--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/generate_macros_xml.pl	Wed Sep 23 09:48:53 2020 +0000
@@ -0,0 +1,841 @@
+#!/usr/bin/env perl
+
+#Usage: perl generate_macros_xml.pl > macros.xml
+
+#Note, this script uses einfo.py to get database info.  It also uses manually compiled data stored at the bottom of this script that is based on: https://www.ncbi.nlm.nih.gov/books/NBK25499/table/chapter4.T._valid_values_of__retmode_and/?report=objectonly
+#The data in the table on that page was manipulated to replace nulls with 'none', remove duplicates, and add missing formats based on correspondence with MLN.
+
+##
+## use einfo to retrieve all the valid databases
+##
+
+print STDERR "Retrieving database list\n";
+
+my $dbxml = `python einfo.py --user_email "planemo@galaxyproject.org" --admin_email "planemo@galaxyproject.org;test@bx.psu.edu"`;
+
+my(@dblist);
+my $dbs     = {};
+my $dbfroms = {};
+my $dbnames = {};
+foreach(split(/\n/,$dbxml))
+  {
+    if(/<DbName>(.+)<\/DbName>/)
+      {
+        my $db = $1;
+        push(@dblist,$db);
+        $dbs->{$db}     = 0;
+        $dbfroms->{$db} = 0;
+        $dbnames->{$db} = $_;
+      }
+  }
+
+##
+## Use einfo to retrieve all the valid links for each database (Note: some databases are not linked)
+##
+
+my $h = {};
+foreach my $db (sort {$dbnames->{$a} cmp $dbnames->{$b}} @dblist)
+  {
+    sleep(2);
+
+    print STDERR "Retrieving info for $db\n";
+
+    my $response = `python einfo.py --db $db --user_email "planemo\@galaxyproject.org" --admin_email "planemo\@galaxyproject.org;test\@bx.psu.edu"`;
+
+    my $dolinks = 0;
+    my $link    = "";
+    my $name    = "";
+
+    foreach(split(/\n/,$response))
+      {
+        if(/<LinkList>/)
+          {
+            $dolinks = 1;
+            #Save whether there exist links from this database
+            $dbfroms->{$db} = 1;
+          }
+        elsif(!$dolinks)
+          {
+            if(/<MenuName>(.+)<\/MenuName>/)
+              {$dbnames->{$db} = "$1 ($db)"}
+          }
+        elsif($dolinks)
+          {
+            if(/<Name>(.+)<\/Name>/)
+              {$link=$1}
+            elsif(/<Menu>(.*)<\/Menu>/)
+              {$name=$1}
+            elsif(/<DbTo>(.+)<\/DbTo>/)
+              {
+                $dbto=$1;
+                push(@{$h->{$db}->{$dbto}},[$link,$name]);
+                $link="";
+                $name="";
+              }
+          }
+      }
+  }
+
+my @sorted_dblist = sort {$dbnames->{$a} cmp $dbnames->{$b}} @dblist;
+
+##
+## Generate XML to govern the valid databases to use with efetch
+##
+
+my $efetch_dbhash = {}; #->{efetch-compatible-db}->{rettype-retmode-galaxy_format} = format_name (galaxy_format)
+while(<DATA>)
+  {
+    chomp;
+    my($db,$galaxy_format,$retmode,$rettype,$format_name) = split(/\t/,$_);
+    $efetch_dbhash->{$db}->{"$rettype-$retmode-$galaxy_format"} =
+      "$format_name ($galaxy_format)";
+  }
+
+#EFetch database select list
+
+print << 'EOXML';
+  <xml name="dbselect_efetch" token_name="db_select" token_label="NCBI Database to Query">
+    <param name="@NAME@" type="select" label="@LABEL@">
+EOXML
+
+foreach my $db (grep {exists($dbs->{$_})}
+                sort {$dbnames->{$a} cmp $dbnames->{$b}}
+                keys(%$efetch_dbhash))
+  {
+    my $selected = '';
+    if($db eq 'pubmed')
+      {$selected = ' selected="True"'}
+    print << "    EOXML";
+      <option value="$db"$selected>$dbnames->{$db}</option>
+    EOXML
+  }
+
+print << 'EOXML';
+    </param>
+  </xml>
+EOXML
+
+#EFetch output formats
+
+print << 'EOXML';
+  <xml name="efetchdb">
+    <conditional name="db">
+      <expand macro="dbselect_efetch" />
+EOXML
+
+foreach my $db (grep {exists($dbs->{$_})}
