Mercurial > repos > iuc > data_manager_mitos
changeset 1:58bcd38cecb6 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 2db6284f6077d80d05227180a809b921b4975c60"
| author | iuc |
|---|---|
| date | Sun, 22 Nov 2020 18:02:48 +0000 |
| parents | c25855a79671 |
| children | 5408a9225788 |
| files | data_manager/data_manager.py data_manager/data_manager_mitos.xml test-data/mitos2_refseq63.json |
| diffstat | 3 files changed, 15 insertions(+), 7 deletions(-) [+] |
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--- a/data_manager/data_manager.py Fri Mar 27 20:34:48 2020 +0000 +++ b/data_manager/data_manager.py Sun Nov 22 18:02:48 2020 +0000 @@ -12,7 +12,7 @@ ZENODO = { "mitos": "2683856", - "mitos2": "3685310" + "mitos2": "4284483" } NAMES = { "mitos1-refdata": "RefSeq39 + MiTFi tRNA models", @@ -71,14 +71,14 @@ 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()) + 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, sort_keys=True)) + json.dump(data_manager_json, fh, sort_keys=True) if __name__ == '__main__':
--- a/data_manager/data_manager_mitos.xml Fri Mar 27 20:34:48 2020 +0000 +++ b/data_manager/data_manager_mitos.xml Sun Nov 22 18:02:48 2020 +0000 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="data_manager_mitos" name="MITOS" tool_type="manage_data" version="0.0.1"> +<tool id="data_manager_mitos" name="MITOS" tool_type="manage_data" version="0.0.2"> <description>reference data downloader</description> <requirements> <requirement type="package" version="3.7">python</requirement> @@ -25,13 +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> @@ -47,6 +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. @@ -74,7 +81,7 @@ - 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. +Data is downloaded from https://zenodo.org/record/4284483. </help> <citations> <citation type="doi">10.1016/j.ympev.2012.08.023</citation>