# HG changeset patch
# User iuc
# Date 1467873662 14400
# Node ID 92bd8a680b9d2b873459c7101df13af8ee24af65

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db

diff -r 000000000000 -r 92bd8a680b9d README.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Thu Jul 07 02:41:02 2016 -0400
@@ -0,0 +1,38 @@
+Galaxy NCBI Entrez Tools
+========================
+
+This repo requires a readme as administrators should very aware of some
+restrictions NCBI places on the use of the Entrez service.
+
+NCBI requests that you please limit large jobs to either weekends or
+between 9:00 PM and 5:00 AM Eastern time during weekdays. This is not a
+request that the Galaxy tool can easily service, so we've included it in
+the disclaimer on every tool quite prominently.
+
+Failure to comply with NCBI's policies may result in an block until
+you/the user contacts NCBI and registers the tool ID and their email.
+
+Note that these are *IP* level blocks so the Galaxy tools uses a
+concatenation of the administrator's emails, and the user email, in
+hopes that NCBI will contact all relevant parties should their system be
+abused.
+
+Additionally, since these are IP level blocks, the Galaxy tool author
+(@erasche) recommends using the following ``jobs_conf.xml`` snippet in
+order to place a system-wide restriction of 1 concurrent Entrez job
+amongst all users.
+
+.. code:: xml
+
+    <destination id="entrez" runner="local">
+    </destination>
+    <limit type="concurrent_jobs" id="entrez">1</limit>
+    <tools>
+      <tool id="ncbi.eutils.efetch" destination="entrez" />
+      <tool id="ncbi.eutils.esearch" destination="entrez" />
+      <tool id="ncbi.eutils.epost" destination="entrez" />
+      <tool id="ncbi.eutils.elink" destination="entrez" />
+      <tool id="ncbi.eutils.einfo" destination="entrez" />
+      <tool id="ncbi.eutils.esummary" destination="entrez" />
+    </tools>
+
diff -r 000000000000 -r 92bd8a680b9d __efetch_build_options.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/__efetch_build_options.py	Thu Jul 07 02:41:02 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 = '''
+<DbName>annotinfo</DbName>
+<DbName>assembly</DbName>
+<DbName>bioproject</DbName>
+<DbName>biosample</DbName>
+<DbName>biosystems</DbName>
+<DbName>blastdbinfo</DbName>
+<DbName>books</DbName>
+<DbName>cdd</DbName>
+<DbName>clinvar</DbName>
+<DbName>clone</DbName>
+<DbName>dbvar</DbName>
+<DbName>gap</DbName>
+<DbName>gapplus</DbName>
+<DbName>gds</DbName>
+<DbName>gencoll</DbName>
+<DbName>gene</DbName>
+<DbName>genome</DbName>
+<DbName>geoprofiles</DbName>
+<DbName>grasp</DbName>
+<DbName>gtr</DbName>
+<DbName>homologene</DbName>
+<DbName>medgen</DbName>
+<DbName>mesh</DbName>
+<DbName>ncbisearch</DbName>
+<DbName>nlmcatalog</DbName>
+<DbName>nuccore</DbName>
+<DbName>nucest</DbName>
+<DbName>nucgss</DbName>
+<DbName>nucleotide</DbName>
+<DbName>omim</DbName>
+<DbName>orgtrack</DbName>
+<DbName>pcassay</DbName>
+<DbName>pccompound</DbName>
+<DbName>pcsubstance</DbName>
+<DbName>pmc</DbName>
+<DbName>popset</DbName>
+<DbName>probe</DbName>
+<DbName>protein</DbName>
+<DbName>proteinclusters</DbName>
+<DbName>pubmed</DbName>
+<DbName>pubmedhealth</DbName>
+<DbName>seqannot</DbName>
+<DbName>snp</DbName>
+<DbName>sra</DbName>
+<DbName>structure</DbName>
+<DbName>taxonomy</DbName>
+<DbName>unigene</DbName>'''.replace( "<DbName>", "").replace( "</DbName>", "").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 = '''      <when value="{format}">
+        <param name="output_format" type="select" label="Output Format">
+          {format_options}
+        </param>
+      </when>'''
+
+FORMAT_OPTION_TPL = '''<option value="{name_type}">{name_type_human}</option>'''
+
+format_names = {}
+
+print '''  <xml name="db">
+    <conditional name="db">
+      <expand macro="dbselect" />'''
+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 '''    </conditional>
+  </xml>'''
+
+CHANGE_FORMAT_TPL = '''
+  <xml name="efetch_formats">
+    <change_format>
+      {formats}
+    </change_format>
+  </xml>
+'''
+
+CHANGE_FORMAT_WHEN_TPL = '''<when input="output_format" value="{key}" format="{value}"/>'''
+# 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 000000000000 -r 92bd8a680b9d ecitmatch.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ecitmatch.py	Thu Jul 07 02:41:02 2016 -0400
@@ -0,0 +1,60 @@
+#!/usr/bin/env python
+import argparse
+import eutils
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='ECitMatch', epilog='')
+    parser.add_argument('--file', type=argparse.FileType('r'), help='Tabular file containing citations to search')
+
+    parser.add_argument('--key', nargs='*', help='Citation Key')
+    parser.add_argument('--journal_title', nargs='*', help='Journal Title')
+    parser.add_argument('--year', nargs='*', help='Year')
+    parser.add_argument('--volume', nargs='*', help='Volume')
+    parser.add_argument('--first_page', nargs='*', help='First Page')
+    parser.add_argument('--author_name', nargs='*', help='Author name')
+
+    # Emails
+    parser.add_argument('--user_email', help="User email")
+    parser.add_argument('--admin_email', help="Admin email")
+    args = parser.parse_args()
+
+    c = eutils.Client(user_email=args.user_email, admin_email=args.admin_email)
+
+    citations = []
+    if args.file is None:
+        for key, journal, year, volume, first_page, author_name in \
+                zip(args.key, args.journal_title, args.year, args.volume, args.first_page, args.author_name):
+            citations.append({
+                'key': key,
+                'journal': journal,