+                sort {$dbnames->{$a} cmp $dbnames->{$b}}
+                keys(%$efetch_dbhash))
+  {
+    print << "    EOXML";
+      <when value="$db">
+        <param name="output_format" type="select" label="Output Format">
+    EOXML
+
+    foreach my $eutils_format (sort {$efetch_dbhash->{$db}->{$a} cmp
+                                       $efetch_dbhash->{$db}->{$b}}
+                               keys(%{$efetch_dbhash->{$db}}))
+      {
+        print << "        EOXML";
+          <option value="$eutils_format">$efetch_dbhash->{$db}->{$eutils_format}</option>
+        EOXML
+      }
+
+    print << "    EOXML";
+        </param>
+      </when>
+    EOXML
+  }
+
+print << 'EOXML';
+    </conditional>
+  </xml>
+EOXML
+
+##
+## Create a select list for the databases linked *from*
+##
+
+print << 'EOXML';
+  <xml name="dbselect" token_name="db_select" token_label="NCBI Database to Query">
+    <param name="@NAME@" type="select" label="@LABEL@">
+EOXML
+
+foreach my $from (@sorted_dblist)
+  {
+    print << "    EOXML";
+      <option value="$from">$dbnames->{$from}</option>
+    EOXML
+  }
+
+print << 'EOXML';
+    </param>
+  </xml>
+EOXML
+
+##
+## Create a select list for the databases linked *to*
+##
+
+print << 'EOXML';
+  <xml name="dbselect_linked" token_name="db_select_linked" token_label="NCBI Database to Use">
+    <param name="@NAME@" type="select" label="@LABEL@">
+EOXML
+
+foreach my $from (grep {$dbfroms->{$_}} @sorted_dblist)
+  {
+    print << "    EOXML";
+      <option value="$from">$dbnames->{$from}</option>
+    EOXML
+  }
+
+print << 'EOXML';
+    </param>
+  </xml>
+EOXML
+
+##
+## Create empty entries for commands that take no *to* database or link
+##
+
+print << 'EOXML';
+  <xml name="none_link_macro">
+            <conditional name="db_to">
+              <param name="db_select_to" type="select" label="To NCBI Database (n/a)">
+                <option value="n/a">Not applicable</option>
+              </param>
+              <when value="n/a">
+                <param name="linkname" type="select" label="Link Name (n/a)">
+                  <option value="n/a">Not applicable</option>
+                </param>
+              </when>
+            </conditional>
+  </xml>
+  <xml name="db_link_macro">
+        <conditional name="db_from_link">
+          <expand macro="dbselect_linked" name="db_select_from_link" label="From NCBI Database" />
+EOXML
+
+foreach(grep {$dbfroms->{$_}} @sorted_dblist)
+  {
+    print << "    EOXML";
+          <when value="$_">
+            <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" />
+          </when>
+    EOXML
+  }
+
+print << 'EOXML';
+        </conditional>
+  </xml>
+EOXML
+
+##
+## This is the master macro for the command selection
+##
+
+print << 'EOXML';
+  <xml name="linkmacro">
+    <conditional name="cmd">
+      <param name="cmd_select" type="select" label="Link Method" help="Fetch UIDs from the 'To' Database that are linked to supplied UIDs in the 'From' database">
+        <option value="neighbor" selected="true">Neighbor (neighbor)</option>
+        <option value="neighbor_history">Neighbor, save result in history server (neighbor_history)</option>
+        <option value="neighbor_score">Neighbor Score (neighbor_score)</option>
+        <option value="acheck">Show available links to any database (acheck)</option>
+        <option value="ncheck">Show available links within the same database (ncheck)</option>
+        <option value="lcheck">Show available links to external sources (LinkOuts) (lcheck)</option>
+        <option value="llinks">Show available URLs and attributes for non-library LinkOut providers (llinks)</option>
