--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Sat Oct 31 12:45:31 2015 -0400
@@ -0,0 +1,687 @@
+<?xml version="1.0"?>
+<macros>
+  <token name="@WRAPPER_VERSION@">1.0</token>
+  <token name="@EMAIL_ARGUMENTS@">
+--user_email $__user_email__
+#set admin_emails = ';'.join(str($__admin_users__).split(','))
+--admin_email $admin_emails
+  </token>
+  <token name="@REFERENCES@"><![CDATA[
+References
+==========
+
+If you use this Galaxy tool in work leading to a scientific
+publication, please cite the following papers:
+
+        ]]></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="stdio">
+    <stdio>
+      <!-- Anything other than zero is an error -->
+      <exit_code range="1:"/>
+      <exit_code range=":-1"/>
+      <!-- In case the return code has not been set propery check stderr too -->
+      <regex match="Error:"/>
+      <regex match="Exception:"/>
+    </stdio>
+  </xml>
+  <xml name="dbselect">
+    <param name="db_select" type="select" label="NCBI Database to Use">
+      <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="epigenomics">Epigenomics</option>
+      <option value="gap">dbGaP</option>
+      <option value="gds">GEO Datasets</option>
+      <option value="gene">Gene</option>
+      <option value="genome">Genome</option>
+      <option value="geoprofiles">GEO Profiles</option>
+      <option value="gtr">Genetic Testing Registry</option>
+      <option value="homologene">HomoloGene</option>
+      <option value="journals">Journals</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">Nucleotide</option>
+      <option value="nucest">EST</option>
+      <option value="nucgss">GSS</option>
+      <option value="omim">OMIM</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="snp">SNP</option>
+      <option value="sra">SRA</option>
+      <option value="structure">Structure</option>
+      <option value="taxonomy">Taxonomy</option>
+      <option value="toolkit">NCBI C++ Toolkit</option>
+      <option value="toolkitall">NCBI C++ Toolkit All</option>
+      <option value="toolkitbook">NCBI C++ Toolkit Book</option>
+      <option value="unigene">UniGene</option>
+    </param>
+  </xml>
+  <xml name="db">
+    <conditional name="db">
+      <param name="db_select" type="select" label="NCBI Database to Use">
+        <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="epigenomics">Epigenomics</option>
+        <option value="gap">dbGaP</option>
+        <option value="gds">GEO Datasets</option>
+        <option value="gene">Gene</option>
+        <option value="genome">Genome</option>
+        <option value="geoprofiles">GEO Profiles</option>
+        <option value="gtr">Genetic Testing Registry</option>
+        <option value="homologene">HomoloGene</option>
+        <option value="journals">Journals</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">Nucleotide</option>
+        <option value="nucest">EST</option>
+        <option value="nucgss">GSS</option>
+        <option value="omim">OMIM</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="snp">SNP</option>
+        <option value="sra">SRA</option>
+        <option value="structure">Structure</option>
+        <option value="taxonomy">Taxonomy</option>
+        <option value="toolkit">NCBI C++ Toolkit</option>
+        <option value="toolkitall">NCBI C++ Toolkit All</option>
+        <option value="toolkitbook">NCBI C++ Toolkit Book</option>
+        <option value="unigene">UniGene</option>
+      </param>
+      <when value="assembly">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+        </param>
+      </when>
+      <when value="bioproject">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+          <option value="xml-xml">Full record</option>
+        </param>
+      </when>
+      <when value="biosample">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+          <option value="full-xml">Full record (XML)</option>
+          <option value="full-text">Full record (plain text)</option>
+        </param>
+      </when>
+      <when value="biosystems">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+          <option value="xml-xml">Full record</option>
+        </param>
+      </when>
+      <when value="blastdbinfo">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+        </param>
+      </when>
+      <when value="books">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+        </param>
+      </when>
+      <when value="cdd">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+        </param>
+      </when>
+      <when value="clinvar">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+        </param>
+      </when>
+      <when value="clone">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+        </param>
+      </when>
+      <when value="dbvar">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+        </param>
+      </when>
+      <when value="epigenomics">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+        </param>
+      </when>
+      <when value="gap">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+        </param>
+      </when>
+      <when value="gds">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+          <option value="summary-text">Summary</option>
