changeset 5:675fd774314e draft

"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit ed32f2e6d8174873cefcbe141084f857f84b0586"

--- a/get_feature_info.py	Fri Apr 13 09:43:28 2018 -0400
+++ b/get_feature_info.py	Thu Oct 31 07:49:30 2019 -0400
@@ -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'}

--- a/get_genetree.py	Fri Apr 13 09:43:28 2018 -0400
+++ b/get_genetree.py	Thu Oct 31 07:49:30 2019 -0400
@@ -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'

--- a/get_genetree.xml	Fri Apr 13 09:43:28 2018 -0400
+++ b/get_genetree.xml	Thu Oct 31 07:49:30 2019 -0400
@@ -29,7 +29,6 @@
 python '$__tool_directory__/get_genetree.py'
 --id_type $input_type
 -i '$input'
--g $species_selector
 --format ${output_format.output_format_selector}
 #if $output_format.output_format_selector == 'json'
     -s ${output_format.sequence.sequence_selector}
@@ -57,10 +56,6 @@
         <param name="input" type="text" label="Ensembl ID">
             <validator type="empty_field" />
         </param>
-        <param name="species_selector" type="select" label="Select Species">
-            <option value="ensembl" selected="true">Vertebrates</option>
-            <option value="ensemblgenomes">Other species</option>
-        </param>
         <conditional name="output_format">
             <param name="output_format_selector" type="select" label="Output format">
                 <option value="json" selected="true">JSON</option>

--- a/get_sequences.py	Fri Apr 13 09:43:28 2018 -0400
+++ b/get_sequences.py	Thu Oct 31 07:49:30 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'}