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comparison abstracts_by_pmids.xml @ 0:d7aea8ba1e30 draft

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"planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
author dlalgroup
date Thu, 24 Sep 2020 03:11:08 +0000
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1 <tool id="abstracts_by_pmids" name="abstracts_by_pmids" version="@VERSION@">
2 <description>For all PMIDs in each row of a table save the according abstracts in additional columns</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros> <expand macro="requirements">
6 <requirement type="package" version="2.0.1">r-argparse</requirement>
7 <requirement type="package" version="0.2.3">r-reutils</requirement>
8 <requirement type="package" version="2.13">r-easypubmed</requirement>
9 <requirement type="package" version="0.9.3">r-textclean</requirement>
10 </expand>
11 <expand macro="stdio"/>
12 <command><![CDATA[Rscript
13 '${__tool_directory__}/abstracts_by_pmids.R'
14 --input '$input'
15 --output '$output'
16 ]]>
17 </command>
18 <inputs>
19 <param argument="--input" label="Input file" name="input" optional="false" type="data" format="tabular" help="input"/>
20 </inputs>
21 <outputs>
22 <data format="tabular" name="output" />
23 </outputs>
24 <tests>
25 <test>
26 <param name="input" value="pubmed_by_queries_output" ftype="tabular"/>
27 <output name="output" value="abstracts_by_pmids_output"/>
28 </test>
29 </tests>
30 <help><![CDATA[
31
32 This tool retrieves for all PMIDs in each row of a table the according abstracts and saves them in additional columns.
33
34 Input:
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.).
36
37 Output:
38 A table with additional columns containing abstract texts.
39
40 ]]></help>
41 <expand macro="citations"/>
42 </tool>