+        </param>
+      </when>
+      <when value="gene">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+          <option value="null-asn.1">text (ASN.1)</option>
+          <option value="null-xml">XML</option>
+          <option value="gene_table-text">Gene table</option>
+        </param>
+      </when>
+      <when value="genome">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+        </param>
+      </when>
+      <when value="geoprofiles">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+        </param>
+      </when>
+      <when value="gtr">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+        </param>
+      </when>
+      <when value="homologene">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+          <option value="null-asn.1">text ASN.1</option>
+          <option value="null-xml">XML</option>
+          <option value="alignmentscores-text">Alignment scores</option>
+          <option value="fasta-text">FASTA</option>
+          <option value="homologene-text">HomoloGene</option>
+        </param>
+      </when>
+      <when value="journals">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+        </param>
+      </when>
+      <when value="medgen">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+        </param>
+      </when>
+      <when value="mesh">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+          <option value="full-text">Full record</option>
+        </param>
+      </when>
+      <when value="ncbisearch">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+        </param>
+      </when>
+      <when value="nlmcatalog">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+          <option value="null-text">Full record</option>
+          <option value="null-xml">XML</option>
+        </param>
+      </when>
+      <when value="nuccore">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+          <option value="null-text">text ASN.1</option>
+          <option value="null-asn.1">binary ASN.1</option>
+          <option value="native-xml">Full record in XML</option>
+          <option value="acc-text">Accession number(s)</option>
+          <option value="fasta-text">FASTA</option>
+          <option value="fasta-xml">TinySeq XML</option>
+          <option value="seqid-text">SeqID string</option>
+          <option value="gb-text">GenBank flat file</option>
+          <option value="gb-xml">GBSeq XML</option>
+          <option value="gbc-xml">INSDSeq XML</option>
+          <option value="ft-text">Feature table</option>
+          <option value="gbwithparts-text">GenBank flat file with full sequence (contigs)</option>
+          <option value="fasta_cds_na-text">CDS nucleotide FASTA</option>
+          <option value="fasta_cds_aa-text">CDS protein FASTA</option>
+        </param>
+      </when>
+      <when value="nucest">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+          <option value="null-text">text ASN.1</option>
+          <option value="null-asn.1">binary ASN.1</option>
+          <option value="native-xml">Full record in XML</option>
+          <option value="acc-text">Accession number(s)</option>
+          <option value="fasta-text">FASTA</option>
+          <option value="fasta-xml">TinySeq XML</option>
+          <option value="seqid-text">SeqID string</option>
+          <option value="gb-text">GenBank flat file</option>
+          <option value="gb-xml">GBSeq XML</option>
+          <option value="gbc-xml">INSDSeq XML</option>
+          <option value="est-text">EST report</option>
+        </param>
+      </when>
+      <when value="nucgss">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+          <option value="null-text">text ASN.1</option>
+          <option value="null-asn.1">binary ASN.1</option>
+          <option value="native-xml">Full record in XML</option>
+          <option value="acc-text">Accession number(s)</option>
+          <option value="fasta-text">FASTA</option>
+          <option value="fasta-xml">TinySeq XML</option>
+          <option value="seqid-text">SeqID string</option>
+          <option value="gb-text">GenBank flat file</option>
+          <option value="gb-xml">GBSeq XML</option>
+          <option value="gbc-xml">INSDSeq XML</option>
+          <option value="gss-text">GSS report</option>
+        </param>
+      </when>
+      <when value="omim">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+        </param>
+      </when>
+      <when value="pcassay">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+        </param>
+      </when>
+      <when value="pccompound">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+        </param>
+      </when>
+      <when value="pcsubstance">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+        </param>
+      </when>
+      <when value="pmc">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+          <option value="null-xml">XML</option>
+          <option value="medline-text">MEDLINE</option>
+        </param>
+      </when>
+      <when value="popset">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+          <option value="null-text">text ASN.1</option>