+                'year': year,
+                'volume': volume,
+                'first_page': first_page,
+                'author_name': author_name,
+            })
+    else:
+        for line in args.file:
+            line = line.strip()
+            if not line.startswith('#'):
+                tmp = line.split('\t')
+                try:
+                    citations.append({
+                        'journal': tmp[0],
+                        'year': tmp[1],
+                        'volume': tmp[2],
+                        'first_page': tmp[3],
+                        'author_name': tmp[4],
+                        'key': tmp[5],
+                    })
+                except KeyError:
+                    print "Could not parse line: %s" % line
+
+    payload = {
+        'db': 'pubmed',
+        'bdata': citations
+    }
+
+    results = c.citmatch(**payload)
+    # We get data back as pipe separated, so just replace those with tabs
+    print results.replace('|', '\t')
diff -r 000000000000 -r 92bd8a680b9d efetch.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/efetch.py	Thu Jul 07 02:41:02 2016 -0400
@@ -0,0 +1,35 @@
+#!/usr/bin/env python
+import argparse
+import eutils
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='EFetch', epilog='')
+    parser.add_argument('db', help='Database to use')
+    parser.add_argument('--user_email', help="User email")
+    parser.add_argument('--admin_email', help="Admin email")
+
+    # ID source
+    parser.add_argument('--id_list', help='list of ids')
+    parser.add_argument('--id', help='Comma separated individual IDs')
+    parser.add_argument('--history_file', help='Fetch results from previous query')
+
+    # Output
+    parser.add_argument('--retmode', help='Retmode')
+    parser.add_argument('--rettype', help='Rettype')
+    args = parser.parse_args()
+
+    c = eutils.Client(history_file=args.history_file, user_email=args.user_email, admin_email=args.admin_email)
+    merged_ids = c.parse_ids(args.id_list, args.id, args.history_file)
+
+    payload = {}
+    if args.history_file is not None:
+        payload.update(c.get_history())
+    else:
+        payload['id'] = ','.join(merged_ids)
+
+    for attr in ('retmode', 'rettype'):
+        if getattr(args, attr, None) is not None:
+            payload[attr] = getattr(args, attr)
+
+    c.fetch(args.db, ftype=args.retmode, **payload)
diff -r 000000000000 -r 92bd8a680b9d egquery.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/egquery.py	Thu Jul 07 02:41:02 2016 -0400
@@ -0,0 +1,20 @@
+#!/usr/bin/env python
+import argparse
+import eutils
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='EGQuery', epilog='')
+    parser.add_argument('term', help='Query')
+    #
+    parser.add_argument('--user_email', help="User email")
+    parser.add_argument('--admin_email', help="Admin email")
+    args = parser.parse_args()
+
+    c = eutils.Client(user_email=args.user_email, admin_email=args.admin_email)
+
+    payload = {
+        'term': args.term,
+    }
+    results = c.gquery(**payload)
+    print results
diff -r 000000000000 -r 92bd8a680b9d einfo.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/einfo.py	Thu Jul 07 02:41:02 2016 -0400
@@ -0,0 +1,18 @@
+#!/usr/bin/env python
+import argparse
+import eutils
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='EInfo', epilog='')
+    parser.add_argument('--db', help='Database to use')
+    parser.add_argument('--user_email', help="User email")
+    parser.add_argument('--admin_email', help="Admin email")
+    args = parser.parse_args()
+
+    c = eutils.Client(user_email=args.user_email, admin_email=args.admin_email)
+    payload = {}
+    if args.db is not None:
+        payload['db'] = args.db
+        payload['version'] = '2.0'
+    print c.info(**payload)
diff -r 000000000000 -r 92bd8a680b9d elink.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/elink.py	Thu Jul 07 02:41:02 2016 -0400
@@ -0,0 +1,59 @@
+#!/usr/bin/env python
+import argparse
+import json
+
+import eutils
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='EFetch', epilog='')
+    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'],
+                        help='ELink command mode')
+    # Only used in case of neighbor_history
+    parser.add_argument('--history_out', type=argparse.FileType('w'),
+                        help='Output history file', default='-')
+
+    parser.add_argument('--user_email', help="User email")
+    parser.add_argument('--admin_email', help="Admin email")
+    # ID Sources
+    parser.add_argument('--id_list', help='list of ids')
+    parser.add_argument('--id', help='Comma separated individual IDs')
+    parser.add_argument('--history_file', help='Fetch results from previous query')
+
+    # TODO: dates, linkname, term, holding
+    # neighbor or neighbor_history and dbfrom is pubmed
+    # parser.add_argument('--datetype', help='Date type')
+    # parser.add_argument('--reldate', help='In past N days')
+    # parser.add_argument('--mindate', help='Minimum date')
+    # parser.add_argument('--maxdate', help='maximum date')
+
+    # Output
+    args = parser.parse_args()
+
+    c = eutils.Client(history_file=args.history_file, user_email=args.user_email, admin_email=args.admin_email)
+    merged_ids = c.parse_ids(args.id_list, args.id, args.history_file)
+
+    payload = {
+        'dbfrom': args.dbfrom,
+        'cmd': args.cmd,
+    }
+    if args.history_file is not None:
+        payload.update(c.get_history())
+    else:
+        payload['id'] = ','.join(merged_ids)
+
+    # DB can be 'none' in a few cases.
