| Previous changeset 5:234d7babf34b (2018-04-13) Next changeset 7:d6bb417dc831 (2020-10-20) |
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Commit message:
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit ed32f2e6d8174873cefcbe141084f857f84b0586" |
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modified:
get_feature_info.py get_feature_info.xml get_genetree.py get_sequences.py |
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| diff -r 234d7babf34b -r 70e4134eb0ed get_feature_info.py --- a/get_feature_info.py Fri Apr 13 09:43:11 2018 -0400 +++ b/get_feature_info.py Thu Oct 31 07:49:48 2019 -0400 |
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| @@ -15,10 +15,6 @@ default='0', help='Expands the search to include any connected features. e.g. If the object is a gene, its transcripts, translations and exons will be returned as well.') -parser.add_option('-s', '--species', type='choice', - choices=['ensembl', 'ensemblgenomes'], default='ensembl', - help='Specify the genome databases for vertebrates and other eukaryotic species') - parser.add_option('-f', '--format', type='choice', choices=['full', 'condensed'], default='full', help='Specify the formats to emit from this endpoint') @@ -27,7 +23,7 @@ raise Exception('-i option must be specified') -server = 'http://rest.%s.org' % options.species +server = 'http://rest.ensembl.org' ext = 'lookup/id' headers = {'Content-Type': 'application/json', 'Accept': 'application/json'} |
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| diff -r 234d7babf34b -r 70e4134eb0ed get_feature_info.xml --- a/get_feature_info.xml Fri Apr 13 09:43:11 2018 -0400 +++ b/get_feature_info.xml Thu Oct 31 07:49:48 2019 -0400 |
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| @@ -10,17 +10,12 @@ -e $expand -f $format_selector -i '$input' --s $species_selector > '$output' ]]> </command> <inputs> <param name="input" type="data" format="txt" label="List of Ensembl IDs" help="Max 1000 IDs" /> - <param name="species_selector" type="select" label="Select species"> - <option value="ensembl" selected="true">Vertebrates</option> - <option value="ensemblgenomes">Other species</option> - </param> <param name="expand" type="boolean" truevalue="1" falsevalue="0" label="Expand the search to include any connected features" help="For example, if the object is a gene, its transcripts, translations and exons will be returned as well" /> <param name="format_selector" type="select" label="Output format"> <option value="full" selected="true">Full</option> |
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| diff -r 234d7babf34b -r 70e4134eb0ed get_genetree.py --- a/get_genetree.py Fri Apr 13 09:43:11 2018 -0400 +++ b/get_genetree.py Thu Oct 31 07:49:48 2019 -0400 |
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| @@ -18,10 +18,6 @@ choices=['protein', 'cdna', 'none'], default='protein', help='The type of sequence to bring back. Setting it to none results in no sequence being returned') -parser.add_option('-g', '--species', type='choice', - choices=['ensembl', 'ensemblgenomes'], default='ensembl', - help='Specify the genome databases for vertebrates and other eukaryotic species') - parser.add_option('-a', '--aligned', type='choice', choices=['0', '1'], default='0', help='Return the aligned string if true. Otherwise, return the original sequence (no insertions)') parser.add_option('-c', '--cigar_line', type='choice', choices=['0', '1'], @@ -35,7 +31,7 @@ if options.input is None: raise Exception('-i option must be specified') -server = 'http://rest.%s.org' % options.species +server = 'http://rest.ensembl.org' if options.id_type == 'gene_id': ext = 'genetree/member/id' |
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| diff -r 234d7babf34b -r 70e4134eb0ed get_sequences.py --- a/get_sequences.py Fri Apr 13 09:43:11 2018 -0400 +++ b/get_sequences.py Thu Oct 31 07:49:48 2019 -0400 |
| [ |
| @@ -12,10 +12,6 @@ parser = optparse.OptionParser() parser.add_option('-i', '--input', help='List of Ensembl IDs') -parser.add_option('-s', '--species', type='choice', - choices=['ensembl', 'ensemblgenomes'], default='ensembl', - help='Specify the genome databases for vertebrates and other eukaryotic species') - parser.add_option('-t', '--type', type='choice', choices=['genomic', 'cds', 'cdna', 'protein'], default='genomic', help='Type of sequence') @@ -27,7 +23,7 @@ if options.input is None: raise Exception('-i option must be specified') -server = 'http://rest.%s.org' % options.species +server = 'http://rest.ensembl.org' ext = 'sequence/id' headers = {'Content-Type': 'text/x-fasta', 'Accept': 'text/x-fasta'} |