Mercurial > repos > mingchen0919 > aurora_skewer
changeset 10:1b637e0a30b6 draft
planemo upload commit 61448862dc9016969191967aeefb7f7acce1e1f9-dirty
| author | mingchen0919 |
|---|---|
| date | Tue, 01 May 2018 00:24:08 -0400 |
| parents | c0e57c994deb |
| children | 70de0b9c4c76 |
| files | build-and-run-job-scripts.sh command-line-arguments.csv expose-outputs-to-galaxy-history.sh expose-outputs.sh getopt_specification.csv helper.R rmarkdown_report.Rmd rmarkdown_report.xml rmarkdown_report_render.R shell-script-template.sh skewer.Rmd skewer.xml skewer_render.R |
| diffstat | 13 files changed, 483 insertions(+), 469 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build-and-run-job-scripts.sh Tue May 01 00:24:08 2018 -0400 @@ -0,0 +1,45 @@ +# run job scripts within the tool outputs directory +cd ${REPORT_FILES_PATH} + +#========== build and run job 1 script ============ +cat >job-1-script.sh <<EOF +skewer \\ + ${X_A} \\ + ${X_B} \\ + -x ${X_x} \\ + -y ${X_y} \\ + -m ${X_m} \\ + -r ${X_r} \\ + -d ${X_D} \\ + -q ${X_q} \\ + -Q ${X_Q} \\ + -l ${X_l} \\ + -j ${X_j} \\ + -M ${X_M} \\ + -b ${X_b} \\ + -c ${X_b} \\ + -n ${X_n} \\ + -u ${X_u} \\ + -f ${X_f} \\ + -z ${X_z} \\ + -qiime ${X_E} \\ + -quiet ${X_F} \\ + -i ${X_i} \\ + -o trim > /dev/null 2>&1 +EOF + +# remove empty input lines +grep -v '\-M \\' temp.sh |\ + grep -v 'None' |\ + grep -v 'NO_ARGUMENT_NO' |\ + sed 's/NO_ARGUMENT_YES//g' > job-1-script.sh + +rm temp.sh + +# run job 1 script +sh job-1-script.sh + +# rename log file +if [ -e trim-trimmed.log ]; then + cp trim-trimmed.log trim-trimmed.txt +fi \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/command-line-arguments.csv Tue May 01 00:24:08 2018 -0400 @@ -0,0 +1,27 @@ +short flag,argument mask,data type,variable name +o,1,character,report +d,1,character,report.files_path +A,1,character,first_reads +B,1,character,second_reads +x,1,character,adapter_first_reads +y,1,character,adapter_second_reads +m,1,character,trimming_mode +r,1,character,maximum_allowed_error_rate +D,1,character,maximum_allowed_indel_error_rate +q,1,character,quality_trimming_3_end +Q,1,character,mean_quality +l,1,character,minimum_read_length +j,1,character,advanced_options.junction_adapter +M,1,character,advanced_options.tab_adapter +b,1,character,advanced_options.barcode +c,1,character,advanced_options.cut +n,1,character,advanced_options.filter_degenerative_reads +u,1,character,advanced_options.filter_undetermined_mate_pair_reads +f,1,character,advanced_options.format +z,1,character,advanced_options.compress +E,1,character,advanced_options.qiime +F,1,character,advanced_options.quiet +i,1,character,advanced_options.intelligent +1,1,character,trimmed_r1 +2,1,character,trimmed_r2 +3,1,character,trimmed_s
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/expose-outputs-to-galaxy-history.sh Tue May 01 00:24:08 2018 -0400 @@ -0,0 +1,24 @@ +# change directory to tool outputs directory +cd ${REPORT_FILES_PATH} + +# copy outputs from tool outputs directory to corresponding galaxy output path +if [ -e "rmarkdown_report.html" ]; then + cp rmarkdown_report.html ${REPORT} +fi + +if [ -e "index.html" ]; then + cp index.html ${REPORT} +fi + + +if [ -e trim-trimmed-pair1.fastq ]; then + cp trim-trimmed-pair1.fastq ${X_1} +fi + +if [ -e trim-trimmed-pair2.fastq ]; then + cp trim-trimmed-pair2.fastq ${X_2} +fi + +if [ -e trim-trimmed.fastq ]; then + cp trim-trimmed.fastq ${X_3} +fi \ No newline at end of file
--- a/expose-outputs.sh Thu Apr 26 14:10:58 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,17 +0,0 @@ -# change directory to tool outputs directory -cd ${REPORT_FILES_PATH} - -# copy outputs from tool outputs directory to corresponding galaxy output path -cp skewer.html ${REPORT} - -if [ -e trim-trimmed-pair1.fastq ]; then - cp trim-trimmed-pair1.fastq ${X_1} -fi - -if [ -e trim-trimmed-pair2.fastq ]; then - cp trim-trimmed-pair2.fastq ${X_2} -fi - -if [ -e trim-trimmed.fastq ]; then - cp trim-trimmed.fastq ${X_3} -fi
