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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">
2 <description>Tool to track publications.</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6
7 <requirements>
8 <expand macro="requirements"/>
9 </requirements>
10
11 <command detect_errors="exit_code"><![CDATA[
12 ln -s '$read' 'read.${read.ext}' &&
13 ln -s '$master' 'master.${master.ext}' &&
14 publication-tracker
15 --read 'read.${read.ext}'
16 --master 'master.${master.ext}'
17 --code '$code'
18 --query '$query'
19 --database '$literature_database'
20 --outdir .
21 \${EMAIL:+--email \$EMAIL}
22 ]]></command>
23
24 <inputs>
25 <expand macro="inputs"/>
26 <param argument="--code" type="text" value="" label="Your search code" help="Type your search code. E.g., 1.1. or 1.2.1.">
27 <sanitizer invalid_char="">
28 <valid initial="string.digits">
29 <add value="." />
30 </valid>
31 </sanitizer>
32 <validator type="regex">^\d+(\.\d+)*\.?$</validator>
33 </param>
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." />
35 <param argument="--master" type="data" format="xlsx" label="Your master table" help="Your master table. Columns ID and Search code must be present." />
36
37 </inputs>
38
39 <outputs>
40 <data name="updated_master_table" format="xlsx" from_work_dir="updated_master_table.xlsx" label="Updated master table" />
41 <data name="to_read" format="xlsx" from_work_dir="to_read.xlsx" label="To read" />
42 </outputs>
43
44 <tests>
45 <!-- Hint: You can use [ctrl+alt+t] after defining the inputs/outputs to auto-scaffold some basic test cases. -->
46 <test>
47 <param name="query" value="hepg2 thioacetamide"/>
48 <param name="code" value="1.1.1."/>
49 <param name="literature_database" value="pubmed"/>
50 <param name="read" value="read_test.xlsx"/>
51 <param name="master" value="master_test.xlsx"/>
52 <output name="to_read" file="read1.xlsx" compare="sim_size" delta="100"/>
53 </test>
54 <test>
55 <param name="query" value="hepg2 heparg thioacetamide spheroid"/>
56 <param name="code" value="1.2.1."/>
57 <param name="literature_database" value="europepmc"/>
58 <param name="read" value="read_test.xlsx"/>
59 <param name="master" value="master_test.xlsx"/>
60 <output name="to_read" file="read2.xlsx" compare="sim_size" delta="100"/>
61 </test>
62 <test>
63 <param name="query" value="lx-2 col1a1"/>
64 <param name="code" value="3.1."/>
65 <param name="literature_database" value="pubmed"/>
66 <param name="read" value="read_test.xlsx"/>
67 <param name="master" value="master_test.xlsx"/>
68 <output name="updated_master_table" file="updated_master_table.xlsx" compare="sim_size" delta="100"/>
69 <output name="to_read" file="read3.xlsx" compare="sim_size" delta="100"/>
70 </test>
71 </tests>
72 <help><![CDATA[
73
74 Publication-Tracker
75 ===================
76 Publication-Tracker allows you to filter for publications which you have read already and automatically update search codes in your master table.
77
78 How It Works
79 ------------
80 - Provide your email address — required by NCBI.
81 - Enter a search term — exactly as you would in PubMed or Europe PMC.
82 - Choose a database — PubMed or Europe PMC.
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.
84 - Upload database of read publications — an Excel file with a column named `id` containing publications you have already read.
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.
86 - Master table with updated search codes will be generated.
87 - File with yet not read publications will be generated.
88
89 Output Files
90 ------------
91
92 - **Publications to read:** List of publications that match your search term and have not been read yet.
93 - **Updated master table:** Master table with updated search codes.
94
95 Notes on Creating Database of Read Publications and Master Table
96 ----------------------------------------------------------------
97
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.
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.
100
101 How to cite
102 ===========
103
104 If you use Publication-Tracker in your research, please cite [DOI TBA].
105 Publication-Tracker was originally developed for the purposes of this publication.
106
107
108 ]]></help>
109 <citations>
110 <citation type="doi">10.1093/bioinformatics/btp163</citation>
111 </citations>
112 </tool>