+    if args.db != "none":
+        payload['db'] = args.db
+
+    results = c.link(**payload)
+
+    if args.cmd == "neighbor_history":
+        history = c.extract_history(results)
+        args.history_out.write(json.dumps(history, indent=4))
+
+    print results
diff -r 000000000000 -r 92bd8a680b9d epost.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/epost.py	Thu Jul 07 02:41:02 2016 -0400
@@ -0,0 +1,27 @@
+#!/usr/bin/env python
+import argparse
+import eutils
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='EPost', epilog='')
+    parser.add_argument('db', help='Database to use')
+    parser.add_argument('--id_list', help='list of ids')
+    parser.add_argument('--id', help='Comma separated individual IDs')
+    parser.add_argument('--history_file', help='Post to new QueryKey in an existing WebEnv')
+    parser.add_argument('--user_email', help="User email")
+    parser.add_argument('--admin_email', help="Admin email")
+
+    args = parser.parse_args()
+
+    c = eutils.Client(history_file=args.history_file, user_email=args.user_email, admin_email=args.admin_email)
+    merged_ids = c.parse_ids(args.id_list, args.id, args.history_file)
+
+    payload = {}
+    if args.history_file is not None:
+        payload.update(c.get_history())
+    else:
+        payload['id'] = ','.join(merged_ids)
+        payload['WebEnv'] = ''
+
+    print c.post(args.db, **payload)
diff -r 000000000000 -r 92bd8a680b9d esearch.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/esearch.py	Thu Jul 07 02:41:02 2016 -0400
@@ -0,0 +1,47 @@
+#!/usr/bin/env python
+import json
+import argparse
+import eutils
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='ESearch', epilog='')
+    parser.add_argument('db', help='Database to use')
+    parser.add_argument('term', help='Query')
+    parser.add_argument('--history_file', help='Filter existing history')
+    parser.add_argument('--datetype', help='Date type')
+    parser.add_argument('--reldate', help='In past N days')
+    parser.add_argument('--mindate', help='Minimum date')
+    parser.add_argument('--maxdate', help='maximum date')
+    # History
+    parser.add_argument('--history_out', type=argparse.FileType('w'),
+                        help='Output history file')
+    parser.add_argument('--user_email', help="User email")
+    parser.add_argument('--admin_email', help="Admin email")
+    args = parser.parse_args()
+
+    c = eutils.Client(history_file=args.history_file, user_email=args.user_email, admin_email=args.admin_email)
+
+    payload = {
+        'db': args.db,
+        'term': args.term,
+        'retstart': 0,
+        'retmax': 20,
+        # hmmm @ retmax
+    }
+    if args.history_file is not None:
+        payload.update(c.get_history())
+    if args.history_out is not None:
+        payload['usehistory'] = 'y'
+
+    for attr in ('datetype', 'reldate', 'mindate', 'maxdate'):
+        if getattr(args, attr, None) is not None:
+            payload[attr] = getattr(args, attr)
+
+    results = c.search(**payload)
+
+    if args.history_out is not None:
+        history = c.extract_history(results)
+        args.history_out.write(json.dumps(history, indent=4))
+
+    print results
diff -r 000000000000 -r 92bd8a680b9d esummary.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/esummary.py	Thu Jul 07 02:41:02 2016 -0400
@@ -0,0 +1,29 @@
+#!/usr/bin/env python
+import argparse
+import eutils
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='ESummary', epilog='')
+    parser.add_argument('db', help='Database to use')
+    parser.add_argument('--id_list', help='list of ids')
+    parser.add_argument('--id', help='Comma separated individual IDs')
+    parser.add_argument('--history_file', help='Filter existing history')
+    parser.add_argument('--user_email', help="User email")
+    parser.add_argument('--admin_email', help="Admin email")
+    args = parser.parse_args()
+
+    c = eutils.Client(history_file=args.history_file, user_email=args.user_email, admin_email=args.admin_email)
+
+    merged_ids = c.parse_ids(args.id_list, args.id, args.history_file)
+
+    payload = {
+        'db': args.db,
+    }
+
+    if args.history_file is not None:
+        payload.update(c.get_history())
+    else:
+        payload['id'] = ','.join(merged_ids)
+
+    print c.summary(**payload)
diff -r 000000000000 -r 92bd8a680b9d esummary.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/esummary.xml	Thu Jul 07 02:41:02 2016 -0400
@@ -0,0 +1,57 @@
+<?xml version="1.0"?>
+<tool id="ncbi_eutils_esummary" name="NCBI ESummary" version="@WRAPPER_VERSION@">
+  <description>fetch summary of history/ids</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <version_command>python esummary.py --version</version_command>
+  <command detect_errors="aggressive" interpreter="python"><![CDATA[esummary.py
+$db_select
+
+@LIST_OR_HIST@
+
+
+@EMAIL_ARGUMENTS@
+> $default]]></command>
+  <inputs>
+    <expand macro="dbselect"/>
+    <expand macro="list_or_hist"/>
+  </inputs>
+  <outputs>
+    <data format="xml" name="default" label="Summary of NCBI Search"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="qss" value="id_list"/>
+      <param name="id_list" value="10239"/>
+      <param name="db_select" value="taxonomy"/>
+      <output name="default" file="esummary.tax.xml" ftype="xml"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+NCBI Entrez ESummary
+====================
+
+Responds to a list of UIDs from a given database with the corresponding
+document summaries.
+
+Example Queries
+---------------
+
+Search against protein:
+
++----------------------+--------------------------------------+
+| Parameter            | Value                                |
++======================+======================================+
+| NCBI Database to Use | Protein                              |
++----------------------+--------------------------------------+
+| ID List              | 28800982 28628843                    |
++----------------------+--------------------------------------+
+
+@REFERENCES@
+
+@DISCLAIMER@
+      ]]></help>
+  <expand macro="citations"/>
+</tool>
diff -r 000000000000 -r 92bd8a680b9d eutils.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/eutils.py	Thu Jul 07 02:41:02 2016 -0400
@@ -0,0 +1,127 @@
+import os
+import json
+import StringIO
+from Bio import Entrez
+Entrez.tool = "GalaxyEutils_1_0"
+BATCH_SIZE = 200
+
+
+class Client(object):
+
+    def __init__(self, history_file=None, user_email=None, admin_email=None):
+        self.using_history = False
+
+        if user_email is not None and admin_email is not None:
+            Entrez.email = ';'.join((admin_email, user_email))
+        elif user_email is not None:
+            Entrez.email = user_email
+        elif admin_email is not None:
+            Entrez.email = admin_email
+        else:
+            Entrez.email = os.environ.get('NCBI_EUTILS_CONTACT', None)
+
+        if Entrez.email is None:
+            raise Exception("Cannot continue without an email; please set "
+                            "administrator email in NCBI_EUTILS_CONTACT")
+
+        if history_file is not None:
+            with open(history_file, 'r') as handle:
+                data = json.loads(handle.read())
+                self.query_key = data['QueryKey']
+                self.webenv = data['WebEnv']
+                self.using_history = True
+
+    def get_history(self):
+        if not self.using_history:
+            return {}
+        else:
+            return {
+                'query_key': self.query_key,
+                'WebEnv': self.webenv,
+            }
+
+    def post(self, database, **payload):
+        return json.dumps(Entrez.read(Entrez.epost(database, **payload)), indent=4)
+
+    def fetch(self, db, ftype=None, **payload):
+        os.makedirs("downloads")
+
+        if 'id' in payload:
+            summary = self.id_summary(db, payload['id'])
+        else:
+            summary = self.history_summary(db)
+
+        count = len(summary)
+        payload['retmax'] = BATCH_SIZE
+
+        # This may be bad. I'm not sure yet. I think it will be ... but UGH.
