<tool id="pubmed_by_queries" name="pubmed_by_queries" version="@VERSION@">
    <description>Download a defined number of abstracts or PMIDs from PubMed for a set of search queries</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
      <requirement type="package" version="2.0.1">r-argparse</requirement>
      <requirement type="package" version="2.13">r-easypubmed</requirement>
    </expand>
    <expand macro="stdio"/>
    <command><![CDATA[Rscript 
      '${__tool_directory__}/pubmed_by_queries.R'
      --input '$input'
      --output '$output'
      --number '$number'
      $abstract
      #if str($key):
      --key '$key'
      #end if
      ]]>
    </command>
    
    <inputs>
      <param argument="--input" label="Input file" name="input" optional="false" type="data" format="tabular" help="input"/>
      <param argument="--abstract" label="Save abstracts instead of PMIDs" name="abstract" type="boolean" truevalue="--abstract" falsevalue="" help="abstract" checked="false"/>
      <param argument="--number" label="Number of PMIDs (or abstracts) to save per  ID" name="number" optional="false" type="integer" help="number" value="5"/>
      <param argument="--key" label="NCBI API key (if available)" name="key" optional="true" type="text" help="key"/>
    </inputs>
    
    <outputs>
      <data format="tabular" name="output" />
    </outputs>
    
    <tests>
        <test>
          <param name="input" value="test_data" ftype="tabular"/>
          <param name="number" value="5"/>
          <param name="abstract" value=""/>
          <output name="output" value="pubmed_by_queries_output"/>
        </test>
    </tests>
    <help><![CDATA[

This tool uses a set of search queries to download a defined number of abstracts or PMIDs for each search query from PubMed. PubMed's search rules and syntax apply.
 
Input:
Table with a list of search queries (biomedical entities of interest) in one column. The column header should start with "ID\_" (e.g., "ID_gene" if search queries are genes).

Output: 
Table with additional columns containing PMIDs or abstracts from PubMed.

Users can obtain an API key from the Settings page of their NCBI account (to create an account, visit http://www.ncbi.nlm.nih.gov/account/).

        ]]></help>
    <expand macro="citations"/>
</tool>