--- a/getopt_specification.csv Thu Apr 26 14:10:58 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,27 +0,0 @@ -short flag,argument mask,data type,variable name -o,1,character,report -d,1,character,report.files_path -A,1,character,first_reads -B,1,character,second_reads -x,1,character,adapter_first_reads -y,1,character,adapter_second_reads -m,1,character,trimming_mode -r,1,character,maximum_allowed_error_rate -D,1,character,maximum_allowed_indel_error_rate -q,1,character,quality_trimming_3_end -Q,1,character,mean_quality -l,1,character,minimum_read_length -j,1,character,advanced_options.junction_adapter -M,1,character,advanced_options.tab_adapter -b,1,character,advanced_options.barcode -c,1,character,advanced_options.cut -n,1,character,advanced_options.filter_degenerative_reads -u,1,character,advanced_options.filter_undetermined_mate_pair_reads -f,1,character,advanced_options.format -z,1,character,advanced_options.compress -E,1,character,advanced_options.qiime -F,1,character,advanced_options.quiet -i,1,character,advanced_options.intelligent -1,1,character,trimmed_r1 -2,1,character,trimmed_r2 -3,1,character,trimmed_s \ No newline at end of file
--- a/helper.R Thu Apr 26 14:10:58 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,82 +0,0 @@ -#' \code{getopt_specification_matrix} returns a getopt specification matrix. -#' -#' @param specification_file a cvs file within the \code{galaxy_tool_directory} which stores getopt specification matrix data. -#' The first column are short flags, the second column are argument masks, the third column -#' is data types. The fourth column are variable names used in the tool XML. These three columns are required. -#' @param gtg_name the name of a running GTG. -getopt_specification_matrix = function(specification_file, - gtg_name = 'gtg', - tool_dir = Sys.getenv('TOOL_DIR')) { - df = read.csv( - paste0(tool_dir, '/', specification_file), - header = TRUE, - stringsAsFactors = FALSE - ) - # check if there are duplicated short flags - short_flags = df[, 1] - if (length(unique(short_flags)) < length(short_flags)) { - cat('----Duplicated short flags found ----\n') - cat('short flags: ', df[, 1][duplicated(df[, 1])], '\n') - stop('Duplicated short flags are not allowed.') - } - - # use short flags to generate long flags - long_flags = paste0('X_', df[, 1]) - - # specification matrix - df2 = data.frame( - long_flags = long_flags, - short_flags = df[, 1], - argument_mask = df[, 2], - data_type = df[, 3] - ) - - as.matrix(df2) -} - - - -#' \code{file_tree} generate file tree of a directory in the format of HTML lists. -#' -#' @param dir the path to the directory for generating the file tree. -#' @param output_dir the REPORT_FILES_PATH folder name, which has the name style: dataset_NUMBER_files. -# define a recursive function to build html string of the file tree -file_tree = function(dir = '.') { - # get the OUTPUT_DIR folder data: dataset_NUMBER_files - report_files_path = Sys.getenv('REPORT_FILES_PATH') - output_dir = tail(strsplit(report_files_path, '/')[[1]], 1) - - files = list.files(path = dir, - recursive = FALSE, - full.names = TRUE) - # files also include directorys, need to remove directorys - files = files[!dir.exists(files)] - dirs = list.dirs(path = dir, - recursive = FALSE, - full.names = TRUE) - tags$ul({ - if (length(files) > 0) { - lapply(files, function(x) { - path_end = tail(strsplit(x, '/')[[1]], 1) - href_path = strsplit(x, paste0(output_dir, '/'))[[1]][2] - li_item = tags$li(tags$a(path_end, href = href_path)) - li_item$attribs = list('data-jstree' = '{"icon":"jstree-file"}') - li_item - }) - } - }, - { - if (length(dirs) > 0) { - lapply(dirs, function(x) { - path_end = tail(strsplit(x, '/')[[1]], 1) - # hide vakata-jstree-3.3.5 folder - if (path_end != 'vakata-jstree-3.3.5') { - # x_path = strsplit(x, paste0(output_dir, '/'))[[1]][2] - li_item = tags$li(path_end, file_tree(x)) - li_item$attribs = list('data-jstree' = '{"icon":"jstree-folder"}') - li_item - } - }) - } - }) -}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rmarkdown_report.Rmd Tue May 01 00:24:08 2018 -0400 @@ -0,0 +1,69 @@ +--- +title: 'Aurora Tool Report' +output: + html_document: + highlight: pygments +--- + +```{r