+        for i in range(0, count, BATCH_SIZE):
+            payload['retstart'] = i
+            file_path = os.path.join('downloads', 'EFetch Results Chunk %s.%s' % (i, ftype))
+            with open(file_path, 'w') as handle:
+                handle.write(Entrez.efetch(db, **payload).read())
+
+    def id_summary(self, db, id_list):
+        payload = {
+            'db': db,
+            'id': id_list,
+        }
+        return Entrez.read(Entrez.esummary(**payload))
+
+    def history_summary(self, db):
+        if not self.using_history:
+            raise Exception("History must be available for this method")
+
+        payload = {
+            'db': db,
+            'query_key': self.query_key,
+            'WebEnv': self.webenv,
+        }
+        return Entrez.read(Entrez.esummary(**payload))
+
+    def summary(self, **payload):
+        return Entrez.esummary(**payload).read()
+
+    def link(self, **payload):
+        return Entrez.elink(**payload).read()
+
+    def extract_history(self, xml_data):
+        parsed_data = Entrez.read(StringIO.StringIO(xml_data))
+        history = {}
+        for key in ('QueryKey', 'WebEnv'):
+            if key in parsed_data:
+                history[key] = parsed_data[key]
+
+        return history
+
+    def search(self, **payload):
+        return Entrez.esearch(**payload).read()
+
+    def info(self, **kwargs):
+        return Entrez.einfo(**kwargs).read()
+
+    def gquery(self, **kwargs):
+        return Entrez.egquery(**kwargs).read()
+
+    def citmatch(self, **kwargs):
+        return Entrez.ecitmatch(**kwargs).read()
+
+    @classmethod
+    def parse_ids(cls, id_list, id, history_file):
+        """Parse IDs passed on --cli or in a file passed to the cli
+        """
+        merged_ids = []
+        if id is not None:
+            for pid in id.replace('__cn__', ',').replace('\n', ',').split(','):
+                if pid is not None and len(pid) > 0:
+                    merged_ids.append(pid)
+
+        if id_list is not None:
+            with open(id_list, 'r') as handle:
+                merged_ids += [x.strip() for x in handle.readlines()]
+
+        # Exception hanlded here for uniformity
+        if len(merged_ids) == 0 and history_file is None:
+            raise Exception("Must provide history file or IDs")
+
+        return merged_ids
diff -r 000000000000 -r 92bd8a680b9d eutils.pyc
Binary file eutils.pyc has changed
diff -r 000000000000 -r 92bd8a680b9d macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Jul 07 02:41:02 2016 -0400
@@ -0,0 +1,847 @@
+<?xml version="1.0"?>
+<macros>
+  <token name="@WRAPPER_VERSION@">1.1</token>
+  <token name="@EMAIL_ARGUMENTS@">
+--user_email "$__user_email__"
+#set admin_emails = ';'.join(str($__admin_users__).split(','))
+--admin_email "$admin_emails"
+  </token>
+  <!--  TODO: citation -->
+  <token name="@REFERENCES@"><![CDATA[
+  ]]></token>
+  <token name="@DISCLAIMER@"><![CDATA[
+Usage Guidelines and Requirements
+=================================
+
+Frequency, Timing, and Registration of E-utility URL Requests
+-------------------------------------------------------------
+
+In order not to overload the E-utility servers, NCBI recommends that users
+limit large jobs to either weekends or between 9:00 PM and 5:00 AM Eastern time
+during weekdays. Failure to comply with this policy may result in an IP address
+being blocked from accessing NCBI.
+
+Minimizing the Number of Requests
+---------------------------------
+
+If a task requires searching for and/or downloading a large number of
+records, it is much more efficient to use the Entrez History to upload
+and/or retrieve these records in batches rather than using separate
+requests for each record. Please refer to Application 3 in Chapter 3
+for an example. Many thousands of IDs can be uploaded using a single
+EPost request, and several hundred records can be downloaded using one
+EFetch request.
+
+
+Disclaimer and Copyright Issues
+-------------------------------
+
+In accordance with requirements of NCBI's E-Utilities, we must provide
+the following disclaimer:
+
+Please note that abstracts in PubMed may incorporate material that may
+be protected by U.S. and foreign copyright laws. All persons
+reproducing, redistributing, or making commercial use of this
+information are expected to adhere to the terms and conditions asserted
+by the copyright holder. Transmission or reproduction of protected
+items beyond that allowed by fair use (PDF) as defined in the copyright
+laws requires the written permission of the copyright owners. NLM
+provides no legal advice concerning distribution of copyrighted
+materials. Please consult your legal counsel. If you wish to do a large
+data mining project on PubMed data, you can enter into a licensing
+agreement and lease the data for free from NLM. For more information on
+this please see `http://www.nlm.nih.gov/databases/leased.html <http://www.nlm.nih.gov/databases/leased.html>`__
+
+The `full disclaimer <http://www.ncbi.nlm.nih.gov/About/disclaimer.html>`__ is available on
+their website
+
+Liability
+~~~~~~~~~
+
+For documents and software available from this server, the
+U.S. Government does not warrant or assume any legal liability or
+responsibility for the accuracy, completeness, or usefulness of any
+information, apparatus, product, or process disclosed.
+
+Endorsement
+~~~~~~~~~~~
+
+NCBI does not endorse or recommend any commercial
+products, processes, or services. The views and opinions of authors
+expressed on NCBI's Web sites do not necessarily state or reflect those
+of the U.S. Government, and they may not be used for advertising or
+product endorsement purposes.
+
+External Links
+~~~~~~~~~~~~~~
+
+Some NCBI Web pages may provide links to other Internet
+sites for the convenience of users. NCBI is not responsible for the
+availability or content of these external sites, nor does NCBI endorse,
+warrant, or guarantee the products, services, or information described
+or offered at these other Internet sites. Users cannot assume that the
+external sites will abide by the same Privacy Policy to which NCBI
+adheres. It is the responsibility of the user to examine the copyright
+and licensing restrictions of linked pages and to secure all necessary
+permissions.
