Mercurial > repos > matthias > data_manager_megan_tools

comparison data_manager/data_manager.py @ 6:2aadd067ea24 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit 00e65802fca3de53129deae7b6df0fd0111400d8-dirty
author matthias
date Mon, 05 Nov 2018 03:30:04 -0500
parents 4b46c7c32984
children
comparison
equal deleted inserted replaced
5:ba3aab283a68 6:2aadd067ea24
27 "gi2seed-May2015X.bin.zip":"Protein accession to SEED (May2015X)", 27 "gi2seed-May2015X.bin.zip":"Protein accession to SEED (May2015X)",
28 "gi2kegg-Aug2016X-ue.bin.zip":"Protein accession to KEGG (Aug2016X). Only for use with the Ultimate Edition of MEGAN." 28 "gi2kegg-Aug2016X-ue.bin.zip":"Protein accession to KEGG (Aug2016X). Only for use with the Ultimate Edition of MEGAN."
29 } 29 }
30 30
31 FILE2TYPE = { 31 FILE2TYPE = {
32 "prot_acc2tax-June2018X1.abin.zip":"acc2tax", 32 "prot_acc2tax-June2018X1.abin.zip":"acc2taxa",
33 "nucl_acc2tax-June2018.abin.zip":"acc2tax", 33 "nucl_acc2tax-June2018.abin.zip":"acc2taxa",
34 "acc2interpro-June2018X.abin.zip":"acc2interpro", 34 "acc2interpro-June2018X.abin.zip":"acc2interpro2go",
35 "acc2eggnog-Oct2016X.abin.zip":"acc2eggnog", 35 "acc2eggnog-Oct2016X.abin.zip":"acc2eggnog",
36 "acc2seed-May2015XX.abin.zip":"acc2seed", 36 "acc2seed-May2015XX.abin.zip":"acc2seed",
37 "acc2kegg-Dec2017X1-ue.abin.zip":"acc2kegg", 37 "acc2kegg-Dec2017X1-ue.abin.zip":"acc2kegg",
38 "SSURef_Nr99_132_tax_silva_to_NCBI_synonyms.map.gz":"syn2taxa", 38 "SSURef_Nr99_132_tax_silva_to_NCBI_synonyms.map.gz":"syn2taxa",
39 "SSURef_NR99_128_tax_silva_to_NCBI_synonyms.map.gz":"syn2taxa", 39 "SSURef_NR99_128_tax_silva_to_NCBI_synonyms.map.gz":"syn2taxa",
40 "prot_gi2tax-Aug2016X.bin.zip":"gi2tax", 40 "prot_gi2tax-Aug2016X.bin.zip":"gi2taxa",
41 "nucl_gi2tax-Aug2016.bin.zip":"gi2tax", 41 "nucl_gi2tax-Aug2016.bin.zip":"gi2taxa",
42 "gi2eggnog-June2016X.bin.zip":"gi2eggnog", 42 "gi2eggnog-June2016X.bin.zip":"gi2eggnog",
43 "gi2interpro-June2016X.bin.zip":"gi2interpro", 43 "gi2interpro-June2016X.bin.zip":"gi2interpro2go",
44 "gi2seed-May2015X.bin.zip":"gi2seed-", 44 "gi2seed-May2015X.bin.zip":"gi2seed-",
45 "gi2kegg-Aug2016X-ue.bin.zip":"gi2kegg" 45 "gi2kegg-Aug2016X-ue.bin.zip":"gi2kegg"
46 } 46 }
47 47
48 def url_download(fname, workdir): 48 def url_download(fname, workdir):
89 data_manager_entry = {} 89 data_manager_entry = {}
90 data_manager_entry['value'] = fname.split(".")[0] 90 data_manager_entry['value'] = fname.split(".")[0]
91 data_manager_entry['name'] = FILE2NAME[fname] 91 data_manager_entry['name'] = FILE2NAME[fname]
92 data_manager_entry['type'] = FILE2TYPE[fname] 92 data_manager_entry['type'] = FILE2TYPE[fname]
93 data_manager_entry['path'] = path 93 data_manager_entry['path'] = path
94
95 data_manager_json = dict(data_tables=dict(megan_tools=data_manager_entry)) 94 data_manager_json = dict(data_tables=dict(megan_tools=data_manager_entry))
96 95
97 params = json.loads(open(outjson).read()) 96 params = json.loads(open(outjson).read())
98 target_directory = params['output_data'][0]['extra_files_path'] 97 target_directory = params['output_data'][0]['extra_files_path']
99 os.mkdir(target_directory) 98 os.mkdir(target_directory)