Mercurial > repos > iuc > openalex_explorer

comparison openalex.xml @ 0:1678b5f97915 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
author iuc
date Sat, 31 May 2025 12:25:24 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:1678b5f97915
1 <tool id="openalex_explorer" name="OpenAlex explorer" version="0.1.0+galaxy0" profile="23.1">
2 <description>Fetch citing papers from OpenAlex using DOI, openAlex ID, or title</description>
3 <requirements>
4 <requirement type="package" version="3.10">python</requirement>
5 <requirement type="package" version="2.31.0">requests</requirement>
6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[
8 python3 '$__tool_directory__/openalex_fetch.py'
9 $input_type '$identifier'
10 --max-citations '$max_citations'
11 $download_pdfs
12 ]]></command>
13 <inputs>
14 <param name="input_type" type="select" label="Input type" help="Select whether the identifier is an OpenAlex ID, DOI, or Title">
15 <option value="--doi" selected="true">DOI</option>
16 <option value="--id">OpenAlex ID</option>
17 <option value="--title">Title</option>
18 </param>
19 <param name="identifier" type="text" label="Identifier" help="Enter the OpenAlex ID, DOI, or Title depending on your selection above"/>
20 <param name="download_pdfs" type="boolean" truevalue="--download" falsevalue="" label="Download available OA PDFs?" value="false"/>
21 <param name="max_citations" type="select" label="Max citing papers to fetch" help="Limit the number of citing papers to fetch">
22 <option value="10">10</option>
23 <option value="20">20</option>
24 <option value="50" selected="true">50</option>
25 <option value="100">100</option>
26 <option value="all">All</option>
27 </param>
28 </inputs>
29 <outputs>
30 <data name="summary_out" format="txt" label="Citation Summary" from_work_dir="summary.txt"/>
31 <data name="tsv_out" format="tabular" label="Citing Papers TSV" from_work_dir="citing_papers.tsv"/>
32 <collection name="pdf_outputs" label="Downloaded PDFs" type="list" format="pdf">
33 <discover_datasets pattern="__designation_and_ext__" directory="downloads"/>
34 </collection>
35 </outputs>
36 <tests>
37 <test>
38 <param name="input_type" value="--id"/>
39 <param name="identifier" value="W4398182689"/>
40 <param name="max_citations" value="10"/>
41 <param name="download_pdfs" value="false"/>
42 <output name="summary_out" file="expected_summary.txt"/>
43 <output name="tsv_out" file="expected_citing_papers.tsv"/>
44 </test>
45 <test>
46 <param name="input_type" value="--doi"/>
47 <param name="identifier" value="10.1093/nar/gkae410"/>
48 <param name="max_citations" value="50"/>
49 <param name="download_pdfs" value="false"/>
50 <output name="summary_out" file="expected_summary_doi.txt"/>
51 <output name="tsv_out" file="expected_citing_papers_doi.tsv"/>
52 </test>
53 <test>
54 <param name="input_type" value="--title"/>
55 <param name="identifier" value="The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update"/>
56 <param name="max_citations" value="50"/>
57 <param name="download_pdfs" value="false"/>
58 <output name="summary_out" file="expected_summary_title.txt"/>
59 <output name="tsv_out" file="expected_citing_papers_title.tsv"/>
60 </test>
61 <test>
62 <param name="input_type" value="--id"/>
63 <param name="identifier" value="W2088676066"/>
64 <param name="max_citations" value="10"/>
65 <param name="download_pdfs" value="true"/>
66 <output name="summary_out" file="expected_summary_wddownload.txt"/>
67 <output name="tsv_out" file="expected_citing_papers_wddownload.tsv"/>
68 <output_collection name="pdf_outputs" type="list" count="1">
69 <!-- Also working with the line below but I guess count check would be suffice -->
70 <!-- <element name="NAC-MYB-based transcriptional regulation of secondary cell wall biosynthesis in land plants" file="downloads/NAC-MYB-based transcriptional regulation of secondary cell wall biosynthesis in land plants.pdf"/> -->
71 </output_collection>
72 </test>
73 </tests>
74 <help><![CDATA[
75 This tool fetches citing papers from OpenAlex for a paper specified by OpenAlex ID, DOI, or Title.
76
77 You can optionally download available Open Access PDFs.
78
79 **Outputs:**
80
81 - summary.txt: summary of total, OA, and closed access citing papers
82
83 - citing_papers.tsv: list of citing papers with details (title, DOI, OA)
84 ]]></help>
85 <citations>
86 <citation type="doi">10.48550/arXiv.2205.01833</citation>
87 </citations>
88 </tool>