+        ]]></token>
+    <xml name="dbselect"
+        token_name="db_select"
+        token_label="NCBI Database to Use"
+        >
+    <param name="@NAME@" type="select" label="@LABEL@">
+      <option value="annotinfo">Annotation Information</option>
+      <option value="assembly">Assembly</option>
+      <option value="bioproject">BioProject</option>
+      <option value="biosample">BioSample</option>
+      <option value="biosystems">Biosystems</option>
+      <option value="blastdbinfo">Blast Database Information</option>
+      <option value="books">Books</option>
+      <option value="cdd">Conserved Domains</option>
+      <option value="clinvar">Clinical Variants</option>
+      <option value="clone">CLone</option>
+      <option value="dbvar">dbVar</option>
+      <option value="gap">dbGaP</option>
+      <option value="gapplus">gapplus</option>
+      <option value="gds">GEO Datasets</option>
+      <option value="gencoll">Gencoll</option>
+      <option value="gene">Gene</option>
+      <option value="genome">Genome</option>
+      <option value="geoprofiles">GEO Profiles</option>
+      <option value="grasp">grasp</option>
+      <option value="gtr">Genetic Testing Registry</option>
+      <option value="homologene">HomoloGene</option>
+      <option value="medgen">MedGen</option>
+      <option value="mesh">MeSH</option>
+      <option value="ncbisearch">NCBI Web Site</option>
+      <option value="nlmcatalog">NLM Catalog</option>
+      <option value="nuccore">Nuccore</option>
+      <option value="nucest">EST</option>
+      <option value="nucgss">GSS</option>
+      <option value="nucleotide">Nucleotide</option>
+      <option value="omim">OMIM</option>
+      <option value="orgtrack">Orgtrack</option>
+      <option value="pcassay">PubChem BioAssay</option>
+      <option value="pccompound">PubChem Compound</option>
+      <option value="pcsubstance">PubChem Substance</option>
+      <option value="pmc">PubMed Central</option>
+      <option value="popset">PopSet</option>
+      <option value="probe">Probe</option>
+      <option value="protein">Protein</option>
+      <option value="proteinclusters">Protein Clusters</option>
+      <option value="pubmed">PubMed</option>
+      <option value="pubmedhealth">PubMed Health</option>
+      <option value="seqannot">seqannot</option>
+      <option value="snp">SNP</option>
+      <option value="sra">SRA</option>
+      <option value="structure">Structure</option>
+      <option value="taxonomy">Taxonomy</option>
+      <option value="unigene">UniGene</option>
+    </param>
+  </xml>
+  <xml name="db">
+    <conditional name="db">
+      <expand macro="dbselect" />
+      <when value="annotinfo">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="assembly">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="bioproject">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="native-None">BioProject Report</option>
+          <option value="native-xml">RecordSet (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="biosample">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="native-None">BioSample Report</option>
+          <option value="native-xml">BioSampleSet (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="biosystems">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="native-xml">Sys-set (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="blastdbinfo">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="books">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="cdd">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="clinvar">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="clone">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="dbvar">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="gap">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="gapplus">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="gds">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="native-xml">RecordSet (xml)</option>
+          <option value="summary-text">Summary (text)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="gencoll">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="gene">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="gene_table-xml">Gene Table (xml)</option>
+          <option value="native-asn.1">Entrezgene (asn.1)</option>
+          <option value="native-text">Gene Report (text)</option>
+          <option value="native-xml">Entrezgene-Set (xml)</option>
+          <option value="tabular-tabular">Tabular Report (tabular)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="genome">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="geoprofiles">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="grasp">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="gtr">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="homologene">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="alignmentscores-text">Alignment Scores (text)</option>
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="fasta-fasta">FASTA (fasta)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="homologene-text">Homologene Report (text)</option>
+          <option value="native-asn.1">HG-Entry (asn.1)</option>
+          <option value="native-text">Homologene List (text)</option>
+          <option value="native-xml">Entrez-Homologene-Set (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="medgen">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="mesh">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-text">Full Record (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="native-text">MeSH Report (text)</option>
+          <option value="native-xml">RecordSet (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="ncbisearch">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="nlmcatalog">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="native-text">Full Record (text)</option>
+          <option value="native-xml">NLMCatalogRecordSet (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="nuccore">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="acc-text">Accession Number (text)</option>
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="est-xml">EST Report (xml)</option>
+          <option value="fasta-fasta">FASTA (fasta)</option>
+          <option value="fasta-xml">TinySeq (xml)</option>
+          <option value="fasta_cds_aa-fasta">CDS Products (fasta)</option>
+          <option value="fasta_cds_na-fasta">Coding Regions (fasta)</option>
+          <option value="ft-text">Feature Table (text)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="gb-text">GenBank Flatfile (text)</option>
+          <option value="gb-xml">GBSet (xml)</option>
+          <option value="gbc-xml">INSDSet (xml)</option>
+          <option value="gbwithparts-text">GenBank with Contig Sequences (text)</option>
+          <option value="gene_fasta-fasta">FASTA of Gene (fasta)</option>
+          <option value="gp-text">GenPept Flatfile (text)</option>
+          <option value="gp-xml">GBSet (xml)</option>
+          <option value="gpc-xml">INSDSet (xml)</option>
+          <option value="gss-text">GSS Report (text)</option>
