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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
author iuc
date Wed, 24 Mar 2021 08:32:54 +0000
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<tool id="abstracts_by_pmids" name="Get PubMed abstracts" version="@VERSION@" license="MIT">
    <description>by PMID IDs</description>
    <macros>
        <import>macros.xml</import>
    </macros>    
    <requirements>
        <requirement type="package" version="2.0.3">r-argparse</requirement>
        <requirement type="package" version="0.2.3">r-reutils</requirement>
        <requirement type="package" version="2.13">r-easypubmed</requirement>
        <requirement type="package" version="0.9.3">r-textclean</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
    Rscript 
      '${__tool_directory__}/abstracts_by_pmids.R'
      --input '$input'
      --output '$output'
      ]]>
    </command>
    <inputs>
        <param argument="--input" type="data" format="tabular" label="Input file with PMID IDs" />
    </inputs>
    <outputs>
        <data format="tabular" name="output" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="pubmed_by_queries_output" ftype="tabular"/>
            <output name="output">
                <assert_contents>
                    <has_n_lines n="7"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

**What it does**

This tool retrieves for all PMIDs in each row of a table the according abstracts and saves them in additional columns.

-----

**Example**

- Input file:
    Table with rows representing biomedical entities and columns containing the corresponding PMIDs. The names of the PMID columns should start with “PMID\_” (e.g., “PMID_1”, “PMID_2” etc.).

    | PMID_1      | PMID_2      | PMID_2      
    | 33565071    | 33531663    | 33528079    
    | 33377604    | 33334860    | 33277917    

- Output file:
    A table with additional columns containing the abstract texts.

    | PMID_1      | PMID_2      | PMID_2      | ABSTRACT_1  | ABSTRACT_3  | ABSTRACT_3  
    | 33565071    | 33531663    | 33528079    | abc def...    | abc def...    | abc def...    
    | 33377604    | 33334860    | 33277917    | abc def...    | abc def...    | abc def...    

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