Mercurial > repos > mbernt > data_manager_mitos
changeset 2:ae5ddc5a6511 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit b63133897598f2881de7bad1f18fcd69d7d7e9df-dirty"
author | mbernt |
---|---|
date | Wed, 15 Dec 2021 11:01:00 +0000 |
parents | 7548eaf95697 |
children | f5d4f9564759 |
files | data_manager/.data_manager_mitos.xml.swp data_manager/data_manager.py data_manager/data_manager_mitos.xml data_manager_conf.xml test-data/mitos2_refseq63.json test-data/mitos_refseq39.json |
diffstat | 6 files changed, 25 insertions(+), 10 deletions(-) [+] |
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--- a/data_manager/data_manager.py Sat Mar 21 15:32:06 2020 +0000 +++ b/data_manager/data_manager.py Wed Dec 15 11:01:00 2021 +0000 @@ -12,7 +12,7 @@ ZENODO = { "mitos": "2683856", - "mitos2": "3685310" + "mitos2": "4284483" } NAMES = { "mitos1-refdata": "RefSeq39 + MiTFi tRNA models", @@ -53,11 +53,10 @@ if src: src.close() with tarfile.open(tarfname, "r:bz2") as tar: + dirname = tar.getnames()[0] tar.extractall(workdir) os.remove(tarfname) - unzipped = os.listdir(workdir) - assert len(unzipped) == 1 - return unzipped[0] + return dirname def main(tpe, db, outjson): @@ -72,13 +71,14 @@ data_manager_entry['path'] = path data_manager_json = dict(data_tables=dict(mitos=data_manager_entry)) - params = json.loads(open(outjson).read()) + with open(outjson) as fh: + params = json.load(fh) 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)) + json.dump(data_manager_json, fh, sort_keys=True) if __name__ == '__main__':
--- a/data_manager/data_manager_mitos.xml Sat Mar 21 15:32:06 2020 +0000 +++ b/data_manager/data_manager_mitos.xml Wed Dec 15 11:01:00 2021 +0000 @@ -1,6 +1,9 @@ <?xml version="1.0"?> <tool id="data_manager_mitos" name="MITOS" tool_type="manage_data" version="0.0.2"> - <description>reference data downloader</description> + <description>reference data downloader blah</description> + <requirements> + <requirement type="package" version="3.7">python</requirement> + </requirements> <command detect_errors="exit_code"> <![CDATA[ python '$__tool_directory__/data_manager.py' @@ -22,13 +25,13 @@ </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> + <option value="refseq39">RefSeq39 (equivalent to MITOS1 data)</option> </param> </when> </conditional> @@ -44,6 +47,13 @@ </conditional> <output name="out_file" file="mitos_refseq39.json"/> </test> + <test> + <conditional name="type_cond"> + <param name="type_select" value="mitos2"/> + <param name="database" value="refseq63m"/> + </conditional> + <output name="out_file" file="mitos2_refseq63.json"/> + </test> </tests> <help> This data manager downloads MITOS and MITOS2 reference data for use in Galaxy. @@ -53,6 +63,8 @@ - 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 @@ -68,6 +80,8 @@ - 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/4284483. </help> <citations> <citation type="doi">10.1016/j.ympev.2012.08.023</citation>
--- a/data_manager_conf.xml Sat Mar 21 15:32:06 2020 +0000 +++ b/data_manager_conf.xml Wed Dec 15 11:01:00 2021 +0000 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <data_managers> - <data_manager tool_file="data_manager/data_manager_mitos.xml" id="mitos_fetcher" version="0.0.2"> + <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" />
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mitos2_refseq63.json Wed Dec 15 11:01:00 2021 +0000 @@ -0,0 +1,1 @@ +{"data_tables": {"mitos": {"name": "RefSeq63 Metazoa", "path": "refseq63m", "type": "mitos2", "value": "refseq63m"}}} \ No newline at end of file
--- a/test-data/mitos_refseq39.json Sat Mar 21 15:32:06 2020 +0000 +++ b/test-data/mitos_refseq39.json Wed Dec 15 11:01:00 2021 +0000 @@ -1,1 +1,1 @@ -{"data_tables": {"mitos": {"path": "mitos1-refdata", "type": "mitos", "name": "RefSeq39 + MiTFi tRNA models", "value": "mitos1-refdata"}}} \ No newline at end of file +{"data_tables": {"mitos": {"name": "RefSeq39 + MiTFi tRNA models", "path": "mitos1-refdata", "type": "mitos", "value": "mitos1-refdata"}}} \ No newline at end of file