+        <option value="llinkslib">Show available URLs and attributes for all LinkOut Providers (llinkslib)</option>
+        <option value="prlinks">Show available primary LinkOut Provider Links (prlinks)</option>
+      </param>
+      <when value="neighbor">
+        <expand macro="db_db_link_macro" name="link_select" label="Link name" />
+        <param name="output_format" type="select" label="Output Format">
+          <option value="xml">ID File (xml)</option>
+          <option value="json">ID File (json)</option>
+          <option value="text" selected="true">ID File (tabular)</option>
+        </param>
+      </when>
+      <when value="neighbor_history">
+        <expand macro="db_db_link_macro" name="link_select" label="Link name" />
+        <param name="output_format" type="select" label="Output Format">
+          <option value="json">History File (json)</option>
+          <option value="xml" selected="true">History File (xml)</option>
+        </param>
+      </when>
+      <when value="neighbor_score">
+        <expand macro="db_db_link_macro" name="link_select" label="Link name" />
+        <param name="output_format" type="select" label="Output Format">
+          <option value="xml">ID File (xml)</option>
+          <option value="json">ID File (json)</option>
+          <option value="text" selected="true">ID File (tabular)</option>
+        </param>
+      </when>
+      <when value="acheck">
+        <expand macro="db_link_macro" name="db_select_from_link" label="From NCBI Database" />
+        <param name="output_format" type="select" label="Output Format">
+          <option value="xml" selected="True">Link Description File (xml)</option>
+          <option value="json">Link Description File (json)</option>
+        </param>
+      </when>
+      <when value="ncheck">
+        <expand macro="db_link_macro" name="db_select_from_link" label="From NCBI Database" />
+        <param name="output_format" type="select" label="Output Format">
+          <option value="xml" selected="True">Link Description File (xml)</option>
+          <option value="json">Link Description File (json)</option>
+        </param>
+      </when>
+      <when value="lcheck">
+        <expand macro="db_link_macro" name="db_select_from_link" label="From NCBI Database" />
+        <param name="output_format" type="select" label="Output Format">
+          <option value="xml" selected="True">Link Description File (xml)</option>
+          <option value="json">Link Description File (json)</option>
+        </param>
+      </when>
+      <when value="llinks">
+        <expand macro="db_link_macro" name="db_select_from_link" label="From NCBI Database" />
+        <param name="output_format" type="select" label="Output Format">
+          <option value="xml" selected="True">Link Description File (xml)</option>
+          <option value="json">Link Description File (json)</option>
+        </param>
+      </when>
+      <when value="llinkslib">
+        <expand macro="db_link_macro" name="db_select_from_link" label="From NCBI Database" />
+        <param name="output_format" type="select" label="Output Format">
+          <option value="xml" selected="true">Link Description File (xml)</option>
+          <option value="json">Link Description File (json)</option>
+        </param>
+      </when>
+      <when value="prlinks">
+        <expand macro="db_link_macro" name="db_select_from_link" label="From NCBI Database" />
+        <param name="output_format" type="select" label="Output Format">
+          <option value="xml" selected="true">Link Description File (xml)</option>
+          <option value="json">Link Description File (json)</option>
+        </param>
+      </when>
+    </conditional>
+  </xml>
+EOXML
+
+##
