Mercurial > repos > iuc > pubmed_by_queries

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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">
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2 <description>download a defined number of abstracts or PMIDs from PubMed</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="2.0.3">r-argparse</requirement>
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8 <requirement type="package" version="2.13">r-easypubmed</requirement>
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9 </requirements>
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10
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11 <command detect_errors="exit_code"><![CDATA[
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12 Rscript
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13 '${__tool_directory__}/pubmed_by_queries.R'
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14 --input '$input'
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15 --output '$output'
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16 --number '$number'
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17 $abstract
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18 #if $__user__.extra_preferences.get('ncbi_account|apikey', ""):
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19 -k '$credentials'
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20 #end if
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21 ]]>
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22 </command>
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23
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24 <configfiles>
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25 <configfile name="credentials"><![CDATA[
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26 $__user__.extra_preferences.get('ncbi_account|apikey', "")
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27 ]]></configfile>
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28 </configfiles>
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29
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30 <inputs>
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31 <param argument="--input" type="data" format="tabular" label="Input file with query terms" />
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32 <param argument="--abstract" type="boolean" truevalue="--abstract" falsevalue="" checked="false" label="Save abstracts instead of PMIDs"/>
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33 <param argument="--number" type="integer" value="5" min="1" label="Number of PMIDs (or abstracts) to save per ID" />
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34 </inputs>
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35
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36 <outputs>
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37 <data format="tabular" name="output" />
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38 </outputs>
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39
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40 <tests>
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41 <test>
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42 <param name="input" value="test_data" ftype="tabular"/>
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43 <param name="number" value="5"/>
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44 <param name="abstract" value=""/>
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45 <output name="output">
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46 <assert_contents>
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47 <has_n_columns n="7"/>
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48 <has_n_lines n="7"/>
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49 </assert_contents>
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50 </output>
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51 </test>
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52 </tests>
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53 <help><![CDATA[
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54
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55 **What it does**
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56
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57 This tool uses a set of search queries to download a defined number of abstracts or PMIDs for each search query from PubMed.
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58 PubMed's search rules and syntax apply.
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59
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60 **Info**
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61
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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).
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63
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64 -----
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65
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66 **Example**
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67
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68 - Input table:
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69 Table with a list of search queries (biomedical entities of interest) in one column. The column header should start with
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70 "ID\_" (e.g., "ID_gene" if search queries are genes).
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71
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72 | ID_gene
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73 | 33565071
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74 | 33377604
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75
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76 - Output table:
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77 Table with additional columns containing PMIDs or abstracts from PubMed (here: PMIDs)
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78
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79 | ID_gene | PMID_1 | PMID_2 | PMID_3
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80 | SCN1A | 33531663 | 33528079 | 33565071
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81 | SCN9A | 33334860 | 33277917 | 33377604
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82
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83 ]]></help>
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84 <expand macro="citations"/>
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85 </tool>