changeset 6:70e4134eb0ed 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 09:43:11 2018 -0400
+++ b/get_feature_info.py	Thu Oct 31 07:49:48 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_feature_info.xml	Fri Apr 13 09:43:11 2018 -0400
+++ b/get_feature_info.xml	Thu Oct 31 07:49:48 2019 -0400
@@ -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>

--- a/get_genetree.py	Fri Apr 13 09:43:11 2018 -0400
+++ b/get_genetree.py	Thu Oct 31 07:49:48 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_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'}