+## Create selections for valid links for command types neighbor, neighbor_history, and neighbor_score
+##
+
+print << 'EOXML';
+  <xml name="db_db_link_macro">
+        <conditional name="db_from_link">
+          <expand macro="dbselect_linked" name="db_select_from_link" label="From NCBI Database" />
+EOXML
+
+foreach my $from (grep {$dbfroms->{$_}} @sorted_dblist)
+  {
+    print STDERR ("Creating Links From: $from\n");
+
+    print << "    EOXML";
+          <when value="$from">
+            <conditional name="db_to">
+              <param name="db_select_to" type="select" label="To NCBI Database">
+    EOXML
+
+    my @dbtos = (grep {exists($h->{$from}) && exists($h->{$from}->{$_})}
+                 @sorted_dblist);
+    foreach(@dbtos)
+      {
+        print << "        EOXML";
+                <option value="$_">$dbnames->{$_}</option>
+        EOXML
+      }
+    if(scalar(@dbtos) == 0)
+      {
+        #Provide an option for a self-link: from->from
+        print << "        EOXML";
+                <option value="$from">$dbnames->{$from}</option>
+        EOXML
+      }
+
+    print << '    EOXML';
+              </param>
+    EOXML
+
+    if(exists($h->{$from}))
+      {
+        #There do exist links to invalid(/outdated/non-existant) databases that
+        #would result in an error if they are selected, so we use the original
+        #@dblist instead of the keys present in the sub hash of $h->{$from}, and
+        #then check for existence in the sub-hash
+        foreach my $to (grep {exists($h->{$from}->{$_})} @sorted_dblist)
+          {
+            print STDERR ("\tTo: $to Links: ",
+                          join(',',map {$_->[0]} @{$h->{$from}->{$to}}),
+                          "\n");
+
+            print << "            EOXML";
+              <when value="$to">
+                <param name="linkname" type="select" label="Link Name">
+                  <option value="None">All Links</option>
+            EOXML
+
+            foreach(sort {"$a->[1] ($a->[0])" cmp "$b->[1] ($b->[0])"}
+                    @{$h->{$from}->{$to}})
+              {
+                print << "                EOXML";
+                  <option value="$_->[0]">$_->[1] ($_->[0])</option>
+                EOXML
+              }
+
+            print << "            EOXML";
+                </param>
+              </when>
+            EOXML
+
+          }
+      }
+    else
+      {
+        ##
+        ## Add-on selections for self-links for command types neighbor,
+        ## neighbor_history, and neighbor_score
+        ## Note, I'm not sure this would yield a valid result from elink
+        ##
+
+        #This shows $from, but this is the 'when' for db_to conditional
+        print << "        EOXML";
+              <when value="$from">
+                <param name="linkname" type="select" label="Link Name">
+                  <option value="none">All Links</option>
+                </param>
+              </when>
+        EOXML
+      }
+
+    print << '    EOXML';
+            </conditional>
+          </when>
+    EOXML
+  }
+
+##
+## Add-on selections for self-links for command types neighbor,
+## neighbor_history, and neighbor_score
+## Note, I'm not sure this would yield a valid result from elink
+##
+
+foreach my $from (grep {!exists($h->{$_})} @sorted_dblist)
+  {
+    print << "EOXML";
+          <when value=\"$from\">
+            <conditional name=\"db_to\">
+              <param name=\"db_select_to\" type=\"select\" label=\"To NCBI Database\">
+                <option value=\"none\">Not applicable</option>
+              </param>
+              <when value=\"none\">
+                <param name=\"linkname\" type=\"select\" label=\"Link Name\">
