--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/efetch.xml	Sat Oct 31 12:44:54 2015 -0400
@@ -0,0 +1,123 @@
+<?xml version="1.0"?>
+<tool id="ncbi_eutils_efetch" name="NCBI EFetch" version="@WRAPPER_VERSION@">
+  <description>fetch records from NCBI</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <version_command>python efetch.py --version</version_command>
+  <command interpreter="python"><![CDATA[efetch.py
+$db.db_select
+
+@LIST_OR_HIST@
+
+#set retmode, rettype = str($db.output_format).split('-')
+## Otherwise, defaults to a None/empty which implies 'default' to NCBI
+#if retmode != "null":
+--retmode $retmode
+#end if
+--rettype $rettype
+
+@EMAIL_ARGUMENTS@
+$whole
+> $default]]></command>
+  <inputs>
+    <expand macro="db"/>
+    <expand macro="list_or_hist"/>
+    <param checked="false" label="Download all records associated with query" name="whole" type="boolean" truevalue="--whole" falsevalue=""/>
+  </inputs>
+  <outputs>
+    <data format="txt" name="default" label="NCBI EFetch Results">
+      <discover_datasets pattern="__designation__.out" ext="txt"/>
+      <change_format>
+        <when input="output_format" value="abstract-text" format="txt"/>
+        <when input="output_format" value="acc-text" format="txt"/>
+        <when input="output_format" value="alignmentscores-text" format="txt"/>
+        <when input="output_format" value="chr-text" format="txt"/>
+        <when input="output_format" value="docset-text" format="txt"/>
+        <when input="output_format" value="docsum-xml" format="xml"/>
+        <when input="output_format" value="est-text" format="txt"/>
+        <when input="output_format" value="fasta_cds_aa-text" format="fasta"/>
+        <when input="output_format" value="fasta-text" format="fasta"/>
+        <when input="output_format" value="fasta-xml" format="xml"/>
+        <when input="output_format" value="flt-text" format="txt"/>
+        <when input="output_format" value="ft-text" format="txt"/>
+        <when input="output_format" value="full-text" format="txt"/>
+        <when input="output_format" value="full-xml" format="xml"/>
+        <when input="output_format" value="gbc-xml" format="xml"/>
+        <when input="output_format" value="gbwithparts-text" format="genbank"/>
+        <when input="output_format" value="gb-text" format="genbank"/>
+        <when input="output_format" value="gb-xml" format="xml"/>
+        <when input="output_format" value="gene_table-text" format="txt"/>
+        <when input="output_format" value="gpc-xml" format="xml"/>
+        <when input="output_format" value="gp-text" format="txt"/>
+        <when input="output_format" value="gp-xml" format="xml"/>
+        <when input="output_format" value="gss-text" format="txt"/>
+        <when input="output_format" value="homologene-text" format="txt"/>
+        <when input="output_format" value="ipg-xml" format="xml"/>
+        <when input="output_format" value="medline-text" format="txt"/>
+        <when input="output_format" value="native-xml" format="xml"/>
+        <when input="output_format" value="null-asn.1" format="asn1"/>
+        <when input="output_format" value="null-text" format="txt"/>
+        <when input="output_format" value="null-xml" format="xml"/>
+        <when input="output_format" value="rsr-text" format="txt"/>
+        <when input="output_format" value="seqid-text" format="txt"/>
+        <when input="output_format" value="ssexemplar-text" format="txt"/>
+        <when input="output_format" value="summary-text" format="txt"/>
+        <when input="output_format" value="uilist-xml" format="xml"/>
+        <when input="output_format" value="xml-xml" format="xml"/>
+      </change_format>
+    </data>
+  </outputs>
+  <tests>
+    <test>
+      <param name="db_select" value="taxonomy"/>
+      <param name="output_format" value="docsum-xml"/>
+      <param name="qss" value="id_list"/>
+      <param name="id_list" value="10239"/>
+      <output name="default" file="viruses.tax.xml">
+        <!--<discovered_datasets designation="0" ftytpe="xml" file="viruses.tax.xml" />-->
+      </output>
+    </test>
+  </tests>
+  <help><![CDATA[
+NCBI Entrez EFetch
+==================
+
+Responds to a list of UIDs in a given database with the corresponding data
+records in a specified format.
+
+Example Queries
+---------------
+
+Fetch PMIDs 17284678 and 9997 as text abstracts:
+
++----------------------+--------------------------------------+
+| Parameter            | Value                                |
++======================+======================================+
+| NCBI Database to Use | PubMed                               |
++----------------------+--------------------------------------+
+| ID List              | 17284678 9997                        |
++----------------------+--------------------------------------+
+| Output Format        | Abstract                             |
++----------------------+--------------------------------------+
+
+Fetch FASTA for a transcript and its protein product (GIs 312836839 and 34577063)
+
++----------------------+--------------------------------------+
+| Parameter            | Value                                |
++======================+======================================+
+| NCBI Database to Use | Protein                              |
++----------------------+--------------------------------------+
+| ID List              | 312836839 34577063                   |
++----------------------+--------------------------------------+
+| Output Format        | Fasta                                |
++----------------------+--------------------------------------+
+
+@REFERENCES@
+
+@DISCLAIMER@
+      ]]></help>
+  <expand macro="citations"/>
+</tool>