Mercurial > repos > galaxyp > uniprotxml_downloader
changeset 3:1a5690a5eedc draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 6aac77a68426533c8c18c9f6aabd2df56a82de24
| author | galaxyp |
|---|---|
| date | Tue, 02 Jul 2019 21:46:14 -0400 |
| parents | e1abc9a35c64 |
| children | 12692567c7f9 |
| files | uniprotxml_downloader.py uniprotxml_downloader.xml |
| diffstat | 2 files changed, 4 insertions(+), 4 deletions(-) [+] |
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--- a/uniprotxml_downloader.py Fri Dec 16 17:33:05 2016 -0500 +++ b/uniprotxml_downloader.py Tue Jul 02 21:46:14 2019 -0400 @@ -25,8 +25,8 @@ parser.add_option('-c', '--column', dest='column', type='int', default=0, help='The column (zero-based) in the tabular file that contains Taxon IDs' ) parser.add_option('-t', '--taxon', dest='taxon', action='append', default=[], help='NCBI taxon ID to download') parser.add_option('-r', '--reviewed', dest='reviewed', help='Only uniprot reviewed entries') - parser.add_option('-f', '--format', dest='format', choices=['xml', 'fasta'], default='xml',help='output format') - parser.add_option('-o', '--output', dest='output', help='file path for th downloaed uniprot xml') + parser.add_option('-f', '--format', dest='format', choices=['xml', 'fasta'], default='xml', help='output format') + parser.add_option('-o', '--output', dest='output', help='file path for the downloaded uniprot xml') parser.add_option('-v', '--verbose', dest='verbose', action='store_true', default=False, help='Print UniProt Info') parser.add_option('-d', '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stderr') (options, args) = parser.parse_args() @@ -51,7 +51,7 @@ try: def reporthook(n1,n2,n3): pass - url = 'http://www.uniprot.org/uniprot/' + url = 'https://www.uniprot.org/uniprot/' query = "%s%s" % (taxon_query, reviewed) params = {'query' : query, 'force' : 'yes' , 'format' : options.format} if options.debug:
--- a/uniprotxml_downloader.xml Fri Dec 16 17:33:05 2016 -0500 +++ b/uniprotxml_downloader.xml Tue Jul 02 21:46:14 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="uniprotxml_downloader" name="UniProt" version="2.0.0"> +<tool id="uniprotxml_downloader" name="UniProt" version="2.1.0"> <description>download proteome as XML or fasta</description> <requirements> <requirement type="package" version="2.7">python</requirement>