# HG changeset patch
# User iuc
# Date 1465584532 14400
# Node ID 3ebc86b520d7bd153dfd4e44f784855a9054c9e0
# Parent de108f838cb0710137e73f550dd2d56c87714685
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
diff -r de108f838cb0 -r 3ebc86b520d7 __efetch_build_options.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/__efetch_build_options.py Fri Jun 10 14:48:52 2016 -0400
@@ -0,0 +1,267 @@
+#!/usr/bin/env python
+# Daniel Blankenberg
+# Creates the options for tool interface
+import re
+
+# http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi
+db_list = '''
+annotinfo
+assembly
+bioproject
+biosample
+biosystems
+blastdbinfo
+books
+cdd
+clinvar
+clone
+dbvar
+gap
+gapplus
+gds
+gencoll
+gene
+genome
+geoprofiles
+grasp
+gtr
+homologene
+medgen
+mesh
+ncbisearch
+nlmcatalog
+nuccore
+nucest
+nucgss
+nucleotide
+omim
+orgtrack
+pcassay
+pccompound
+pcsubstance
+pmc
+popset
+probe
+protein
+proteinclusters
+pubmed
+pubmedhealth
+seqannot
+snp
+sra
+structure
+taxonomy
+unigene'''.replace( "", "").replace( "", "").split("\n")
+
+
+help = ''' (all)
+ docsum xml Document Summary
+ docsum json Document Summary
+ full text Full Document
+ uilist xml Unique Identifier List
+ uilist text Unique Identifier List
+ full xml Full Document
+
+ bioproject
+ native BioProject Report
+ native xml RecordSet
+
+ biosample
+ native BioSample Report
+ native xml BioSampleSet
+
+ biosystems
+ native xml Sys-set
+
+ gds
+ native xml RecordSet
+ summary text Summary
+
+ gene
+ gene_table xml Gene Table
+ native text Gene Report
+ native asn.1 Entrezgene
+ native xml Entrezgene-Set
+ tabular tabular Tabular Report
+
+ homologene
+ alignmentscores text Alignment Scores
+ fasta fasta FASTA
+ homologene text Homologene Report
+ native text Homologene List
+ native asn.1 HG-Entry
+ native xml Entrez-Homologene-Set
+
+ mesh
+ full text Full Record
+ native text MeSH Report
+ native xml RecordSet
+
+ nlmcatalog
+ native text Full Record
+ native xml NLMCatalogRecordSet
+
+ pmc
+ medline text MEDLINE
+ native xml pmc-articleset
+
+ pubmed
+ abstract xml Abstract
+ medline text MEDLINE
+ native asn.1 Pubmed-entry
+ native xml PubmedArticleSet
+
+ (sequences)
+ acc text Accession Number
+ est xml EST Report
+ fasta fasta FASTA
+ fasta xml TinySeq
+ fasta_cds_aa fasta CDS Products
+ fasta_cds_na fasta Coding Regions
+ ft text Feature Table
+ gb text GenBank Flatfile
+ gb xml GBSet
+ gbc xml INSDSet
+ gbwithparts text GenBank with Contig Sequences
+ gene_fasta fasta FASTA of Gene
+ gp text GenPept Flatfile
+ gp xml GBSet
+ gpc xml INSDSet
+ gss text GSS Report
+ ipg text Identical Protein Report
+ ipg xml IPGReportSet
+ native text Seq-entry
+ native xml Bioseq-set
+ seqid asn.1 Seq-id
+
+ snp
+ chr text Chromosome Report
+ docset text Summary
+ fasta fasta FASTA
+ flt text Flat File
+ native asn.1 Rs
+ native xml ExchangeSet
+ rsr tabular RS Cluster Report
+ ssexemplar text SS Exemplar List
+
+ sra
+ native xml EXPERIMENT_PACKAGE_SET
+ runinfo xml SraRunInfo
+
+ structure
+ mmdb asn.1 Ncbi-mime-asn1 strucseq
+ native text MMDB Report
+ native xml RecordSet
+
+ taxonomy
+ native text Taxonomy List
+ native xml TaxaSet'''.split("\n")
+
+
+db = {}
+for db_name in db_list:
+ db[db_name] = []
+
+section = None
+for line in help:
+ line = re.split('\s{2,}', line.strip())
+ # Ignore empties
+ if len(line) == 0:
+ continue
+ # Section headers have one item
+ elif len(line) == 1:
+ section = line[0]
