Mercurial > repos > mingchen0919 > aurora_fasta_importer
view rmarkdown_report.Rmd @ 0:461163067ced draft
planemo upload
author | mingchen0919 |
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date | Tue, 15 May 2018 00:50:47 -0400 |
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--- title: 'Aurora FASTA importer report' output: html_document: highlight: pygments --- ```{r setup, include=FALSE, warning=FALSE, message=FALSE} knitr::opts_chunk$set(error = TRUE, echo = FALSE) ``` ```{css echo=FALSE} # code chunks scrollable pre code, pre, code { white-space: pre !important; overflow-x: scroll !important; word-break: keep-all !important; word-wrap: initial !important; } ``` ```{r, echo=FALSE} # to make the css theme to work, <link></link> tags cannot be added directly # as <script></script> tags as below. # it has to be added using a code chunk with the htmltool functions!!! css_link = tags$link() css_link$attribs = list(rel="stylesheet", href="vakata-jstree-3.3.5/dist/themes/default/style.min.css") css_link ``` ```{r, eval=FALSE, echo=FALSE} # this code chunk is purely for adding comments # below is to add jQuery and jstree javascripts ``` <script src="https://code.jquery.com/jquery-3.3.1.min.js"></script> <script src="vakata-jstree-3.3.5/dist/jstree.min.js"></script> --- # javascript code below is to build the file tree interface # see this for how to implement opening hyperlink: https://stackoverflow.com/questions/18611317/how-to-get-i-get-leaf-nodes-in-jstree-to-open-their-hyperlink-when-clicked-when --- <script> $(function () { // create an instance when the DOM is ready $('#jstree').jstree().bind("select_node.jstree", function (e, data) { window.open( data.node.a_attr.href, data.node.a_attr.target ) }); }); </script> --- # ADD YOUR DATA ANALYSIS CODE AND MARKUP TEXT BELOW TO EXTEND THIS R MARKDOWN FILE --- ## Job script ```{bash, echo=FALSE} sh ${TOOL_INSTALL_DIR}/build-and-run-job-scripts.sh > ${REPORT_FILES_PATH}/log.txt 2>&1 ``` ```{r echo=FALSE, comment='', results='asis'} cat('```bash\n') cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/curl-download.sh')), sep = '\n') cat('\n```') ```