<?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>