Mercurial > repos > iuc > pmids_to_pubtator_matrix

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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 08:33:56 +0000
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1 <tool id="pmids_to_pubtator_matrix" name="PMIDs to PubTator" version="@VERSION@" license="MIT">
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2 <description>binary matrix</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="1.4.0">r-stringr</requirement>
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9 <requirement type="package" version="1.98_1.2">r-rcurl</requirement>
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10 <requirement type="package" version="1.5.3">r-stringi</requirement>
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11 </requirements>
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12 <command detect_errors="exit_code"><![CDATA[
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13 Rscript
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14 '${__tool_directory__}/pmids_to_pubtator_matrix.R'
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15 --input '$input'
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16 --output '$output'
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17 --number '$number'
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18 $byid
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19 --categories
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20 #for $category in $categories:
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21 '$category'
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22 #end for
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23 ]]>
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24 </command>
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25 <inputs>
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26 <param argument="--input" type="data" format="tabular" label="Input file with PMID IDs" />
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27 <param argument="--categories" type="select" label="categories" multiple="true" display="checkboxes">
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28 <option value="Gene">Genes</option>
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29 <option value="Disease">Diseases</option>
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30 <option value="Mutation">Mutations</option>
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31 <option value="Chemical">Chemicals</option>
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32 <option value="Species">Species</option>
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33 </param>
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34 <param argument="--byid" label="If you want to find common gene IDs / mesh IDs instead of specific scientific terms." name="byid" type="boolean" truevalue="--byid" falsevalue="" help="byid" checked="false"/>
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35 <param argument="--number" label="Number of most frequent terms/IDs to extract." name="number" optional="true" type="integer" help="number" value="50"/>
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36 </inputs>
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37 <outputs>
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38 <data format="tabular" name="output" />
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39 </outputs>
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40 <tests>
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41 <test>
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42 <param name="input" value="pubmed_by_queries_output" ftype="tabular"/>
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43 <param name="categories" value="Gene,Mutation"/>
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44 <output name="output">
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45 <assert_contents>
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46 <has_n_lines n="7"/>
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47 </assert_contents>
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48 </output>
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49 </test>
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50 <test>
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51 <param name="input" value="pubmed_by_queries_output" ftype="tabular"/>
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52 <param name="categories" value="Gene,Disease"/>
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53 <param name="byid" value="True"/>
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54 <output name="output">
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55 <assert_contents>
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56 <has_n_lines n="7"/>
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57 </assert_contents>
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58 </output>
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59 </test>
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60 <test>
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61 <param name="input" value="pubmed_by_queries_output" ftype="tabular"/>
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62 <param name="categories" value="Gene,Disease"/>
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63 <param name="number" value="5"/>
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64 <output name="output">
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65 <assert_contents>
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66 <has_n_lines n="7"/>
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67 </assert_contents>
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68 </output>
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69 </test>
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70 </tests>
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71 <help><![CDATA[
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72
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73 **What it does**
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74
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75 The tool uses all PMIDs per row and extracts "Gene", "Disease", "Mutation", "Chemical" and "Species" terms of the corresponding abstracts,
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76 using PubTator annotations. The user can choose from which categories terms should be extracted. The extracted terms are united in one
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77 large binary matrix, with 0= term not present in abstracts of that row and 1= term present in abstracts of that row.
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78 The user can decide if the scientific terms should be extracted and used as they are or if they should be grouped by their
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79 geneIDs/ meshIDs (several terms are often grouped into one ID). The the user can specify a number of most frequent words to extract per row.
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80
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81 - Input file:
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82
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83 Output of 'abstracts_by_pmids' tool, or tab-delimited table with columns containing PMIDs.
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84 The names of the PMID columns should start with "PMID", e.g. "PMID_1", "PMID_2" etc.
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85
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86 - Output file:
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87
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88 Binary matrix in that each column represents one of the extracted terms.
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89
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90 -----
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91
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92 **Example**
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93
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94 - Input table:
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95
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96 | PMID_1 | PMID_2 | PMID_2
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97 | 33565071 | 33531663 | 33528079
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98 | 33377604 | 33334860 | 33277917
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99
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100 - Extract of output table:
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101
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102 | egfr | hormone | tp53 | scn8a | cacna1a | grin2a
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103 | 1 | 0 | 1 | 0 | 1 | 0
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104 | 1 | 1 | 1 | 1 | 0 | 1
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105
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106
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107 ]]></help>
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108 <expand macro="citations"/>
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109 </tool>