setup, include=FALSE, warning=FALSE, message=FALSE} +knitr::opts_chunk$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 +``` + +```{r echo=FALSE,warning=FALSE,results='asis'} +# display content of the job-script.sh file. +cat('```bash\n') +cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/job-1-script.sh')), sep = '\n') +cat('\n```') +``` + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rmarkdown_report.xml Tue May 01 00:24:08 2018 -0400 @@ -0,0 +1,161 @@ +<tool name="aurora_skewer" id='aurora_skewer_report' version="2.0.1"> + <description>A fast and accurate adapter trimmer for next-generation sequencing single or paired end reads. + </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 $report.files_path + + -A '$first_reads' + -B '$second_reads' + -x '$adapter_first_reads' + -y '$adapter_second_reads' + -m '$trimming_mode' + -r '$maximum_allowed_error_rate' + -D '$maximum_allowed_indel_error_rate' + -q '$quality_trimming_3_end' + -Q '$mean_quality' + -l '$minimum_read_length' + -j '$advanced_options.junction_adapter' + -M '$advanced_options.tab_adapter' + -b '$advanced_options.barcode' + -c '$advanced_options.cut' + -n '$advanced_options.filter_degenerative_reads' + -u '$advanced_options.filter_undetermined_mate_pair_reads' + -f '$advanced_options.format' + -z '$advanced_options.compress' + -E '$advanced_options.qiime' + -F '$advanced_options.quiet' + -i '$advanced_options.intelligent' + -1 '$trimmed_r1' + -2 '$trimmed_r2' + -3 '$trimmed_s' + + + ]]></command> + <inputs> + <param type="data" name="first_reads" label="First reads" optional="False" format="fastq,fastqsanger" + multiple="False"/> + <param type="data" name="second_reads" label="Second reads" + help="If it is single end reads, ignore this input field and use the "first reads" field only." + optional="True" format="fastq,fastqsanger" multiple="False"/> + <param type="data" name="adapter_first_reads" argument="-x" label="Adapter sequence/file for the first reads." + optional="True" format="fasta,fa" multiple="False"/> + <param type="data" name="adapter_second_reads" argument="-y" label="Adapter sequence/file for the second reads" + optional="True" format="fasta,fa" multiple="False"/> + <param type="select" name="trimming_mode" argument="-m" label="trimming mode" optional="False" multiple="False"> + <option value="None" selected="true">--select a model--</option> + <option value="head" selected="false">5’ end trimming (single end reads)</option> + <option value="tail" selected="false">3’ end trimming (single end reads)</option> + <option value="any" selected="false">anywhere adapter detection and trimming (single end reads)</option> + <option value="pe" selected="false">paired-end trimming</option> + <option value="mp" selected="false">mate-pair trimming</option> + <option value="ap" selected="false">amplicon trimming</option> + </param> + <param type="float" name="maximum_allowed_error_rate" argument="-r" label="Maximum allowed error rate" + optional="False" value="0.1" min="0" max="0.5"/> + <param type="float" name="maximum_allowed_indel_error_rate" argument="-d" + label="Maximum allowed indel error rate" + help="The valid range of indel error rate is [0, maximum allowed error rate]" optional="False" + value="0.03" min="0"/> + <param type="integer" name="quality_trimming_3_end" argument="-q" label="3’ end quality trimming" + optional="False" value="0"/> + <param type="integer" name="mean_quality" argument="-Q" label="Reads filtering by average quality" + optional="False" value="0"/> + <param type="integer" name="minimum_read_length" argument="-l" + label="Minimum read length allowed after trimming" optional="False" value="18"/> + <section name="advanced_options" title="Advanced options" expanded="False"> + <param type="data" name="junction_adapter" argument="-j" + label="Junction adapter sequence/file for Nextera Mate Pair reads" optional="True" format="fasta,fa" + multiple="False"/> + <param type="text" name="tab_adapter" argument="-M" + label="TAB delimited file indicates valid forward/reverse adapter pairing" optional="True"/> + <param type="boolean" name="barcode" argument="-b" + label="Whether