+                  <option value=\"none\">Not applicable</option>
+                </param>
+              </when>
+            </conditional>
+          </when>
+EOXML
+  }
+
+##
+## This is the corresponding code for using the selections to add the respective command line options
+##
+
+print << 'EOXML';
+    </conditional>
+  </xml>
+EOXML
+
+print << 'EOXML';
+  <token name="@LINK_TOKEN@">
+    <![CDATA[
+#if $cmd.db_from_link.db_to.db_select_to == 'n/a':
+    none
+#else:
+    $cmd.db_from_link.db_to.db_select_to
+#end if
+
+$cmd.db_from_link.db_select_from_link
+
+$cmd.cmd_select
+
+#if $cmd.output_format == 'json':
+    --retmode json
+#elif $cmd.output_format == 'text':
+    --retmode uilist
+#else:
+    --retmode xml
+#end if
+
+#if $cmd.db_from_link.db_to.linkname != 'None' and $cmd.cmd_select in ('neighbor', 'neighbor_history', 'neighbor_score'):
+    --linkname $cmd.db_from_link.db_to.linkname
+#end if
+    ]]>
+  </token>
+EOXML
+
+sub startXML
+  {
+    print << '    EOXML';
+<?xml version="1.0"?>
+<macros>
+  <token name="@PROFILE@">18.01</token>
+  <token name="@WRAPPER_VERSION@">1.70</token>
+  <token name="@EMAIL_ARGUMENTS@">
+--user_email "$__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 `https://www.nlm.nih.gov/databases/download/data_distrib_main.html <https://www.nlm.nih.gov/databases/download/data_distrib_main.html>`__
+
+The `full disclaimer <https://www.ncbi.nlm.nih.gov/home/about/policies/>`__ 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>
+  <token name="@LIST_OR_HIST@">
+#if $query_source.qss == "history_json":
+    --history_file $query_source.history_file
+#else if $query_source.qss == "history_xml":
+    --history_xml $query_source.history_xml
+#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
+#else if $query_source.qss == "id_xml":
+    --id_xml $query_source.id_xml
+#else if $query_source.qss == "id_json":
+    --id_json $query_source.id_json
+#end if
+  </token>
+  <xml name="list_or_hist">
+    <conditional name="query_source">
+      <param name="qss" type="select" label="Enter Query IDs by..." help="Files output by ELink or ESearch are acceptable.  Query IDs in an ELink result are ignored.">
+        <option value="history_json">History File (JSON)</option>
+        <option value="history_xml">History File (XML)</option>
+        <option value="id_file" selected="True">ID file (Tabular)</option>
+        <option value="id_xml">ID File (XML)</option>
+        <option value="id_json">ID File (JSON)</option>
+        <option value="id_list">Paste IDs</option>
+      </param>
+      <when value="history_json">
+        <param label="History File (JSON)" name="history_file" type="data" format="json" help="A JSON file containing the WebEnv ID and Query Key referencing the search on the NCBI history server"/>
+      </when>
+      <when value="history_xml">
+        <param label="History File (XML)" name="history_xml" type="data" format="xml" help="An XML file containing the WebEnv ID and Query Key referencing the search on the NCBI history server"/>
+      </when>
+      <when value="id_file">
+        <param label="ID File (Text)" name="id_file" type="data" format="text,tabular" help="A Text file containing one ID per line"/>
+      </when>
+      <when value="id_xml">
+        <param label="ID File (XML)" name="id_xml" type="data" format="xml" help="ESearch or ELink Result XML file"/>
+      </when>
+      <when value="id_json">
+        <param label="ID File (JSON)" name="id_json" type="data" format="json" help="ESearch or ELink Result JSON file"/>
+      </when>
+      <when value="id_list">
+        <param label="Paste ID List" name="id_list" type="text" area="true" help="Newline/Comma separated list of IDs"/>