+          <option value="null-asn.1">binary ASN.1</option>
+          <option value="native-xml">Full record in XML</option>
+          <option value="acc-text">Accession number(s)</option>
+          <option value="fasta-text">FASTA</option>
+          <option value="fasta-xml">TinySeq XML</option>
+          <option value="seqid-text">SeqID string</option>
+          <option value="gb-text">GenBank flat file</option>
+          <option value="gb-xml">GBSeq XML</option>
+          <option value="gbc-xml">INSDSeq XML</option>
+        </param>
+      </when>
+      <when value="probe">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+        </param>
+      </when>
+      <when value="protein">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+          <option value="null-text">text ASN.1</option>
+          <option value="null-asn.1">binary ASN.1</option>
+          <option value="native-xml">Full record in XML</option>
+          <option value="acc-text">Accession number(s)</option>
+          <option value="fasta-text">FASTA</option>
+          <option value="fasta-xml">TinySeq XML</option>
+          <option value="seqid-text">SeqID string</option>
+          <option value="ft-text">Feature table</option>
+          <option value="gp-text">GenPept flat file</option>
+          <option value="gp-xml">GBSeq XML</option>
+          <option value="gpc-xml">INSDSeq XML</option>
+          <option value="ipg-xml">Identical Protein XML</option>
+        </param>
+      </when>
+      <when value="proteinclusters">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+        </param>
+      </when>
+      <when value="pubmed">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+          <option value="null-asn.1">text ASN.1</option>
+          <option value="null-xml">XML</option>
+          <option value="medline-text">MEDLINE</option>
+          <option value="uilist-text">PMID list</option>
+          <option value="abstract-text">Abstract</option>
+        </param>
+      </when>
+      <when value="pubmedhealth">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+        </param>
+      </when>
+      <when value="snp">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+          <option value="null-asn.1">text ASN.1</option>
+          <option value="null-xml">XML</option>
+          <option value="flt-text">Flat file</option>
+          <option value="fasta-text">FASTA</option>
+          <option value="rsr-text">RS Cluster report</option>
+          <option value="ssexemplar-text">SS Exemplar list</option>
+          <option value="chr-text">Chromosome report</option>
+          <option value="docset-text">Summary</option>
+          <option value="uilist-xml">UID list (XML)</option>
+          <option value="uilist-text">UID list (text)</option>
+        </param>
+      </when>
+      <when value="sra">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+          <option value="full-xml">XML</option>
+        </param>
+      </when>
+      <when value="structure">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+        </param>
+      </when>
+      <when value="taxonomy">
+        <param name="output_format" type="select" label="Output Format">
+          <option value="docsum-xml">Document summary</option>
+          <option value="uilist-xml">List of UIDs (XML)</option>
+          <option value="uilist-text">List of UIDs (plain text)</option>
+          <option value="null-xml">XML</option>
+          <option value="uilist-xml">TaxID list (XML)</option>
+          <option value="uilist-text">TaxID list (text)</option>
+        </param>
+      </when>
+    </conditional>
+  </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="ncbi_history"/>
+      </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="ncbi_history" 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="db_select_to">
+    <param name="db_select_to" type="select" label="To NCBI Database">
+      <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="epigenomics">Epigenomics</option>
+      <option value="gap">dbGaP</option>
+      <option value="gds">GEO Datasets</option>
+      <option value="gene">Gene</option>
+      <option value="genome">Genome</option>
+      <option value="geoprofiles">GEO Profiles</option>
+      <option value="gtr">Genetic Testing Registry</option>
+      <option value="homologene">HomoloGene</option>
+      <option value="journals">Journals</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">Nucleotide</option>
+      <option value="nucest">EST</option>
+      <option value="nucgss">GSS</option>
+      <option value="omim">OMIM</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="snp">SNP</option>
+      <option value="sra">SRA</option>
+      <option value="structure">Structure</option>
+      <option value="taxonomy">Taxonomy</option>
+      <option value="toolkit">NCBI C++ Toolkit</option>
+      <option value="toolkitall">NCBI C++ Toolkit All</option>
+      <option value="toolkitbook">NCBI C++ Toolkit Book</option>
+      <option value="unigene">UniGene</option>
+    </param>
+  </xml>
+  <xml name="requirements">
+    <requirements>
+      <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>