Mercurial > repos > dlalgroup > abstracts_by_pmids

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"planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
author dlalgroup
date Thu, 24 Sep 2020 05:16:41 +0000
parents d7aea8ba1e30
children
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dlalgroup
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1 <tool id="abstracts_by_pmids" name="abstracts_by_pmids" version="@VERSION@">
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dlalgroup
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2 <description>For all PMIDs in each row of a table save the according abstracts in additional columns</description>
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dlalgroup
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros> <expand macro="requirements">
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6 <requirement type="package" version="2.0.1">r-argparse</requirement>
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7 <requirement type="package" version="0.2.3">r-reutils</requirement>
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8 <requirement type="package" version="2.13">r-easypubmed</requirement>
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9 <requirement type="package" version="0.9.3">r-textclean</requirement>
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10 </expand>
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11 <expand macro="stdio"/>
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12 <command><![CDATA[Rscript
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13 '${__tool_directory__}/abstracts_by_pmids.R'
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14 --input '$input'
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15 --output '$output'
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16 ]]>
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17 </command>
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18 <inputs>
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19 <param argument="--input" label="Input file" name="input" optional="false" type="data" format="tabular" help="input"/>
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20 </inputs>
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21 <outputs>
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22 <data format="tabular" name="output" />
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23 </outputs>
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24 <tests>
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25 <test>
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26 <param name="input" value="pubmed_by_queries_output" ftype="tabular"/>
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27 <output name="output" value="abstracts_by_pmids_output"/>
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28 </test>
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29 </tests>
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30 <help><![CDATA[
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31
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32 This tool retrieves for all PMIDs in each row of a table the according abstracts and saves them in additional columns.
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33
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34 Input:
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35 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.).
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36
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37 Output:
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38 A table with additional columns containing abstract texts.
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39
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40 ]]></help>
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41 <expand macro="citations"/>
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42 </tool>