+          <option value="ipg-text">Identical Protein Report (text)</option>
+          <option value="ipg-xml">IPGReportSet (xml)</option>
+          <option value="native-text">Seq-entry (text)</option>
+          <option value="native-xml">Bioseq-set (xml)</option>
+          <option value="seqid-asn.1">Seq-id (asn.1)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="nucest">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="acc-text">Accession Number (text)</option>
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="est-xml">EST Report (xml)</option>
+          <option value="fasta-fasta">FASTA (fasta)</option>
+          <option value="fasta-xml">TinySeq (xml)</option>
+          <option value="fasta_cds_aa-fasta">CDS Products (fasta)</option>
+          <option value="fasta_cds_na-fasta">Coding Regions (fasta)</option>
+          <option value="ft-text">Feature Table (text)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="gb-text">GenBank Flatfile (text)</option>
+          <option value="gb-xml">GBSet (xml)</option>
+          <option value="gbc-xml">INSDSet (xml)</option>
+          <option value="gbwithparts-text">GenBank with Contig Sequences (text)</option>
+          <option value="gene_fasta-fasta">FASTA of Gene (fasta)</option>
+          <option value="gp-text">GenPept Flatfile (text)</option>
+          <option value="gp-xml">GBSet (xml)</option>
+          <option value="gpc-xml">INSDSet (xml)</option>
+          <option value="gss-text">GSS Report (text)</option>
+          <option value="ipg-text">Identical Protein Report (text)</option>
+          <option value="ipg-xml">IPGReportSet (xml)</option>
+          <option value="native-text">Seq-entry (text)</option>
+          <option value="native-xml">Bioseq-set (xml)</option>
+          <option value="seqid-asn.1">Seq-id (asn.1)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="nucgss">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="acc-text">Accession Number (text)</option>
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="est-xml">EST Report (xml)</option>
+          <option value="fasta-fasta">FASTA (fasta)</option>
+          <option value="fasta-xml">TinySeq (xml)</option>
+          <option value="fasta_cds_aa-fasta">CDS Products (fasta)</option>
+          <option value="fasta_cds_na-fasta">Coding Regions (fasta)</option>
+          <option value="ft-text">Feature Table (text)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="gb-text">GenBank Flatfile (text)</option>
+          <option value="gb-xml">GBSet (xml)</option>
+          <option value="gbc-xml">INSDSet (xml)</option>
+          <option value="gbwithparts-text">GenBank with Contig Sequences (text)</option>
+          <option value="gene_fasta-fasta">FASTA of Gene (fasta)</option>
+          <option value="gp-text">GenPept Flatfile (text)</option>
+          <option value="gp-xml">GBSet (xml)</option>
+          <option value="gpc-xml">INSDSet (xml)</option>
+          <option value="gss-text">GSS Report (text)</option>
+          <option value="ipg-text">Identical Protein Report (text)</option>
+          <option value="ipg-xml">IPGReportSet (xml)</option>
+          <option value="native-text">Seq-entry (text)</option>
+          <option value="native-xml">Bioseq-set (xml)</option>
+          <option value="seqid-asn.1">Seq-id (asn.1)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="nucleotide">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="acc-text">Accession Number (text)</option>
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="est-xml">EST Report (xml)</option>
+          <option value="fasta-fasta">FASTA (fasta)</option>
+          <option value="fasta-xml">TinySeq (xml)</option>
+          <option value="fasta_cds_aa-fasta">CDS Products (fasta)</option>
+          <option value="fasta_cds_na-fasta">Coding Regions (fasta)</option>
+          <option value="ft-text">Feature Table (text)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="gb-text">GenBank Flatfile (text)</option>
+          <option value="gb-xml">GBSet (xml)</option>
+          <option value="gbc-xml">INSDSet (xml)</option>
+          <option value="gbwithparts-text">GenBank with Contig Sequences (text)</option>
+          <option value="gene_fasta-fasta">FASTA of Gene (fasta)</option>
+          <option value="gp-text">GenPept Flatfile (text)</option>
+          <option value="gp-xml">GBSet (xml)</option>
+          <option value="gpc-xml">INSDSet (xml)</option>
+          <option value="gss-text">GSS Report (text)</option>
+          <option value="ipg-text">Identical Protein Report (text)</option>
+          <option value="ipg-xml">IPGReportSet (xml)</option>
+          <option value="native-text">Seq-entry (text)</option>
+          <option value="native-xml">Bioseq-set (xml)</option>
+          <option value="seqid-asn.1">Seq-id (asn.1)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="omim">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="orgtrack">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="pcassay">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="pccompound">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="pcsubstance">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="pmc">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="medline-text">MEDLINE (text)</option>
+          <option value="native-xml">pmc-articleset (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="popset">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="probe">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="protein">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="proteinclusters">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="pubmed">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="abstract-xml">Abstract (xml)</option>
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="medline-text">MEDLINE (text)</option>
+          <option value="native-asn.1">Pubmed-entry (asn.1)</option>
+          <option value="native-xml">PubmedArticleSet (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="pubmedhealth">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="seqannot">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="snp">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="chr-text">Chromosome Report (text)</option>
+          <option value="docset-text">Summary (text)</option>
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="fasta-fasta">FASTA (fasta)</option>
+          <option value="flt-text">Flat File (text)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="native-asn.1">Rs (asn.1)</option>
+          <option value="native-xml">ExchangeSet (xml)</option>
+          <option value="rsr-tabular">RS Cluster Report (tabular)</option>
+          <option value="ssexemplar-text">SS Exemplar List (text)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="sra">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="native-xml">EXPERIMENT_PACKAGE_SET (xml)</option>