+      </when>
+    </conditional>
+  </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 = {https://www.ncbi.nlm.nih.gov/books/NBK25500/}
+      }</citation>
+    </citations>
+  </xml>
+  <xml name="requirements">
+    <requirements>
+      <requirement type="package" version="1.70">biopython</requirement>
+    </requirements>
+  </xml>
+  <token name="@EFETCH_FORMAT_TOKEN@">
+    <![CDATA[
+
+    ## This token must go at the end of the efetch command
+
+    #set rettype, retmode, format = str($db.output_format).split('-')
+
+    #if retmode != "none":
+      --retmode $retmode
+    #end if
+    ## Otherwise, defaults to a None/empty which implies 'default' to NCBI
+
+    #if rettype != "none":
+        --rettype $rettype
+    #end if
+
+    --galaxy_format $format
+
+    ]]>
+  </token>
+    EOXML
+  }
+
+sub endXML
+  {
+    print << '    EOXML';
+</macros>
+    EOXML
+  }
+
+BEGIN {startXML()}
+END   {endXML()}
+
+
+##
+## Output formats for efetch mapped to galaxy formats
+##
+
+#Based on:
+#https://www.ncbi.nlm.nih.gov/books/NBK25499/table/chapter4.T._valid_values_of__retmode_and/?report=objectonly
+
+#Note: While json works for esearch and elink, the only database that supports
+#json (according to an NLM support ticket I have about this) is snp
+
+#The output_format param value for these will be "rettype-retmode-format"
+
+#db	galaxy	retmode	rettype	format_name
+__DATA__
+bioproject	tabular	text	uilist	List of UIDs
+bioproject	xml	xml	docsum	Document summary
+bioproject	xml	xml	uilist	List of UIDs
+bioproject	xml	xml	xml	Full record
+biosample	tabular	text	uilist	List of UIDs
+biosample	txt	text	full	Full record
+biosample	xml	xml	docsum	Document summary
+biosample	xml	xml	full	Full record
+biosample	xml	xml	uilist	List of UIDs
+biosystems	tabular	text	uilist	List of UIDs
+biosystems	xml	xml	docsum	Document summary
+biosystems	xml	xml	uilist	List of UIDs
+biosystems	xml	xml	xml	Full record
+clinvar	tabular	text	uilist	List of UIDs
+clinvar	xml	xml	clinvarset	ClinVar Set
+clinvar	xml	xml	docsum	Document summary
+clinvar	xml	xml	uilist	List of UIDs
+clinvar	xml	none	none	Full
+gds	tabular	text	uilist	List of UIDs
+gds	txt	text	summary	Summary
+gds	xml	xml	docsum	Document summary
+gds	xml	xml	uilist	List of UIDs
+gds	xml	none	none	Full
+gene	txt	text	gene_table	Gene table
+gene	tabular	text	uilist	List of UIDs
+gene	txt	asn.1	none	text ASN.1
+gene	xml	xml	docsum	Document summary
+gene	xml	xml	none	Full
+gene	xml	xml	uilist	List of UIDs
+gtr	tabular	text	uilist	List of UIDs
+gtr	xml	xml	docsum	Document summary
+gtr	xml	xml	gtracc	GTR Test Report
+gtr	xml	xml	uilist	List of UIDs
+gtr	xml	none	none	Full
+homologene	fasta	text	fasta	FASTA
+homologene	tabular	text	alignmentscores	Alignment scores
+homologene	tabular	text	uilist	List of UIDs
+homologene	txt	asn.1	none	text ASN.1
+homologene	txt	text	homologene	HomoloGene
+homologene	xml	xml	docsum	Document summary
+homologene	xml	xml	none	Full
+homologene	xml	xml	uilist	List of UIDs
+mesh	tabular	text	uilist	List of UIDs
+mesh	txt	text	full	Full record
+mesh	xml	xml	docsum	Document summary
+mesh	xml	xml	uilist	List of UIDs
+nlmcatalog	tabular	text	uilist	List of UIDs
+nlmcatalog	txt	text	none	Full record
+nlmcatalog	xml	xml	docsum	Document summary
+nlmcatalog	xml	xml	none	Full
+nlmcatalog	xml	xml	uilist	List of UIDs
+nuccore	binary	asn.1	none	binary ASN.1
+nuccore	fasta	text	fasta	FASTA
+nuccore	fasta	text	fasta_cds_aa	CDS protein FASTA
+nuccore	fasta	text	fasta_cds_na	CDS nucleotide FASTA
+nuccore	genbank	text	gb	GenBank flat file
+nuccore	genbank	text	gbwithparts	GenBank flat file with full sequence (contigs)
+nuccore	tabular	text	acc	Accession number(s)
+nuccore	txt	text	ft	Feature table