to demultiplex reads according to adapters/primers" optional="False" checked="False" + truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/> + <param type="text" name="cut" argument="-c" + label="To hard clip off the 5’ leading bases of the forward primer and reverse primer respectively as the barcodes in amplicon mode" + optional="False" value="0, 0"/> + <param type="boolean" name="filter_degenerative_reads" argument="-n" + label="Whether to filter out highly degenerative reads" optional="False" checked="False" + truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/> + <param type="boolean" name="filter_undetermined_mate_pair_reads" argument="-u" + label="Whether to filter out undetermined mate-pair reads" optional="False" checked="False" + truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/> + <param type="select" name="format" argument="-f" label="Format of FASTQ quality value" optional="False" + multiple="False"> + <option value="sanger" selected="false">sanger</option> + <option value="solexa" selected="false">solexa</option> + <option value="auto" selected="true">auto</option> + </param> + <param type="boolean" name="compress" argument="-z" label="Whether to compress output in GZIP format" + optional="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/> + <param type="boolean" name="qiime" argument="-qiime" label="Whether to prepare files required by QIIME" + optional="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/> + <param type="boolean" name="quiet" argument="--quiet" label="Whether in quiet mode" optional="False" + truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/> + <param type="boolean" name="intelligent" argument="-i" label="Whether to intelligently redistribute reads" + optional="False" checked="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/> + </section> + </inputs> + <outputs> + <data name="report" format="html" label="${tool.name} report on ${on_string}" hidden="false"/> + <data name="trimmed_r1" format="fastq" label="${tool.name} trimmed first reads on ${on_string}" hidden="false"/> + <data name="trimmed_r2" format="fastq" label="${tool.name} trimmed second reads on ${on_string}" + hidden="false"/> + <data name="trimmed_s" format="fastq" label="${tool.name} trimmed single end reads on ${on_string}" + hidden="false"/> + </outputs> + <help> + <![CDATA[Read the `tool manual <http://download2.nust.na/pub4/sourceforge/s/project/sk/skewer/skewer_manual.pdf>`_ if you are not sure what parameter values to use.]]></help> + <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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rmarkdown_report_render.R Tue May 01 00:24:08 2018 -0400 @@ -0,0 +1,157 @@ +##============ Sink warnings and errors to a file ============== +## use the sink() function to wrap all code within it. +##============================================================== +zz = file(paste0(Sys.getenv('REPORT_FILES_PATH'), '/.r_rendering.log.txt')) +sink(zz) +sink(zz, type = 'message') + +#============== preparation ==================================== +# import libraries +#------------------------------------------------------------------ +# ADD MORE LIBRARIES HERE IF YOUR TOOL DEPENDS ON OTHER R LIBRARIES +#------------------------------------------------------------------ +library('getopt') +library('rmarkdown') +library('htmltools') +#------------------------------------------------------------------ +options(stringsAsFactors = FALSE) + + +# define two helper functions +#-----: helper function 1 +#' \code{getopt_specification_matrix} returns a getopt specification matrix. +#' +#' @param specification_file a cvs file within the \code{galaxy_tool_directory} which stores getopt specification matrix data. +#' The first column are short flags, the second column are argument masks, the third column +#' is data types. The fourth column are variable names used in the tool XML. These three columns are required. +#' @param gtg_name the name of a running GTG. +getopt_specification_matrix = function(specification_file, + gtg_name = 'gtg', + tool_dir = Sys.getenv('TOOL_INSTALL_DIR')) { + df = read.csv( + paste0(tool_dir, '/', specification_file), + header = TRUE, + stringsAsFactors = FALSE + ) + # check if there are duplicated short flags + short_flags = df[, 1] + if (length(unique(short_flags)) < length(short_flags)) { + cat('----Duplicated short flags found ----\n') + cat('short flags: ', df[, 1][duplicated(df[, 1])], '\n') + stop('Duplicated short flags are not allowed.') + } + + # use short flags to generate long flags + long_flags = paste0('X_', df[, 1]) + + # specification matrix + df2 = data.frame( + long_flags = long_flags, + short_flags = df[, 1], + argument_mask = df[, 2], + data_type = df[, 3] + ) + + as.matrix(df2) +} + +#-----: helper function 2 +#' \code{file_tree} generate file tree of a directory in the format of HTML lists. +#' +#' @param dir the path to the directory for generating the file tree. +#' @param output_dir the REPORT_FILES_PATH folder name, which has the name style: dataset_NUMBER_files. +# define a recursive function to build html string of the file tree +file_tree = function(dir = '.') { + # get the OUTPUT_DIR folder data: dataset_NUMBER_files + report_files_path = Sys.getenv('REPORT_FILES_PATH') + output_dir = tail(strsplit(report_files_path, '/')[[1]], 1) + + files = list.files(path = dir, + recursive = FALSE, + full.names = TRUE) + # files also include directorys, need to remove directorys + files = files[!dir.exists(files)] + dirs = list.dirs(path = dir, + recursive = FALSE, + full.names = TRUE) + tags$ul({ + if (length(files) > 0) { + lapply(files, function(x) { + path_end = tail(strsplit(x, '/')[[1]], 1) + href_path = strsplit(x, paste0(output_dir, '/'))[[1]][2] + li_item = tags$li(tags$a(path_end, href = href_path)) + li_item$attribs = list('data-jstree' = '{"icon":"jstree-file"}') + li_item + }) + } + }, + { + if (length(dirs) > 0) { + lapply(dirs, function(x) { + path_end = tail(strsplit(x, '/')[[1]], 1) + # hide vakata-jstree-3.3.5 folder + if (path_end != 'vakata-jstree-3.3.5') { + # x_path = strsplit(x, paste0(output_dir, '/'))[[1]][2] + li_item = tags$li(path_end, file_tree(x)) + li_item$attribs = list('data-jstree' = '{"icon":"jstree-folder"}') + li_item + } + }) + } + }) +} +#----------------- end of help functions ------------------------- + + +# import getopt specification matrix from a csv file +opt = getopt(getopt_specification_matrix('command-line-arguments.csv', + tool_dir = Sys.getenv('TOOL_INSTALL_DIR'))) +# define environment variables for all input values. this is useful when we +# want to use input values by other programming language in r markdown +do.call(Sys.setenv, opt[-1]) +#=============================================================== + + +#======================== render Rmd files ========================= +# copy jstree javascript library to tool output directory +file.copy( + from = paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/vakata-jstree-3.3.5'), + to = Sys.getenv('REPORT_FILES_PATH'), + recursive = TRUE +) + +# if '_site.yml' file exists, this tool is assumed to render a website. +# otherwise, it renders a single html. +if (file.exists(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/_site.yml'))) { + # render a website + system(command = 'cp -r ${TOOL_INSTALL_DIR}/*.Rmd ${REPORT_FILES_PATH}') + system(command = 'cp -r ${TOOL_INSTALL_DIR}/_site.yml ${REPORT_FILES_PATH}') + render_site(input = Sys.getenv('REPORT_FILES_PATH')) +} else { + # render a single html + system(command = 'cp -r ${TOOL_INSTALL_DIR}/rmarkdown_report.Rmd ${REPORT_FILES_PATH}') + # add a few lines to 'rmarkdown_report.Rmd' to generate file tree outputs + jstree_lines = ' +## Outputs + +```{r, echo=FALSE} +tags$div(id="jstree", file_tree(Sys.getenv(\'REPORT_FILES_PATH\'))) +```' + write( + x = jstree_lines, + append = TRUE, + file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/rmarkdown_report.Rmd') + ) + render(input = paste0(Sys.getenv('REPORT_FILES_PATH'), '/rmarkdown_report.Rmd')) +} +#=============================================================== + + +#============== expose outputs to galaxy history =============== +system(command = 'sh ${TOOL_INSTALL_DIR}/expose-outputs-to-galaxy-history.sh') +#=============================================================== + + +##--------end of code rendering .Rmd templates---------------- +sink() +##=========== End of sinking output=============================
