view abstracts_by_pmids.xml @ 0:01f691e9ba03 draft default tip

"planemo upload for repository https://github.com/dlal-group/simtext commit e55e96337165eebd0e2b365bcd0ae48ebb358ebc-dirty"

<tool id="abstracts_by_pmids" name="abstracts_by_pmids" version="@VERSION@">
    <description>For all PMIDs in each row of a table save the according abstracts in additional columns</description>
    <macros>
        <import>macros.xml</import>
    </macros>    <expand macro="requirements">
      <requirement type="package" version="2.0.1">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>
    </expand>
    <expand macro="stdio"/>
    <command><![CDATA[Rscript 
      '${__tool_directory__}/abstracts_by_pmids.R'
      --input '$input'
      --output '$output'
      ]]>
    </command>
    <inputs>
      <param argument="--input" label="Input file" name="input" optional="false" type="data" format="tabular" help="input"/>
    </inputs>
    <outputs>
      <data format="tabular" name="output" />
    </outputs>
    <tests>
        <test>
          <param name="input" value="pubmed_by_queries_output" ftype="tabular"/>
          <output name="output" value="abstracts_by_pmids_output"/>
        </test>
    </tests>
    <help><![CDATA[

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

Input: 
able 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.).

Output: 
A table with additional columns containing abstract texts.

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