# HG changeset patch # User mingchen0919 # Date 1524764295 14400 # Node ID 7c9170b7d9f65b9f46154c274e5f9c51500996ec # Parent c5c297020c36cc3b525bb2bcc879f02b40d0236e planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311 diff -r c5c297020c36 -r 7c9170b7d9f6 expose-outputs.sh --- a/expose-outputs.sh Thu Apr 26 12:49:35 2018 -0400 +++ b/expose-outputs.sh Thu Apr 26 13:38:15 2018 -0400 @@ -2,16 +2,5 @@ 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 +cp star.html ${REPORT} +cp Aligned.out.sorted.bam ${X_S} \ No newline at end of file diff -r c5c297020c36 -r 7c9170b7d9f6 getopt_specification.csv --- a/getopt_specification.csv Thu Apr 26 12:49:35 2018 -0400 +++ b/getopt_specification.csv Thu Apr 26 13:38:15 2018 -0400 @@ -1,27 +1,9 @@ -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 +short flag,argument mask,data type,variable name +o,1,character,report +d,1,character,report.files_path +A,1,character,genomeFastaFiles +B,1,character,sjdbGTFfile +C,1,character,sjdbOverhang +F,1,character,first_reads +R,1,character,second_reads +S,1,character,sorted_bam \ No newline at end of file diff -r c5c297020c36 -r 7c9170b7d9f6 shell-script-template.sh --- a/shell-script-template.sh Thu Apr 26 12:49:35 2018 -0400 +++ b/shell-script-template.sh Thu Apr 26 13:38:15 2018 -0400 @@ -1,48 +1,47 @@ -# SHELL_SCRIPT file name -SHELL_SCRIPT='skewer.sh' - # run SHELL_SCRIPT within tool outputs directory cd ${REPORT_FILES_PATH} -# build job-script.sh +#--------- index genome -------- +# create genome directory for genome indexes +mkdir -p ${X_d}/genomeDir + cat >temp.sh < /dev/null 2>&1 +STAR \\ + --runMode genomeGenerate \\ + --genomeDir ${X_d}/genomeDir \\ + --genomeFastaFiles $( echo ${X_A} | sed 's/,/ /g' ) \\ + --sjdbGTFfile ${X_B} \\ + --sjdbOverhang ${X_C} \\ + > /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} +grep -v None temp.sh > index-genome.sh + +# run star +sh index-genome.sh +#---- mapping --------- +cat >temp.sh < /dev/null 2>&1 +EOF + +grep -v None temp.sh > mapping.sh + +# run mapping +sh mapping.sh + +# remove temp.sh rm temp.sh -# run SHELL_SCRIPT -sh ${SHELL_SCRIPT} +#----- SAM to sorted BAM ------ +echo "samtools sort -o Aligned.out.sorted.bam Aligned.out.sam" > sam2bam.sh +sh sam2bam.sh -# rename log file -if [ -e trim-trimmed.log ]; then - cp trim-trimmed.log trim-trimmed.txt -fi \ No newline at end of file +#----- evaluate mapping ------- +echo "samtools flagstat Aligned.out.sorted.bam > flagstat.txt" > flagstat.sh +sh flagstat.sh diff -r c5c297020c36 -r 7c9170b7d9f6 skewer.Rmd --- a/skewer.Rmd Thu Apr 26 12:49:35 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,78 +0,0 @@ ---- -title: 'Skewer report' -output: - html_document: - highlight: pygments ---- - -```{r setup, include=FALSE, warning=FALSE, message=FALSE} -knitr::opts_knit$set(progress = FALSE) -knitr::opts_chunk$set(error = TRUE, echo = FALSE) -``` - -```{r, echo=FALSE} -# to make the css theme to work, tags cannot be added directly -# as tags as below. -# it has to be added using a code chunk with the htmltool functions!!! -css_link = tags$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 -``` - - - -```{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 -``` - - -```{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')) -) -``` - diff -r c5c297020c36 -r 7c9170b7d9f6 skewer.xml --- a/skewer.xml Thu Apr 26 12:49:35 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,165 +0,0 @@ - - A fast and accurate adapter trimmer for next-generation sequencing single or paired end reads. - - - pandoc - r-getopt - r-rmarkdown - skewer - - - - - - - - - - - - - - - - - - - - - - - - -

- - - - - - - - - - - - - - - -