--- a/shell-script-template.sh Thu Apr 26 14:10:58 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,48 +0,0 @@ -# SHELL_SCRIPT file name -SHELL_SCRIPT='skewer.sh' - -# run SHELL_SCRIPT within tool outputs directory -cd ${REPORT_FILES_PATH} - -# build job-script.sh -cat >temp.sh <<EOF -skewer \\ - ${X_A} \\ - ${X_B} \\ - -x ${X_x} \\ - -y ${X_y} \\ - -m ${X_m} \\ - -r ${X_r} \\ - -d ${X_D} \\ - -q ${X_q} \\ - -Q ${X_Q} \\ - -l ${X_l} \\ - -j ${X_j} \\ - -M ${X_M} \\ - -b ${X_b} \\ - -c ${X_b} \\ - -n ${X_n} \\ - -u ${X_u} \\ - -f ${X_f} \\ - -z ${X_z} \\ - -qiime ${X_E} \\ - -quiet ${X_F} \\ - -i ${X_i} \\ - -o trim > /dev/null 2>&1 -EOF - -# remove empty input lines -grep -v '\-M \\' temp.sh |\ - grep -v 'None' |\ - grep -v 'NO_ARGUMENT_NO' |\ - sed 's/NO_ARGUMENT_YES//g' > ${SHELL_SCRIPT} - -rm temp.sh - -# run SHELL_SCRIPT -sh ${SHELL_SCRIPT} - -# rename log file -if [ -e trim-trimmed.log ]; then - cp trim-trimmed.log trim-trimmed.txt -fi \ No newline at end of file
--- a/skewer.Rmd Thu Apr 26 14:10:58 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,78 +0,0 @@ ---- -title: 'Skewer report' -output: - html_document: - highlight: pygments ---- - -```{r setup, include=FALSE, warning=FALSE, message=FALSE} -knitr::opts_knit$set(progress = FALSE) -knitr::opts_chunk$set(error = TRUE, echo = FALSE) -``` - -```{r, echo=FALSE} -# to make the css theme to work, <link></link> tags cannot be added directly -# as <script></script> tags as below. -# it has to be added using a code chunk with the htmltool functions!!! -css_link = tags$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> - -```{r, eval=FALSE, echo=FALSE} -# this code chunk is purely for adding comments -# 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> - -```{css} -# code chunks scrollable -pre code, pre, code { - white-space: pre !important; - overflow-x: scroll !important; - word-break: keep-all !important; - word-wrap: initial !important; -} -``` ------------------------------------------ - -## Job script - -```{bash echo=FALSE} -sh ${TOOL_INSTALL_DIR}/shell-script-template.sh -``` - -```{r echo=FALSE,warning=FALSE,results='asis'} -# display content of the job-script.sh file. -cat('```bash\n') -cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/skewer.sh')), sep = '\n') -cat('\n```') -``` - - ------------------------------------------ -## Output - -```{r, echo=FALSE} -# create a div container to store the file tree interface -tags$div( - id="jstree", - file_tree(Sys.getenv('REPORT_FILES_PATH')) -) -``` -
--- a/skewer.xml Thu Apr 26 14:10:58 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,165 +0,0 @@ -<tool id="aurora_skewer" name="aurora_skewer" version="2.0.0"> - <description>A fast and accurate adapter trimmer for next-generation sequencing single or paired end reads. - </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> - <requirement type="package" version="0.2.2">skewer</requirement> - </requirements> - <stdio> - <regex match="XXX" source="stderr" level="warning" - description="Check the warnings_and_errors.txt file for more details."/> - </stdio> - <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 $report.files_path/.r_rendering.log.txt && - -Rscript '${__tool_directory__}/'skewer_render.R - - -o '$report' - -d '$report.files_path' - -A '$first_reads' - -B '$second_reads' - -x '$adapter_first_reads' - -y '$adapter_second_reads' - -m '$trimming_mode' - -r '$maximum_allowed_error_rate' - -D '$maximum_allowed_indel_error_rate' - -q '$quality_trimming_3_end' - -Q '$mean_quality' - -l '$minimum_read_length' - -j '$advanced_options.junction_adapter' - -M '$advanced_options.tab_adapter' - -b '$advanced_options.barcode' - -c '$advanced_options.cut' - -n '$advanced_options.filter_degenerative_reads' - -u '$advanced_options.filter_undetermined_mate_pair_reads' - -f '$advanced_options.format' - -z '$advanced_options.compress' - -E '$advanced_options.qiime' - -F '$advanced_options.quiet' - -i '$advanced_options.intelligent' - -1 '$trimmed_r1' - -2 '$trimmed_r2' - -3 '$trimmed_s' -]]></command> - <inputs> - <param type="data" name="first_reads" label="First reads" optional="False" format="fastq,fastqsanger" - multiple="False"/> - <param type="data" name="second_reads" label="Second reads" - help="If it is single end reads, ignore this input field and use the "first reads" field only." - optional="True" format="fastq,fastqsanger" multiple="False"/> - <param type="data" name="adapter_first_reads" argument="-x" label="Adapter sequence/file for the first reads." - optional="True" format="fasta,fa" multiple="False"/> - <param type="data" name="adapter_second_reads" argument="-y" label="Adapter sequence/file for the second reads" - optional="True" format="fasta,fa" multiple="False"/> - <param type="select" name="trimming_mode" argument="-m" label="trimming mode" optional="False" multiple="False"> - <option value="None" selected="true">--select a model--</option> - <option value="head" selected="false">5’ end trimming (single end reads)</option> - <option value="tail" selected="false">3’ end trimming (single end reads)</option> - <option value="any" selected="false">anywhere adapter detection and trimming (single end reads)</option> - <option value="pe" selected="false">paired-end trimming</option> - <option value="mp" selected="false">mate-pair trimming</option> - <option value="ap" selected="false">amplicon trimming</option> - </param> - <param type="float" name="maximum_allowed_error_rate" argument="-r" label="Maximum allowed error rate" - optional="False" value="0.1" min="0" max="0.5"/> - <param type="float" name="maximum_allowed_indel_error_rate" argument="-d" - label="Maximum allowed indel error rate" - help="The valid range of indel error rate is [0, maximum allowed error rate]" optional="False" - value="0.03" min="0"/> - <param type="integer" name="quality_trimming_3_end" argument="-q" label="3’ end quality trimming" - optional="False" value="0"/> - <param type="integer" name="mean_quality" argument="-Q" label="Reads filtering by average quality" - optional="False" value="0"/> - <param type="integer" name="minimum_read_length" argument="-l" - label="Minimum read length allowed after trimming" optional="False" value="18"/> - <section name="advanced_options" title="Advanced options" expanded="False"> - <param type="data" name="junction_adapter" argument="-j" - label="Junction adapter sequence/file for Nextera Mate Pair reads" optional="True" format="fasta,fa" - multiple="False"/> - <param type="text" name="tab_adapter" argument="-M" - label="TAB delimited file indicates valid forward/reverse adapter pairing" optional="True"/> - <param type="boolean" name="barcode" argument="-b" - label="Whether to demultiplex reads according to adapters/primers" optional="False" checked="False" - truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/> - <param type="text" name="cut" argument="-c" - label="To hard clip off the 5’ leading bases of the forward primer and reverse primer respectively as the barcodes in amplicon mode" - optional="False" value="0, 0"/> - <param type="boolean" name="filter_degenerative_reads" argument="-n" - label="Whether to filter out highly degenerative reads" optional="False" checked="False" - truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/> - <param type="boolean" name="filter_undetermined_mate_pair_reads" argument="-u" - label="Whether to filter out undetermined mate-pair reads" optional="False" checked="False" - truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/> - <param type="select" name="format" argument="-f" label="Format of FASTQ quality value" optional="False" - multiple="False"> - <option value="sanger" selected="false">sanger</option> - <option value="solexa" selected="false">solexa</option> - <option value="auto" selected="true">auto</option> - </param> - <param type="boolean" name="compress" argument="-z" label="Whether to compress output in GZIP