<tool id="pubmed_by_queries" name="PubMed query" version="@VERSION@" license="MIT">
    <description>download a defined number of abstracts or PMIDs from PubMed</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="2.0.3">r-argparse</requirement>
        <requirement type="package" version="2.13">r-easypubmed</requirement>
    </requirements>

    <command detect_errors="exit_code"><![CDATA[
    Rscript 
      '${__tool_directory__}/pubmed_by_queries.R'
      --input '$input'
      --output '$output'
      --number '$number'
      $abstract
      #if $__user__.extra_preferences.get('ncbi_account|apikey', ""):
        -k '$credentials'
      #end if  
      ]]>
    </command>

    <configfiles>
        <configfile name="credentials"><![CDATA[
        $__user__.extra_preferences.get('ncbi_account|apikey', "")
        ]]></configfile>
    </configfiles>

    <inputs>
        <param argument="--input" type="data" format="tabular" label="Input file with query terms" />
        <param argument="--abstract" type="boolean" truevalue="--abstract" falsevalue="" checked="false" label="Save abstracts instead of PMIDs"/>
        <param argument="--number" type="integer" value="5" min="1" label="Number of PMIDs (or abstracts) to save per ID" />
    </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">
                <assert_contents>
                    <has_n_columns n="7"/>
                    <has_n_lines n="7"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

**What it does**

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.

**Info**

To speed up the the download of PubMed data 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/) and add it to the Galaxy user-preferences (User/ Preferences/ Manage Information).

-----

**Example**

- Input table:
    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).

    | ID_gene
    | 33565071
    | 33377604

- Output table:
    Table with additional columns containing PMIDs or abstracts from PubMed (here: PMIDs)

    | ID_gene   | PMID_1        |  PMID_2       |  PMID_3
    | SCN1A       | 33531663  | 33528079  | 33565071
    | SCN9A       | 33334860  | 33277917  | 33377604

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