| Previous changeset 4:3b686142e9c2 (2018-04-13) Next changeset 6:7af66c2b3831 (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_genetree.py get_sequences.py get_sequences.xml |
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| diff -r 3b686142e9c2 -r 0fa1d1cc417d get_feature_info.py --- a/get_feature_info.py Fri Apr 13 09:43:51 2018 -0400 +++ b/get_feature_info.py Thu Oct 31 07:50:07 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 3b686142e9c2 -r 0fa1d1cc417d get_genetree.py --- a/get_genetree.py Fri Apr 13 09:43:51 2018 -0400 +++ b/get_genetree.py Thu Oct 31 07:50:07 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 3b686142e9c2 -r 0fa1d1cc417d get_sequences.py --- a/get_sequences.py Fri Apr 13 09:43:51 2018 -0400 +++ b/get_sequences.py Thu Oct 31 07:50:07 2019 -0400 |
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| @@ -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'} |
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| diff -r 3b686142e9c2 -r 0fa1d1cc417d get_sequences.xml --- a/get_sequences.xml Fri Apr 13 09:43:51 2018 -0400 +++ b/get_sequences.xml Thu Oct 31 07:50:07 2019 -0400 |
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| @@ -7,7 +7,6 @@ <command detect_errors="exit_code"> <![CDATA[ python '$__tool_directory__/get_sequences.py' --s $species_selector --expand_3prime $expand_3prime --expand_5prime $expand_5prime -t $type_selector @@ -18,10 +17,6 @@ <inputs> <param name="input" type="data" format="txt" label="List of Ensembl 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_3prime" type="integer" value="0" min="0" label="expand_3prime" help="Expand each sequence downstream of the sequence by this many basepairs. Only available when using genomic sequence type." /> <param name="expand_5prime" type="integer" value="0" min="0" label="expand_5prime" help="Expand each sequence downstream of the sequence by this many basepairs. Only available when using genomic sequence type." /> <param name="type_selector" type="select" label="Type" help="Type of sequence. Defaults to genomic where applicable, i.e. not translations. cDNA refers to the spliced transcript sequence with UTR; CDS refers to the spliced transcript sequence without UTR"> |