Mercurial > repos > mingchen0919 > aurora_fasta_importer
view rmarkdown_report.xml @ 0:461163067ced draft
planemo upload
author | mingchen0919 |
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date | Tue, 15 May 2018 00:50:47 -0400 |
parents | |
children | dfd29c07d6ca |
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<tool name="aurora_tool" id='aurora_tool_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 -f $upload_fasta -u $url_fasta -O $output_fasta ]]></command> <inputs> <param type="data" name="upload_fasta" format="fa,fna,fasta" label="Fasta file from history" optional="True"/> <param type="text" name="url_fasta" label="URL to downloadable fasta file"/> </inputs> <outputs> <data format="html" name="report" label="${tool.name} report on ${on_string}" /> <data format="fasta" name="output_fasta" label="${tool.name} fasta on ${on_string}" /> </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>