Mercurial > repos > iuc > abstracts_by_pmids
comparison abstracts_by_pmids.xml @ 0:ff904894ccaa draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
author | iuc |
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date | Wed, 24 Mar 2021 08:32:54 +0000 |
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1 <tool id="abstracts_by_pmids" name="Get PubMed abstracts" version="@VERSION@" license="MIT"> | |
2 <description>by PMID IDs</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <requirements> | |
7 <requirement type="package" version="2.0.3">r-argparse</requirement> | |
8 <requirement type="package" version="0.2.3">r-reutils</requirement> | |
9 <requirement type="package" version="2.13">r-easypubmed</requirement> | |
10 <requirement type="package" version="0.9.3">r-textclean</requirement> | |
11 </requirements> | |
12 <command detect_errors="exit_code"><![CDATA[ | |
13 Rscript | |
14 '${__tool_directory__}/abstracts_by_pmids.R' | |
15 --input '$input' | |
16 --output '$output' | |
17 ]]> | |
18 </command> | |
19 <inputs> | |
20 <param argument="--input" type="data" format="tabular" label="Input file with PMID IDs" /> | |
21 </inputs> | |
22 <outputs> | |
23 <data format="tabular" name="output" /> | |
24 </outputs> | |
25 <tests> | |
26 <test> | |
27 <param name="input" value="pubmed_by_queries_output" ftype="tabular"/> | |
28 <output name="output"> | |
29 <assert_contents> | |
30 <has_n_lines n="7"/> | |
31 </assert_contents> | |
32 </output> | |
33 </test> | |
34 </tests> | |
35 <help><![CDATA[ | |
36 | |
37 **What it does** | |
38 | |
39 This tool retrieves for all PMIDs in each row of a table the according abstracts and saves them in additional columns. | |
40 | |
41 ----- | |
42 | |
43 **Example** | |
44 | |
45 - Input file: | |
46 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.). | |
47 | |
48 | PMID_1 | PMID_2 | PMID_2 | |
49 | 33565071 | 33531663 | 33528079 | |
50 | 33377604 | 33334860 | 33277917 | |
51 | |
52 - Output file: | |
53 A table with additional columns containing the abstract texts. | |
54 | |
55 | PMID_1 | PMID_2 | PMID_2 | ABSTRACT_1 | ABSTRACT_3 | ABSTRACT_3 | |
56 | 33565071 | 33531663 | 33528079 | abc def... | abc def... | abc def... | |
57 | 33377604 | 33334860 | 33277917 | abc def... | abc def... | abc def... | |
58 | |
59 ]]></help> | |
60 <expand macro="citations"/> | |
61 </tool> |