- - - - - `_ if you are not sure what parameter values to use.]]> - - - - - - diff -r c5c297020c36 -r 7c9170b7d9f6 skewer_render.R --- a/skewer_render.R Thu Apr 26 12:49:35 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 ${TOOL_INSTALL_DIR}/expose-outputs.sh') -#=============================================================== - - -##--------end of code rendering .Rmd templates---------------- -sink() -##=========== End of sinking output============================= \ No newline at end of file diff -r c5c297020c36 -r 7c9170b7d9f6 star.Rmd --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/star.Rmd Thu Apr 26 13:38:15 2018 -0400 @@ -0,0 +1,117 @@ +--- +title: 'STAR: RNA-Seq aligner' +output: + html_document: + highlight: pygments +--- + +```{css echo=FALSE} +pre code, pre, code { + white-space: pre !important; + overflow-x: scroll !important; + word-break: keep-all !important; + word-wrap: initial !important; +} +``` + +```{r setup, include=FALSE, warning=FALSE, message=FALSE} +knitr::opts_knit$set(progress = FALSE) +knitr::opts_chunk$set(error = TRUE, echo = FALSE) +``` + +```{r, echo=FALSE} +# to make the css theme to work, tags cannot be added directly +# as tags as below. +# it has to be added using a code chunk with the htmltool functions!!! +css_link = tags$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 +``` + + + +```{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 +``` + +----------------------------------------- + + +## Job scripts + +```{bash, echo=FALSE} +sh ${TOOL_INSTALL_DIR}/shell-script-template.sh +``` + +### Index genome + +```{r echo=FALSE,results='asis'} +# display content of the job-script.sh file. +cat('```bash\n') +cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/index-genome.sh')), sep = '\n') +cat('\n```') +``` + +### Mapping + +```{r echo=FALSE,results='asis'} +# display content of the job-script.sh file. +cat('```bash\n') +cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/mapping.sh')), sep = '\n') +cat('\n```') +``` + +### SAM to sorted BAM + +```{r echo=FALSE,warning=FALSE,results='asis'} +# display content of the job-script.sh file. +cat('```bash\n') +cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/sam2bam.sh')), sep = '\n') +cat('\n```') +``` + +### Mapping evaluation + +```{r echo=FALSE,warning=FALSE,results='asis'} +# display content of the job-script.sh file. +cat('```bash\n') +cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/flagstat.sh')), sep = '\n') +cat('\n```') +``` + + +### Mapping evaluation results + +```{r echo=FALSE,warning=FALSE,results='asis'} +# display content of the job-script.sh file. +cat('```bash\n') +cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/flagstat.txt')), sep = '\n') +cat('\n```') +``` + + +----------------------------------------- +## Output + +```{r, echo=FALSE} +# create a div container to store the file tree interface +tags$div( + id="jstree", + file_tree(Sys.getenv('REPORT_FILES_PATH')) +) +``` + diff -r c5c297020c36 -r 7c9170b7d9f6 star.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/star.xml Thu Apr 26 13:38:15 2018 -0400 @@ -0,0 +1,92 @@ + + ultrafast universal RNA-seq aligner + + + pandoc + r-getopt + r-rmarkdown + star + samtools + + + + + + + + + + + + + + + + + + + + + + diff -r c5c297020c36 -r 7c9170b7d9f6 star_render.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/star_render.R Thu Apr 26 13:38:15 2018 -0400 @@ -0,0 +1,52 @@ +##============ 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'), '/star.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