename') + parser.add_argument('--type', action='store', help='mitos version') + parser.add_argument('--db', action='store', help='db name') + args = parser.parse_args() + + main(args.type, args.db, args.out) |
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| diff -r 000000000000 -r 26a6f95e82c8 data_manager/data_manager_mitos.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_mitos.xml Fri Mar 27 17:50:23 2020 -0400 |
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| @@ -0,0 +1,86 @@ +<?xml version="1.0"?> +<tool id="data_manager_mitos" name="MITOS" tool_type="manage_data" version="0.0.1"> + <description>reference data downloader</description> + <requirements> + <requirement type="package" version="3.7">python</requirement> + </requirements> + <command detect_errors="exit_code"> + <![CDATA[ + python '$__tool_directory__/data_manager.py' + --out '${out_file}' + --type '$type_cond.type_select' + --db '$type_cond.database' + ]]> + </command> + <inputs> + <conditional name="type_cond"> + <param name="type_select" type="select" label="MITOS version"> + <option value="mitos">MITOS</option> + <option value="mitos2">MITOS2</option> + </param> + <when value="mitos"> + <param name="database" type="select" label="Reference data version"> + <option value="mitos1-refdata">RefSeq39 + MiTFi tRNA models</option> + </param> + </when> + <when value="mitos2"> + <param name="database" type="select" label="Reference data version"> + <option value="refseq39">RefSeq39 (equivalent to MITOS1 data)</option> + <option value="refseq63m">RefSeq63 Metazoa</option> + <option value="refseq63f">RefSeq63 Fungi</option> + <option value="refseq63o">RefSeq63 Opisthokonta</option> + <option value="refseq89m">RefSeq89 Metazoa</option> + <option value="refseq89f">RefSeq89 Fungi</option> + <option value="refseq89o">RefSeq89 Opisthokonta</option> + </param> + </when> + </conditional> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json" /> + </outputs> + <tests> + <test> + <conditional name="type_cond"> + <param name="type_select" value="mitos"/> + <param name="database" value="mitos1-refdata"/> + </conditional> + <output name="out_file" file="mitos_refseq39.json"/> + </test> + </tests> + <help> +This data manager downloads MITOS and MITOS2 reference data for use in Galaxy. + +For MITOS the reference data includes + +- protein data bases derived from RefSeq release 39 (see Bernt et al. 2012) +- covariance models for tRNAs and rRNAs as described in Jühling et al 2012 + +Data is downloaded from https://zenodo.org/record/2683856. + +For MITOS2 the reference data sets are available for three different taxons + +- Metazoa +- Fungi +- Opisthokonta + +these have been computed for RefSeq release 63 and 89. In addition the reference data +for MITOS1 has been converted to be usable in MITOS2. +contains + +The reference data sets contain: + +- protein data bases derived from the corresponding RefSeq release Donath et al. 2019 +- covariance models computed for the data in the RefSeq releas based on the MITOS1 models +- in addition for Metazoa Release 63 also hidden markov models are available as described in Al Arab et al. 2017 + +Data is downloaded from https://zenodo.org/record/3685310. + </help> + <citations> + <citation type="doi">10.1016/j.ympev.2012.08.023</citation> + <citation type="doi">10.1093/nar/gkr1131</citation> + <citation type="doi">10.1016/j.ympev.2016.09.024</citation> + <citation type="doi">10.1093/nar/gkz833</citation> + </citations> +</tool> + |
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| diff -r 000000000000 -r 26a6f95e82c8 data_manager_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Fri Mar 27 17:50:23 2020 -0400 |
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| @@ -0,0 +1,20 @@ +<?xml version="1.0"?> +<data_managers> + <data_manager tool_file="data_manager/data_manager_mitos.xml" id="mitos_fetcher" version="0.0.1"> + <data_table name="mitos"> + <output> + <column name="value" /> + <column name="name" /> + <column name="type" /> + <column name="path" output_ref="out_file"> + <move type="directory" relativize_symlinks="True"> + <source>${path}</source> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">mitos/${path}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/mitos/${path}</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + </data_manager> +</data_managers> |
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| diff -r 000000000000 -r 26a6f95e82c8 test-data/mitos.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mitos.loc Fri Mar 27 17:50:23 2020 -0400 |
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| @@ -0,0 +1,4 @@ +mitos1-refdata RefSeq39 + MiTFi tRNA models mitos /tmp/tmpbtwefN/tmpiplugx/tmpydhEfm/database/data_manager_tool-datacoy8bz/mitos/mitos1-refdata +mitos1-refdata RefSeq39 + MiTFi tRNA models mitos /tmp/tmpGIPfAb/tmpfKzrSO/tmpOaxm5C/database/data_manager_tool-data6ViNKD/mitos/mitos1-refdata +mitos1-refdata RefSeq39 + MiTFi tRNA models mitos /tmp/tmpoaKkwC/tmprSa8eg/tmpT61Fpn/database/data_manager_tool-data0wohya/mitos/mitos1-refdata +mitos1-refdata RefSeq39 + MiTFi tRNA models mitos /tmp/tmpo_lErk/tmpzfa6qz/tmpCY3yzt/database/data_manager_tool-dataCMEecR/mitos/mitos1-refdata |
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| diff -r 000000000000 -r 26a6f95e82c8 test-data/mitos_refseq39.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mitos_refseq39.json Fri Mar 27 17:50:23 2020 -0400 |
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| @@ -0,0 +1,1 @@ +{"data_tables": {"mitos": {"name": "RefSeq39 + MiTFi tRNA models", "path": "mitos1-refdata", "type": "mitos", "value": "mitos1-refdata"}}} \ No newline at end of file |
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| diff -r 000000000000 -r 26a6f95e82c8 tool-data/mitos.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/mitos.loc.sample Fri Mar 27 17:50:23 2020 -0400 |
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| @@ -0,0 +1,8 @@ +# consists of 4 tab separated columns: +# - value identifier +# - name the name shown in the tool form +# - type mitos/mitos2 +# - path the directory containing the reference data +# +# example: +# mitos1-refdata RefSeq39 + MiTFi tRNA models mitos /tmp/tmpSp4v2Y/tmpR7DRNf/tmp53wbgs/database/data_manager_tool-dataWhw0Ns/mitos/mitos1-refdata |
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| diff -r 000000000000 -r 26a6f95e82c8 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri Mar 27 17:50:23 2020 -0400 |
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| @@ -0,0 +1,8 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of data downloaded for the megan tools --> + <table name="mitos" comment_char="#"> + <columns>value, name, type, path</columns> + <file path="tool-data/mitos.loc" /> + </table> +</tables> |
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| diff -r 000000000000 -r 26a6f95e82c8 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Fri Mar 27 17:50:23 2020 -0400 |
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| @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of indexes in the Bowtie2 mapper format --> + <table name="mitos" comment_char="#"> + <columns>value, name, type, path</columns> + <file path="${__HERE__}/test-data/mitos.loc" /> + </table> +</tables> |