Mercurial > repos > mingchen0919 > aurora_bdss_url
view rmarkdown_report.xml @ 2:0d15928a648c draft
planemo upload for repository https://github.com/feltus/BDSS
author | mingchen0919 |
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date | Mon, 11 Jun 2018 23:50:10 -0400 |
parents | b12c945daf86 |
children | 86f38533b2ab |
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<tool name="aurora_bdss_url" id='aurora_bdss_url_report' version="1.0.0"> <description> some description </description> <requirements> <requirement type="package" version="1.15.0.6-0">pandoc</requirement> <requirement type="package" version="1.20.0">r-getopt</requirement> <requirement type="package" version="1.6">r-rmarkdown</requirement> </requirements> <command><![CDATA[ ######### each aurora tool generates a html file and have an files path directory associated with it. mkdir -p $report.files_path && ######### three important paths: ######### 1. path to tool installation directory ######### 2. path to report html ######### 3. path to files_path directory associated with the report output. export TOOL_INSTALL_DIR='${__tool_directory__}' && export REPORT='$report' && export REPORT_FILES_PATH='$report.files_path' && ############ create a hidden file to store r markdown rendering log touch $report.files_path/.r_rendering.log.txt && ############ finally run the render.R script Rscript '${__tool_directory__}/rmarkdown_report_render.R' -o $report -d $report.files_path -u $urls ]]></command> <inputs> <param type="text" name="urls" area="true" size="5x25" label="data URLs" help="Multiple URLs should be separated with comma or space"/> </inputs> <outputs> <data format="html" name="report" label="${tool.name} report on ${on_string}"/> <data name="output" label="BDSS downloaded data"> <discover_datasets pattern="__name_and_ext__" directory="download_dir" visible="true"/> </data> </outputs> <citations> <citation type="bibtex"><![CDATA[ @article{allaire2016rmarkdown, title={rmarkdown: Dynamic Documents for R, 2016}, author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff and Wickham, Hadley and Atkins, Aron and Hyndman, Rob}, journal={R package version 0.9}, volume={6}, year={2016} } ]]></citation> <citation type="bibtex"><![CDATA[ @book{xie2015dynamic, title={Dynamic Documents with R and knitr}, author={Xie, Yihui}, volume={29}, year={2015}, publisher={CRC Press} } ]]></citation> <citation type="bibtex"><![CDATA[ @online{jstree, author={Bozhanov, Ivan}, year = 2018, url = {https://www.jstree.com/} } ]]></citation> </citations> </tool>