+          <option value="runinfo-xml">SraRunInfo (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="structure">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="mmdb-asn.1">Ncbi-mime-asn1 strucseq (asn.1)</option>
+          <option value="native-text">MMDB Report (text)</option>
+          <option value="native-xml">RecordSet (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="taxonomy">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="native-text">Taxonomy List (text)</option>
+          <option value="native-xml">TaxaSet (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+      <when value="unigene">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-json">Document Summary (json)</option>
+          <option value="docsum-xml">Document Summary (xml)</option>
+          <option value="full-text">Full Document (text)</option>
+          <option value="full-xml">Full Document (xml)</option>
+          <option value="uilist-text">Unique Identifier List (text)</option>
+          <option value="uilist-xml">Unique Identifier List (xml)</option>
+        </param>
+      </when>
+    </conditional>
+  </xml>
+
+  <xml name="efetch_formats">
+    <change_format>
+      <when input="output_format" value="fasta_cds_na-fasta" format="fasta"/>
+      <when input="output_format" value="ipg-xml" format="xml"/>
+      <when input="output_format" value="gbc-xml" format="xml"/>
+      <when input="output_format" value="medline-text" format="text"/>
+      <when input="output_format" value="native-None" format="text"/>
+      <when input="output_format" value="mmdb-asn.1" format="asn1"/>
+      <when input="output_format" value="seqid-asn.1" format="asn1"/>
+      <when input="output_format" value="acc-text" format="text"/>
+      <when input="output_format" value="summary-text" format="text"/>
+      <when input="output_format" value="gene_fasta-fasta" format="fasta"/>
+      <when input="output_format" value="native-text" format="text"/>
+      <when input="output_format" value="gbwithparts-text" format="text"/>
+      <when input="output_format" value="gpc-xml" format="xml"/>
+      <when input="output_format" value="fasta_cds_aa-fasta" format="fasta"/>
+      <when input="output_format" value="gp-text" format="text"/>
+      <when input="output_format" value="gss-text" format="text"/>
+      <when input="output_format" value="ipg-text" format="text"/>
+      <when input="output_format" value="uilist-xml" format="xml"/>
+      <when input="output_format" value="docsum-xml" format="xml"/>
+      <when input="output_format" value="rsr-tabular" format="tabular"/>
+      <when input="output_format" value="uilist-text" format="text"/>
+      <when input="output_format" value="gb-text" format="text"/>
+      <when input="output_format" value="chr-text" format="text"/>
+      <when input="output_format" value="alignmentscores-text" format="text"/>
+      <when input="output_format" value="native-asn.1" format="asn1"/>
+      <when input="output_format" value="gp-xml" format="xml"/>
+      <when input="output_format" value="tabular-tabular" format="tabular"/>
+      <when input="output_format" value="ssexemplar-text" format="text"/>
+      <when input="output_format" value="docsum-json" format="json"/>
+      <when input="output_format" value="fasta-xml" format="xml"/>
+      <when input="output_format" value="runinfo-xml" format="xml"/>
+      <when input="output_format" value="flt-text" format="text"/>
+      <when input="output_format" value="fasta-fasta" format="fasta"/>
+      <when input="output_format" value="full-text" format="text"/>
+      <when input="output_format" value="gb-xml" format="xml"/>
+      <when input="output_format" value="abstract-xml" format="xml"/>
+      <when input="output_format" value="full-xml" format="xml"/>
+      <when input="output_format" value="ft-text" format="text"/>
+      <when input="output_format" value="homologene-text" format="text"/>
+      <when input="output_format" value="est-xml" format="xml"/>
+      <when input="output_format" value="gene_table-xml" format="xml"/>
+      <when input="output_format" value="docset-text" format="text"/>
+      <when input="output_format" value="native-xml" format="xml"/>
+    </change_format>
+  </xml>
+  <token name="@LIST_OR_HIST@">
+#if $query_source.qss == "history":
+    --history_file $query_source.history_file
+#else if $query_source.qss == "id_file":
+    --id_list $query_source.id_file
+#else if $query_source.qss == "id_list":
+    --id $query_source.id_list
+#end if
+    </token>
+  <xml name="list_or_hist">
+    <conditional name="query_source">
+      <param name="qss" type="select" label="Select source for IDs">
+        <option value="history">NCBI WebEnv History</option>
+        <option value="id_file">File containing IDs (one per line)</option>
+        <option value="id_list">Direct Entry</option>
+      </param>
+      <when value="history">
+        <param label="History File" name="history_file" type="data" format="json"/>
+      </when>
+      <when value="id_file">
+        <param label="ID List" name="id_file" type="data" format="text,tabular"/>
+      </when>
+      <when value="id_list">
+        <param label="ID List" name="id_list" type="text" area="true" help="Newline/Comma separated list of IDs"/>
+      </when>
+    </conditional>
+  </xml>
+  <xml name="history_out">
+    <data format="json" name="history" label="NCBI Entrez WebEnv History">
+      <yield/>
+    </data>
+  </xml>
+  <xml name="citations">
+    <citations>
+      <citation type="bibtex">@Book{ncbiEutils,
+          author = {Eric Sayers},
+          title = {Entrez Programming Utilities Help},
+          year = {2010},
+          publisher = {National Center for Biotechnology Information, Bethesda, Maryland},
+          note = {http://ww.ncbi.nlm.nih.gov/books/NBK25500/}
+      }</citation>
+    </citations>
+  </xml>
+  <xml name="requirements">
+    <requirements>
+      <requirement type="package" version="2.7">python</requirement>
+      <requirement type="package" version="1.66">biopython</requirement>
+    </requirements>
+  </xml>
+  <xml name="linkname">
+    <param name="linkname" type="select" label="To NCBI Database">
+        <!-- TODO: http://eutils.ncbi.nlm.nih.gov/entrez/query/static/entrezlinks.html -->
+    </param>
+  </xml>
+</macros>
diff -r 000000000000 -r 92bd8a680b9d test-data/ecitmatch.results.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ecitmatch.results.tsv	Thu Jul 07 02:41:02 2016 -0400
@@ -0,0 +1,2 @@
+	1991	88	3248	mann bj	citation_1	2014248
+
diff -r 000000000000 -r 92bd8a680b9d test-data/ecitmatch.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ecitmatch.tsv	Thu Jul 07 02:41:02 2016 -0400
@@ -0,0 +1,2 @@
+#journal	year	volume	first page	author	key
+proc natl acad sci u s a	1991	88	3248	mann bj	citation_1
diff -r 000000000000 -r 92bd8a680b9d test-data/egquery.1.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/egquery.1.xml	Thu Jul 07 02:41:02 2016 -0400
@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE Result PUBLIC "-//NLM//DTD eSearchResult, January 2004//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/egquery.dtd">
+<Result>
+   
+    <Term>bacteriophage</Term>
+    