+ db[section] = []
+ # Format lines have 2+
+ elif len(line) == 2:
+ parent_format = line[0]
+ description = line[1]
+
+ if parent_format not in db[section]:
+ db[section].append((parent_format, None, description))
+ elif len(line) == 3:
+ parent_format = line[0]
+ format_modifier = line[1]
+ description = line[2]
+
+ if parent_format not in db[section]:
+ db[section].append((parent_format, format_modifier, description))
+
+
+all_formats = db['(all)']
+del db['(all)']
+sequences_formats = db['(sequences)']
+del db['(sequences)']
+del db['']
+
+for key in db:
+ db[key] += all_formats
+
+for key in ('nuccore', 'nucest', 'nucgss', 'nucleotide'):
+ db[key] += sequences_formats
+
+MACRO_TPL = '''
+
+'''
+
+WHEN_TPL = '''
+
+ {format_options}
+
+ '''
+
+FORMAT_OPTION_TPL = ''''''
+
+format_names = {}
+
+print '''
+
+ '''
+for key in sorted(db):
+ format_options = []
+
+ for (parent_format, format_modifier, description) in sorted(db[key]):
+ name_human = description
+ if format_modifier:
+ name_human += ' (%s)' % format_modifier
+ format_string = '%s-%s' % (parent_format, format_modifier)
+
+ format_options.append(FORMAT_OPTION_TPL.format(
+ name_type=format_string,
+ name_type_human=name_human,
+ ))
+
+ format_names[format_string] = format_modifier
+
+ print WHEN_TPL.format(
+ format=key,
+ format_options='\n '.join(format_options)
+ )
+
+print '''
+ '''
+
+CHANGE_FORMAT_TPL = '''
+
+
+ {formats}
+
+
+'''
+
+CHANGE_FORMAT_WHEN_TPL = ''''''
+# Format options
+
+
+whens = []
+for (k, v) in format_names.items():
+ if v is None:
+ v = 'text'
+ elif v == 'asn.1':
+ v = 'asn1'
+
+ whens.append(CHANGE_FORMAT_WHEN_TPL.format(
+ key=k, value=v
+ ))
+
+print CHANGE_FORMAT_TPL.format(formats='\n '.join(whens))
diff -r de108f838cb0 -r 3ebc86b520d7 elink.py
--- a/elink.py Thu Apr 07 17:36:58 2016 -0400
+++ b/elink.py Fri Jun 10 14:48:52 2016 -0400
@@ -1,7 +1,8 @@
#!/usr/bin/env python
import argparse
+import json
+
import eutils
-import json
if __name__ == '__main__':
@@ -9,8 +10,8 @@
parser.add_argument('db', help='Database to use, sometimes "none" (e.g. *check)')
parser.add_argument('dbfrom', help='Database containing input UIDs')
parser.add_argument('cmd', choices=['neighbor', 'neighbor_score',
- 'neighbor_history', 'acheck', 'ncheck', 'lcheck',
- 'llinks', 'llinkslib', 'prlinks'],
+ 'neighbor_history', 'acheck', 'ncheck', 'lcheck',
+ 'llinks', 'llinkslib', 'prlinks'],
help='ELink command mode')
# Only used in case of neighbor_history
parser.add_argument('--history_out', type=argparse.FileType('w'),
diff -r de108f838cb0 -r 3ebc86b520d7 eutils.py
--- a/eutils.py Thu Apr 07 17:36:58 2016 -0400
+++ b/eutils.py Fri Jun 10 14:48:52 2016 -0400
@@ -27,6 +27,7 @@
if history_file is not None:
with open(history_file, 'r') as handle:
data = json.loads(handle.read())
+ print data
self.query_key = data['QueryKey']
self.webenv = data['WebEnv']
self.using_history = True
diff -r de108f838cb0 -r 3ebc86b520d7 eutils.pyc
Binary file eutils.pyc has changed
diff -r de108f838cb0 -r 3ebc86b520d7 macros.xml
--- a/macros.xml Thu Apr 07 17:36:58 2016 -0400
+++ b/macros.xml Fri Jun 10 14:48:52 2016 -0400
@@ -1,6 +1,6 @@
- 1.0
+ 1.1
--user_email "$__user_email__"
#set admin_emails = ';'.join(str($__admin_users__).split(','))
@@ -90,6 +90,7 @@
token_label="NCBI Database to Use"
>
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#if $query_source.qss == "history":
--history_file $query_source.history_file
@@ -576,5 +842,5 @@
-
+