+nuccore	tabular	text	seqid	SeqID string
+nuccore	tabular	text	uilist	List of UIDs
+nuccore	txt	text	none	text ASN.1
+nuccore	xml	xml	docsum	Document summary
+nuccore	xml	xml	fasta	TinySeq
+nuccore	xml	xml	gb	GBSeq
+nuccore	xml	xml	gbc	INSDSeq
+nuccore	xml	xml	native	Full record
+nuccore	xml	xml	uilist	List of UIDs
+nucest	binary	asn.1	none	binary ASN.1
+nucest	fasta	text	fasta	FASTA
+nucest	genbank	text	gb	GenBank flat file
+nucest	tabular	text	acc	Accession number(s)
+nucest	tabular	text	seqid	SeqID string
+nucest	tabular	text	uilist	List of UIDs
+nucest	txt	text	est	EST report
+nucest	txt	text	none	text ASN.1
+nucest	xml	xml	docsum	Document summary
+nucest	xml	xml	fasta	TinySeq
+nucest	xml	xml	gb	GBSeq
+nucest	xml	xml	gbc	INSDSeq
+nucest	xml	xml	native	Full record
+nucest	xml	xml	uilist	List of UIDs
+nucgss	binary	asn.1	none	binary ASN.1
+nucgss	fasta	text	fasta	FASTA
+nucgss	genbank	text	gb	GenBank flat file
+nucgss	tabular	text	acc	Accession number(s)
+nucgss	tabular	text	seqid	SeqID string
+nucgss	tabular	text	uilist	List of UIDs
+nucgss	txt	text	gss	GSS report
+nucgss	txt	text	none	text ASN.1
+nucgss	xml	xml	docsum	Document summary
+nucgss	xml	xml	fasta	TinySeq
+nucgss	xml	xml	gb	GBSeq
+nucgss	xml	xml	gbc	INSDSeq
+nucgss	xml	xml	native	Full record
+nucgss	xml	xml	uilist	List of UIDs
+pmc	tabular	text	uilist	List of UIDs
+pmc	txt	text	medline	MEDLINE
+pmc	xml	xml	docsum	Document summary
+pmc	xml	xml	none	FULL
+pmc	xml	xml	uilist	List of UIDs
+popset	binary	asn.1	none	binary ASN.1
+popset	fasta	text	fasta	FASTA
+popset	genbank	text	gb	GenBank flat file
+popset	tabular	text	acc	Accession number(s)
+popset	tabular	text	seqid	SeqID string
+popset	tabular	text	uilist	List of UIDs
+popset	txt	text	none	text ASN.1
+popset	xml	xml	docsum	Document summary
+popset	xml	xml	fasta	TinySeq
+popset	xml	xml	gb	GBSeq
+popset	xml	xml	gbc	INSDSeq
+popset	xml	xml	native	Full record
+popset	xml	xml	uilist	List of UIDs
+protein	binary	asn.1	none	binary ASN.1
+protein	fasta	text	fasta	FASTA
+protein	tabular	text	acc	Accession number(s)
+protein	txt	text	ft	Feature table
+protein	tabular	text	seqid	SeqID string
+protein	tabular	text	uilist	List of UIDs
+protein	txt	text	gp	GenPept flat file
+protein	txt	text	none	text ASN.1
+protein	xml	xml	docsum	Document summary
+protein	xml	xml	fasta	TinySeq
+protein	xml	xml	gp	GBSeq
+protein	xml	xml	gpc	INSDSeq
+protein	xml	xml	ipg	Identical Protein
+protein	xml	xml	native	Full record
+protein	xml	xml	uilist	List of UIDs
+pubmed	tabular	text	uilist	List of UIDs
+pubmed	txt	asn.1	none	text ASN.1
+pubmed	txt	text	abstract	Abstract
+pubmed	txt	text	medline	MEDLINE
+pubmed	xml	xml	docsum	Document summary
+pubmed	xml	xml	none	Full
+pubmed	xml	xml	uilist	List of UIDs
+sequences	fasta	text	fasta	FASTA
+sequences	tabular	text	acc	Accession number(s)
+sequences	tabular	text	seqid	SeqID string
+sequences	tabular	text	uilist	List of UIDs
+sequences	txt	text	none	text ASN.1
+sequences	xml	xml	docsum	Document summary
+sequences	xml	xml	uilist	List of UIDs
+sequences	xml	none	none	Full
+snp	fasta	text	fasta	FASTA
+snp	json	json	docsum	Document summary
+snp	json	json	uilist	List of UIDs
+snp	tabular	text	ssexemplar	SS Exemplar list
+snp	tabular	text	uilist	List of UIDs
+snp	txt	asn.1	none	text ASN.1
+snp	txt	text	chr	Chromosome report
+snp	txt	text	docset	Summary
+snp	txt	text	flt	Flat file
+snp	txt	text	rsr	RS Cluster report
+snp	xml	xml	docsum	Document summary
+snp	xml	xml	none	XML
+snp	xml	xml	uilist	List of UIDs
+sra	tabular	text	uilist	List of UIDs
+sra	xml	xml	docsum	Document summary
+sra	xml	xml	full	Full
+taxonomy	tabular	text	uilist	List of UIDs
+taxonomy	xml	xml	none	Full
+taxonomy	xml	xml	docsum	Document summary
+taxonomy	xml	xml	uilist	List of UIDs