+    <eGQueryResult>
diff -r 000000000000 -r 92bd8a680b9d test-data/esearch.pubmed.2014-01-pnas.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/esearch.pubmed.2014-01-pnas.xml	Thu Jul 07 02:41:02 2016 -0400
@@ -0,0 +1,25 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE eSearchResult PUBLIC "-//NLM//DTD esearch 20060628//EN" "http://eutils.ncbi.nlm.nih.gov/eutils/dtd/20060628/esearch.dtd">
+<eSearchResult><Count>524</Count><RetMax>20</RetMax><RetStart>0</RetStart><IdList>
+<Id>24620368</Id>
+<Id>24613929</Id>
+<Id>24596955</Id>
+<Id>24596954</Id>
+<Id>24571024</Id>
+<Id>24555201</Id>
+<Id>24555200</Id>
+<Id>24550301</Id>
+<Id>24520173</Id>
+<Id>24520172</Id>
+<Id>24497494</Id>
+<Id>24497493</Id>
+<Id>24488973</Id>
+<Id>24488972</Id>
+<Id>24488971</Id>
+<Id>24481254</Id>
+<Id>24481253</Id>
+<Id>24481252</Id>
+<Id>24477693</Id>
+<Id>24477692</Id>
+</IdList><TranslationSet><Translation>     <From>PNAS[ta]</From>     <To>"Proc Natl Acad Sci U S A"[Journal]</To>    </Translation></TranslationSet><TranslationStack>   <TermSet>    <Term>"Proc Natl Acad Sci U S A"[Journal]</Term>    <Field>Journal</Field>    <Count>124812</Count>    <Explode>N</Explode>   </TermSet>   <TermSet>    <Term>2014/01/01[PDAT]</Term>    <Field>PDAT</Field>    <Count>0</Count>    <Explode>N</Explode>   </TermSet>   <TermSet>    <Term>2014/02/01[PDAT]</Term>    <Field>PDAT</Field>    <Count>0</Count>    <Explode>N</Explode>   </TermSet>   <OP>RANGE</OP>   <OP>AND</OP>  </TranslationStack><QueryTranslation>"Proc Natl Acad Sci U S A"[Journal] AND 2014/01/01[PDAT] : 2014/02/01[PDAT]</QueryTranslation></eSearchResult>
+
diff -r 000000000000 -r 92bd8a680b9d test-data/esearch.pubmed.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/esearch.pubmed.xml	Thu Jul 07 02:41:02 2016 -0400
@@ -0,0 +1,25 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE eSearchResult PUBLIC "-//NLM//DTD esearch 20060628//EN" "http://eutils.ncbi.nlm.nih.gov/eutils/dtd/20060628/esearch.dtd">
+<eSearchResult><Count>2651</Count><RetMax>20</RetMax><RetStart>0</RetStart><IdList>
+<Id>16578858</Id>
+<Id>11186225</Id>
+<Id>11121081</Id>
+<Id>11121080</Id>
+<Id>11121079</Id>
+<Id>11121078</Id>
+<Id>11121077</Id>
+<Id>11121076</Id>
+<Id>11121075</Id>
+<Id>11121074</Id>
+<Id>11121073</Id>
+<Id>11121072</Id>
+<Id>11121071</Id>
+<Id>11121070</Id>
+<Id>11121069</Id>
+<Id>11121068</Id>
+<Id>11121067</Id>
+<Id>11121066</Id>
+<Id>11121065</Id>
+<Id>11121064</Id>
+</IdList><TranslationSet><Translation>     <From>PNAS[ta]</From>     <To>"Proc Natl Acad Sci U S A"[Journal]</To>    </Translation></TranslationSet><TranslationStack>   <TermSet>    <Term>"Proc Natl Acad Sci U S A"[Journal]</Term>    <Field>Journal</Field>    <Count>124812</Count>    <Explode>N</Explode>   </TermSet>   <TermSet>    <Term>97[vi]</Term>    <Field>vi</Field>    <Count>77218</Count>    <Explode>N</Explode>   </TermSet>   <OP>AND</OP>   <OP>GROUP</OP>  </TranslationStack><QueryTranslation>"Proc Natl Acad Sci U S A"[Journal] AND 97[vi]</QueryTranslation></eSearchResult>
+
diff -r 000000000000 -r 92bd8a680b9d test-data/esummary.tax.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/esummary.tax.xml	Thu Jul 07 02:41:02 2016 -0400
@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE eSummaryResult PUBLIC "-//NLM//DTD esummary v1 20041029//EN" "http://eutils.ncbi.nlm.nih.gov/eutils/dtd/20041029/esummary-v1.dtd">
+<eSummaryResult>
+<DocSum>
+	<Id>10239</Id>
+	<Item Name="Status" Type="String">active</Item>
+	<Item Name="Rank" Type="String">superkingdom</Item>
+	<Item Name="Division" Type="String">viruses</Item>
+	<Item Name="ScientificName" Type="String">Viruses</Item>
+	<Item Name="CommonName" Type="String"></Item>
+	<Item Name="TaxId" Type="Integer">10239</Item>
+	<Item Name="AkaTaxId" Type="Integer">0</Item>
+	<Item Name="Genus" Type="String"></Item>
+	<Item Name="Species" Type="String"></Item>
+	<Item Name="Subsp" Type="String"></Item>
+	<Item Name="ModificationDate" Type="Date">2010/11/23 00:00</Item>
+</DocSum>
+
+</eSummaryResult>
+
diff -r 000000000000 -r 92bd8a680b9d test-data/example.history.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.history.json	Thu Jul 07 02:41:02 2016 -0400
@@ -0,0 +1,4 @@
+{
+    "QueryKey": "1", 
+    "WebEnv": "NCID_1_9485527_130.14.22.215_9001_1430928295_33285243_0MetA0_S_MegaStore_F_1"
+}
diff -r 000000000000 -r 92bd8a680b9d test-data/pm-tax-neighbor.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pm-tax-neighbor.xml	Thu Jul 07 02:41:02 2016 -0400
@@ -0,0 +1,24 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE eLinkResult PUBLIC "-//NLM//DTD elink 20101123//EN" "http://eutils.ncbi.nlm.nih.gov/eutils/dtd/20101123/elink.dtd">
+<eLinkResult>
+
+  <LinkSet>
+    <DbFrom>taxonomy</DbFrom>
+    <IdList>
+      <Id>510899</Id>
+    </IdList>
+    
+    <LinkSetDb>
+      <DbTo>pubmed</DbTo>
+      <LinkName>taxonomy_pubmed_entrez</LinkName>
+      
+        <Link>
+				<Id>22241621</Id>
+			</Link>
+      
+    </LinkSetDb>
+    
+    
+  </LinkSet>
+</eLinkResult>
+
diff -r 000000000000 -r 92bd8a680b9d test-data/pubmed.metadata.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pubmed.metadata.xml	Thu Jul 07 02:41:02 2016 -0400
@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE eInfoResult PUBLIC "-//NLM//DTD einfo 20130322//EN" "http://eutils.ncbi.nlm.nih.gov/eutils/dtd/20130322/einfo.dtd">
+<eInfoResult>
+	<DbInfo>
+	<DbName>pubmed</DbName>
+	<MenuName>PubMed</MenuName>
+	<Description>PubMed bibliographic record</Description>
diff -r 000000000000 -r 92bd8a680b9d test-data/viruses.tax.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/viruses.tax.xml	Thu Jul 07 02:41:02 2016 -0400
@@ -0,0 +1,29 @@
+<?xml version="1.0"?>
+<!DOCTYPE TaxaSet PUBLIC "-//NLM//DTD Taxon, 14th January 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/taxon.dtd">
+<TaxaSet><Taxon>
+    <TaxId>10239</TaxId>
+    <ScientificName>Viruses</ScientificName>
+    <OtherNames>
+        <BlastName>viruses</BlastName>
+        <Synonym>Vira</Synonym>
+        <Synonym>Viridae</Synonym>
+    </OtherNames>
+    <ParentTaxId>1</ParentTaxId>
+    <Rank>superkingdom</Rank>
+    <Division>Viruses</Division>
+    <GeneticCode>
+        <GCId>1</GCId>
+        <GCName>Standard</GCName>
+    </GeneticCode>
+    <MitoGeneticCode>
+        <MGCId>0</MGCId>
+        <MGCName>Unspecified</MGCName>
+    </MitoGeneticCode>
+    <Lineage/>
+    <CreateDate>1995/02/27 09:24:00</CreateDate>
+    <UpdateDate>2010/11/23 11:40:11</UpdateDate>
+    <PubDate>1993/04/20 01:00:00</PubDate>
+</Taxon>
+
+</TaxaSet>
+
diff -r 000000000000 -r 92bd8a680b9d tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Jul 07 02:41:02 2016 -0400
@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <set_environment version="1.0">
+    <environment_variable action="set_to" name="NCBI_EUTILS_CONTACT">/please set the administrator's contact email in the corresponding env.sh file/</environment_variable>
+  </set_environment>
+  <package name="biopython" version="1.66">
+    <repository changeset_revision="8433ee4531ff" name="package_biopython_1_66" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" />
+  </package>
+</tool_dependency>