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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 08:34:22 +0000
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1 <tool id="pubmed_by_queries" name="PubMed query" version="@VERSION@" license="MIT">
2 <description>download a defined number of abstracts or PMIDs from PubMed</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="2.13">r-easypubmed</requirement>
9 </requirements>
10
11 <command detect_errors="exit_code"><![CDATA[
12 Rscript
13 '${__tool_directory__}/pubmed_by_queries.R'
14 --input '$input'
15 --output '$output'
16 --number '$number'
17 $abstract
18 #if $__user__.extra_preferences.get('ncbi_account|apikey', ""):
19 -k '$credentials'
20 #end if
21 ]]>
22 </command>
23
24 <configfiles>
25 <configfile name="credentials"><![CDATA[
26 $__user__.extra_preferences.get('ncbi_account|apikey', "")
27 ]]></configfile>
28 </configfiles>
29
30 <inputs>
31 <param argument="--input" type="data" format="tabular" label="Input file with query terms" />
32 <param argument="--abstract" type="boolean" truevalue="--abstract" falsevalue="" checked="false" label="Save abstracts instead of PMIDs"/>
33 <param argument="--number" type="integer" value="5" min="1" label="Number of PMIDs (or abstracts) to save per ID" />
34 </inputs>
35
36 <outputs>
37 <data format="tabular" name="output" />
38 </outputs>
39
40 <tests>
41 <test>
42 <param name="input" value="test_data" ftype="tabular"/>
43 <param name="number" value="5"/>
44 <param name="abstract" value=""/>
45 <output name="output">
46 <assert_contents>
47 <has_n_columns n="7"/>
48 <has_n_lines n="7"/>
49 </assert_contents>
50 </output>
51 </test>
52 </tests>
53 <help><![CDATA[
54
55 **What it does**
56
57 This tool uses a set of search queries to download a defined number of abstracts or PMIDs for each search query from PubMed.
58 PubMed's search rules and syntax apply.
59
60 **Info**
61
62 To speed up the the download of PubMed data users can obtain an API key from the Settings page of their NCBI account (to create an account, visit http://www.ncbi.nlm.nih.gov/account/) and add it to the Galaxy user-preferences (User/ Preferences/ Manage Information).
63
64 -----
65
66 **Example**
67
68 - Input table:
69 Table with a list of search queries (biomedical entities of interest) in one column. The column header should start with
70 "ID\_" (e.g., "ID_gene" if search queries are genes).
71
72 | ID_gene
73 | 33565071
74 | 33377604
75
76 - Output table:
77 Table with additional columns containing PMIDs or abstracts from PubMed (here: PMIDs)
78
79 | ID_gene | PMID_1 | PMID_2 | PMID_3
80 | SCN1A | 33531663 | 33528079 | 33565071
81 | SCN9A | 33334860 | 33277917 | 33377604
82
83 ]]></help>
84 <expand macro="citations"/>
85 </tool>