Mercurial > repos > recetox > aoptk_publication_tracker

annotate aoptk_publication_tracker.xml @ 0:0f01dc62c4f3 draft default tip

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planemo upload for repository https://github.com/rdurnik/aoptk commit df42dbae2ad18cec86a3b927123fdc3f1c82287c
author recetox
date Wed, 04 Feb 2026 09:43:20 +0000
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1 <tool id="aoptk_publication_tracker" name="aoptk publication tracker" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="25.1" license="MIT">
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2 <description>Tool to track publications.</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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7 <requirements>
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8 <expand macro="requirements"/>
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9 </requirements>
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11 <command detect_errors="exit_code"><![CDATA[
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12 ln -s '$read' 'read.${read.ext}' &&
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13 ln -s '$master' 'master.${master.ext}' &&
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14 publication-tracker
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15 --read 'read.${read.ext}'
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16 --master 'master.${master.ext}'
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17 --code '$code'
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18 --query '$query'
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19 --database '$literature_database'
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20 --outdir .
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21 \${EMAIL:+--email \$EMAIL}
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22 ]]></command>
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23
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24 <inputs>
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25 <expand macro="inputs"/>
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26 <param argument="--code" type="text" value="" label="Your search code" help="Type your search code. E.g., 1.1. or 1.2.1.">
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27 <sanitizer invalid_char="">
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28 <valid initial="string.digits">
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29 <add value="." />
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30 </valid>
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31 </sanitizer>
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32 <validator type="regex">^\d+(\.\d+)*\.?$</validator>
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33 </param>
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34 <param argument="--read" type="data" format="xlsx" label="Your database of read publications" help="Your database of read publications. Column id must be present." />
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35 <param argument="--master" type="data" format="xlsx" label="Your master table" help="Your master table. Columns ID and Search code must be present." />
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36
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37 </inputs>
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38
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39 <outputs>
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40 <data name="updated_master_table" format="xlsx" from_work_dir="updated_master_table.xlsx" label="Updated master table" />
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41 <data name="to_read" format="xlsx" from_work_dir="to_read.xlsx" label="To read" />
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42 </outputs>
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43
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44 <tests>
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45 <!-- Hint: You can use [ctrl+alt+t] after defining the inputs/outputs to auto-scaffold some basic test cases. -->
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46 <test>
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47 <param name="query" value="hepg2 thioacetamide"/>
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48 <param name="code" value="1.1.1."/>
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49 <param name="literature_database" value="pubmed"/>
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50 <param name="read" value="read_test.xlsx"/>
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51 <param name="master" value="master_test.xlsx"/>
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52 <output name="to_read" file="read1.xlsx" compare="sim_size" delta="100"/>
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53 </test>
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54 <test>
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55 <param name="query" value="hepg2 heparg thioacetamide spheroid"/>
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56 <param name="code" value="1.2.1."/>
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57 <param name="literature_database" value="europepmc"/>
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58 <param name="read" value="read_test.xlsx"/>
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59 <param name="master" value="master_test.xlsx"/>
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60 <output name="to_read" file="read2.xlsx" compare="sim_size" delta="100"/>
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61 </test>
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62 <test>
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63 <param name="query" value="lx-2 col1a1"/>
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64 <param name="code" value="3.1."/>
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65 <param name="literature_database" value="pubmed"/>
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66 <param name="read" value="read_test.xlsx"/>
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67 <param name="master" value="master_test.xlsx"/>
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68 <output name="updated_master_table" file="updated_master_table.xlsx" compare="sim_size" delta="100"/>
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69 <output name="to_read" file="read3.xlsx" compare="sim_size" delta="100"/>
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70 </test>
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71 </tests>
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72 <help><![CDATA[
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73
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74 Publication-Tracker
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75 ===================
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76 Publication-Tracker allows you to filter for publications which you have read already and automatically update search codes in your master table.
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77
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78 How It Works
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79 ------------
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80 - Provide your email address — required by NCBI.
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81 - Enter a search term — exactly as you would in PubMed or Europe PMC.
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82 - Choose a database — PubMed or Europe PMC.
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83 - Assign a search code — a unique identifier for your search, e.g., 1.1. or 1.2.1. Maintain rationale behind this search code in Search-code table.
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84 - Upload database of read publications — an Excel file with a column named `id` containing publications you have already read.
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85 - Upload master table — an Excel file with columns `ID` and `Search code`. This is where you will map your publications to their corresponding search codes.
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86 - Master table with updated search codes will be generated.
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87 - File with yet not read publications will be generated.
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88
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89 Output Files
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90 ------------
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91
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92 - **Publications to read:** List of publications that match your search term and have not been read yet.
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93 - **Updated master table:** Master table with updated search codes.
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94
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95 Notes on Creating Database of Read Publications and Master Table
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96 ----------------------------------------------------------------
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97
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98 - **Database of read publications:** Must be an Excel file with a column named `id` containing the PubMed IDs (or other identifier if not available) of the publications you have read.
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99 - **Master table:** Must be an Excel file with columns `ID` (PubMed ID or other identifier) and `Search code`. This table will be updated with new search codes.
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100
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101 How to cite
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102 ===========
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103
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104 If you use Publication-Tracker in your research, please cite [DOI TBA].
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105 Publication-Tracker was originally developed for the purposes of this publication.
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106
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107
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108 ]]></help>
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109 <citations>
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110 <citation type="doi">10.1093/bioinformatics/btp163</citation>
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111 </citations>
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112 </tool>