format" - optional="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/> - <param type="boolean" name="qiime" argument="-qiime" label="Whether to prepare files required by QIIME" - optional="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/> - <param type="boolean" name="quiet" argument="--quiet" label="Whether in quiet mode" optional="False" - truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/> - <param type="boolean" name="intelligent" argument="-i" label="Whether to intelligently redistribute reads" - optional="False" checked="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/> - </section> - </inputs> - <outputs> - <data name="report" format="html" label="${tool.name} report on ${on_string}" hidden="false"/> - <data name="trimmed_r1" format="fastq" label="${tool.name} trimmed first reads on ${on_string}" hidden="false"/> - <data name="trimmed_r2" format="fastq" label="${tool.name} trimmed second reads on ${on_string}" - hidden="false"/> - <data name="trimmed_s" format="fastq" label="${tool.name} trimmed single end reads on ${on_string}" - hidden="false"/> - </outputs> - <help> - <![CDATA[Read the `tool manual <http://download2.nust.na/pub4/sourceforge/s/project/sk/skewer/skewer_manual.pdf>`_ if you are not sure what parameter values to use.]]></help> - <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[@article{jiang2014skewer, - title={Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads}, - author={Jiang, Hongshan and Lei, Rong and Ding, Shou-Wei and Zhu, Shuifang}, - journal={BMC bioinformatics}, - volume={15}, - number={1}, - pages={182}, - year={2014}, - publisher={BioMed Central} -}]]></citation> - </citations> -</tool>
--- a/skewer_render.R Thu Apr 26 14:10:58 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,52 +0,0 @@ -##============ Sink warnings and errors to a file ============== -## use the sink() function to wrap all code within it. -##============================================================== -zz = file(paste0(Sys.getenv('REPORT_FILES_PATH'), '/.r_rendering.log.txt')) -sink(zz) -sink(zz, type = 'message') - -#============== preparation ==================================== -options(stringsAsFactors = FALSE) -# import libraries -#------------------------------------------------------------------ -# ADD MORE LIBRARIES HERE IF YOUR TOOL DEPENDS ON OTHER R LIBRARIES -#------------------------------------------------------------------ -library('getopt') -library('rmarkdown') -library('htmltools') - - -# load helper functions -source(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/helper.R')) -# import getopt specification matrix from a csv file -opt = getopt(getopt_specification_matrix('getopt_specification.csv', - tool_dir=Sys.getenv('TOOL_INSTALL_DIR'))) -# define environment variables for all input values. this is useful when we -# want to use input values by other programming language in r markdown -do.call(Sys.setenv, opt[-1]) -#=============================================================== - - -#======================== render Rmd files ========================= -# NOTICE: -# we should copy all rmarkdown files from tool install directory to REPORT_FILES_PATH directory. -# and render rmarkdown files in the REPORT_FILES_PATH directory. -file.copy(from = paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/vakata-jstree-3.3.5'), - to = Sys.getenv('REPORT_FILES_PATH'), recursive = TRUE) -system(command = 'cp -r ${TOOL_INSTALL_DIR}/*.Rmd ${REPORT_FILES_PATH}') - -#----------------BELOW IS WHERE YOU NEED TO CUSTOMIZE --------------------- -render(input = paste0(Sys.getenv('REPORT_FILES_PATH'), '/skewer.Rmd')) -# add more lines below if there are more Rmd files to be rendered - -#=============================================================== - - -#============== expose outputs to galaxy history =============== -system(command = 'sh ${TOOL_INSTALL_DIR}/expose-outputs.sh') -#=============================================================== - - -##--------end of code rendering .Rmd templates---------------- -sink() -##=========== End of sinking output============================= \ No newline at end of file