--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/elink.xml	Sat Oct 31 12:44:05 2015 -0400
@@ -0,0 +1,237 @@
+<?xml version="1.0"?>
+<tool id="ncbi_eutils_elink" name="NCBI ELink" version="@WRAPPER_VERSION@">
+  <description>link UIDs from one database to another</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <version_command>python elink.py --version</version_command>
+  <command interpreter="python"><![CDATA[elink.py
+#if $cmd.cmd_select in ('neighbor', 'neighbor_score', 'neighbor_history'):
+$cmd.db_select_to
+#else:
+"none"
+#end if
+
+$db_select_from
+$cmd.cmd_select
+
+@EMAIL_ARGUMENTS@
+
+@LIST_OR_HIST@
+
+#if $cmd.cmd_select == "neighbor_history":
+    --history_out $history
+#end if
+
+> $default]]></command>
+  <inputs>
+    <param name="db_select_from" type="select" label="From 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>
+    <conditional name="cmd">
+      <param name="cmd_select" type="select" label="ELink command to execute">
+        <option value="neighbor">Neighbor: Fetch a set of UIDs in DB linked to input UIDs in DBFROM</option>
+        <option value="neighbor_score">Scored Neighbors: Fetch a set of UIDs within the same database as the input UIDs along with computed similarity scores</option>
+        <option value="neighbor_history">Neighbor (history): Fetch a set of UIDs in DB linked to input UIDs from DBFROM, and store on history server</option>
+        <option value="acheck">ACheck: List all links available from a set of UIDs</option>
+        <option value="ncheck">NCheck: Check for the existence of links within the same database for a set of UIDs</option>
+        <option value="lcheck">LCheck: Check for the existence of external links (LinkOuts) for a set of UIDs</option>
+        <option value="llinks">Links: For each input UID, list the URLs and attributes for the LinkOut providers that are not libraries</option>
+        <option value="llinkslib">LinksLib: For each input UID, list the URLs and attributes for the LinkOut providers (including libraries)</option>
+        <option value="prlinks">Provider Links: List the primary LinkOut provider for each input UID</option>
+      </param>
+      <when value="neighbor">
+        <expand macro="db_select_to"/>
+      </when>
+      <when value="neighbor_score">
+        <expand macro="db_select_to"/>
+      </when>
+      <when value="neighbor_history">
+        <expand macro="db_select_to"/>
+      </when>
+      <when value="acheck">
+        <expand macro="db_select_to"/>
+      </when>
+      <when value="ncheck"/>
+      <when value="lcheck"/>
+      <when value="llinks"/>
+      <when value="llinkslib"/>
+      <when value="prlinks"/>
+    </conditional>
+    <expand macro="list_or_hist"/>
+  </inputs>
+  <outputs>
+    <data format="xml" name="default" label="NCBI Linked IDs from $db_select_from"/>
+    <expand macro="history_out">
+      <filter>cmd['cmd_select'] == 'neighbor_history'</filter>
+    </expand>
+  </outputs>
+  <tests>
+    <test>
+      <param name="cmd_select" value="neighbor"/>
+      <param name="db_select_to" value="pubmed"/>
+      <param name="db_select_from" value="taxonomy"/>
+      <param name="qss" value="id_list"/>
+      <param name="id_list" value="510899"/>
+      <output name="default" file="pm-tax-neighbor.xml"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+NCBI Entrez ELink
+=================
+
+Responds to a list of UIDs in a given database with either a list of related
+UIDs (and relevancy scores) in the same database or a list of linked UIDs in
+another Entrez database; checks for the existence of a specified link from a
+list of one or more UIDs; creates a hyperlink to the primary LinkOut provider
+for a specific UID and database, or lists LinkOut URLs and attributes for
+multiple UIDs.
+
+Commands
+--------
+
+Example Queries
+---------------
+
+Link from protein to gene
+
++----------------------+--------------------------------------+
+| Parameter            | Value                                |
++======================+======================================+
+| From NCBI Database   | Protein                              |
++----------------------+--------------------------------------+
+| Elink Command        | Neighbor                             |
++----------------------+--------------------------------------+
+| To NCBI Database     | Gene                                 |
++----------------------+--------------------------------------+
+| ID List              | 15718680 157427902                   |
++----------------------+--------------------------------------+
+
+Find related articles to PMID 20210808 with scores
+
++----------------------+--------------------------------------+
+| Parameter            | Value                                |
++======================+======================================+
+| From NCBI Database   | PubMed                               |
++----------------------+--------------------------------------+
+| Elink Command        | Scored Neighbors                     |
++----------------------+--------------------------------------+
+| To NCBI Database     | PubMed                               |
++----------------------+--------------------------------------+
+| ID List              | 20210808                             |
++----------------------+--------------------------------------+
+
+List all possible links from two protein GIs
+
++----------------------+--------------------------------------+
+| Parameter            | Value                                |
++======================+======================================+
+| From NCBI Database   | Protein                              |
++----------------------+--------------------------------------+
+| Elink Command        | ACheck                               |
++----------------------+--------------------------------------+
+| ID List              | 15718680 157427902                   |
++----------------------+--------------------------------------+
+
+List all possible links from two protein GIs to PubMed
+
++----------------------+--------------------------------------+
+| Parameter            | Value                                |
++======================+======================================+
+| From NCBI Database   | Protein                              |
++----------------------+--------------------------------------+
+| Elink Command        | ACheck                               |
++----------------------+--------------------------------------+
+| To NCBI Database     | PubMed                               |
++----------------------+--------------------------------------+
+| ID List              | 15718680 157427902                   |
++----------------------+--------------------------------------+
+
+Check whether two nuccore sequences have "related sequences" links.
+
++----------------------+--------------------------------------+
+| Parameter            | Value                                |
++======================+======================================+
+| From NCBI Database   | Nuccore                              |
++----------------------+--------------------------------------+
+| Elink Command        | NCheck                               |
++----------------------+--------------------------------------+
+| ID List              | 21614549 219152114                   |
++----------------------+--------------------------------------+
+
+List the LinkOut URLs for non-library providers for two pubmed abstracts.
+
++----------------------+--------------------------------------+
+| Parameter            | Value                                |
++======================+======================================+
+| From NCBI Database   | Pubmed                               |
++----------------------+--------------------------------------+
+| Elink Command        | Links                                |
++----------------------+--------------------------------------+
+| ID List              | 19880848 19822630                    |
++----------------------+--------------------------------------+
+
+Find links to full text providers for two PubMed abstracts.
+
++----------------------+--------------------------------------+
+| Parameter            | Value                                |
++======================+======================================+
+| From NCBI Database   | Pubmed                               |
++----------------------+--------------------------------------+
+| Elink Command        | Provider Links                       |
++----------------------+--------------------------------------+
+| ID List              | 19880848 19822630                    |
++----------------------+--------------------------------------+
+
+@REFERENCES@
+
+@DISCLAIMER@
+      ]]></help>
+  <expand macro="citations"/>
+</tool>