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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/make_data_paper_sketches commit 34f4e0604adc2a2ba4902ce6b8e6df2460eda292
author ecology
date Tue, 15 Oct 2024 20:33:48 +0000
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1 <tool id="data_paper_from_EML" name="Make data paper sketches" version="0.1.0+galaxy0" profile="21.05">
2 <description>from EML</description>
3 <requirements>
4 <requirement type="package" version="4.3.3">r-base</requirement>
5 <requirement type="package" version="1.1.39">libxslt</requirement>
6 <requirement type="package" version="3.5">pandoc</requirement>
7 <requirement type="package" version="1.1.4">r-dplyr</requirement>
8 <requirement type="package" version="2.11.2">r-mapview</requirement>
9 <requirement type="package" version="1.4.6">r-xslt</requirement>
10 <requirement type="package" version="1.3.6">r-xml2</requirement>
11 <requirement type="package" version="2.1.1">phantomjs</requirement>
12
13 </requirements>
14 <command detect_errors="exit_code"><![CDATA[
15
16 Rscript '$__tool_directory__/map_geographical_coverage.R' '$inputmetadatafile' &&
17
18 xsltproc -o datapaper.html '$__tool_directory__/emldown_templates/bootstrap2.xsl' '${inputmetadatafile}' &&
19 pandoc datapaper.html -o data_paper.docx
20
21 ]]></command>
22 <inputs>
23 <param name="inputmetadatafile" type="data" format="xml" label="EML metadata file" help="Insert only metadata using EML standard"/>
24 </inputs>
25 <outputs>
26 <data name="datapaper_docx" from_work_dir="data_paper.docx" format="docx" label="data_paper.docx"/>
27 </outputs>
28 <tests>
29 <test>
30 <param name="inputmetadatafile" value="EML.xml"/>
31 <output name='datapaper_docx'>
32 <assert_contents>
33 <has_size value="31756" delta="50"/>
34 </assert_contents>
35 </output>
36 </test>
37 </tests>
38 <help><![CDATA[
39
40 **What it does?**
41 --------------------
42
43 This tool derived from the archived R Opensci emldown package thanks to French Fund for open science "OpenMetaPaper" project emldown R code improvements https://github.com/TanguyGen/emldown and creation fo the MetaShRIMPS R Shiny App <https://github.com/TanguyGen/metaCure> is made to produce draft of data paper from Ecological Metadata Language (EML) based metadata documents.
44
45 **How to use it?**
46 --------------------
47
48 You need to input an EML (Ecological Metadata Language) metadata file (xml format) and run the tool that will produce a draft of data paper in docx format that you can edit.
49
50
51 ]]></help>
52
53 <citations>
54 <citation type="bibtex">@misc{githubsurvey2023,
55 author = {Tanguy Genthon},
56 title = {{Metadata Shiny for Retroactive Information Management and Production of data paper Sketches}},
57 publisher = {Github},
58 url = {https://github.com/TanguyGen/metaCure},
59 year = {2023}
60 }
61 }</citation>
62 <citation type="bibtex">@misc{githubsurvey2023b,
63 author = {Tanguy Genthon},
64 title = {{Produce beautifull website from EML}},
65 publisher = {Github},
66 url = {https://github.com/TanguyGen/emldown},
67 year = {2023}
68 }
69 }</citation>
70 </citations>
71 </tool>