Mercurial > repos > mingchen0919 > aurora_statonlab_hmmscan_merger
changeset 1:aee65d1b1840 draft
planemo upload commit b399babf7f0e3755704fb13dda1f5981495f6958
| author | mingchen0919 |
|---|---|
| date | Sun, 16 Sep 2018 17:39:54 -0400 |
| parents | e4299abb3568 |
| children | ae3909607532 |
| files | _site.yml command-line-arguments.csv index.Rmd rmarkdown_report.Rmd rmarkdown_report.sh rmarkdown_report.xml rmarkdown_report_render.R |
| diffstat | 7 files changed, 75 insertions(+), 81 deletions(-) [+] |
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--- a/_site.yml Sun Sep 16 13:28:55 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,19 +0,0 @@ -name: "Aurora Tool Website" -output_dir: "." -navbar: - title: "Aurora Tool" - type: inverse - left: - - text: "Job 1" - href: 01_rmarkdown.html - - text: "Job 2" - menu: - - text: "Sub-job 1" - href: 02_rmarkdown.html - - text: "Sub-job 2" - href: 03_rmarkdown.html - -output: - html_document: - theme: cosmo - highlight: textmate \ No newline at end of file
--- a/command-line-arguments.csv Sun Sep 16 13:28:55 2018 -0400 +++ b/command-line-arguments.csv Sun Sep 16 17:39:54 2018 -0400 @@ -1,3 +1,4 @@ -short flag,argument mask,data type,variable name -o,1,character,report -d,1,character,report.files_path \ No newline at end of file +short flag,argument mask,data type,variable name +o,1,character,report +d,1,character,report.files_path +p,1,character,hmmscan_pfam_tblouts
--- a/index.Rmd Sun Sep 16 13:28:55 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,53 +0,0 @@ - - -```{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> - -```{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 - $('#jstree').jstree().bind("select_node.jstree", function (e, data) { - window.open( data.node.a_attr.href, data.node.a_attr.target ) - }); - }); -</script> - -## Outputs - -```{r, echo=FALSE} -# create a div container to store the file tree interface -library(htmltools) -tags$div( - id="jstree", - file_tree(Sys.getenv('REPORT_FILES_PATH')) -) -```
--- a/rmarkdown_report.Rmd Sun Sep 16 13:28:55 2018 -0400 +++ b/rmarkdown_report.Rmd Sun Sep 16 17:39:54 2018 -0400 @@ -1,5 +1,5 @@ --- -title: 'Aurora Tool Report' +title: '' output: html_document: highlight: pygments @@ -53,5 +53,67 @@ # ADD YOUR DATA ANALYSIS CODE AND MARKUP TEXT BELOW TO EXTEND THIS R MARKDOWN FILE --- +#### Significant genes grouped by pfam target name across multiple organisms + +--- + +```{r message=FALSE} +library(tidyverse) +library(knitr) +tblout_files = strsplit(opt$X_p, ',')[[1]] +common_pfams = read.csv(tblout_files[1])[, 'target_name'] +for (f in tblout_files[-1]) { + common_pfams = intersect(common_pfams, read.csv(f)[, 'target_name']) +} + +pfams_df = read.csv(tblout_files[1], stringsAsFactors = FALSE) +pfams_df = pfams_df[pfams_df$target_name %in% common_pfams, c('target_name', 'accession', 'query_name')] +pfams_df = pfams_df %>% group_by(target_name) %>% + mutate(query_name = paste0(unique(query_name), collapse = ',')) %>% + distinct() %>% + arrange(target_name) +first_file_name = tail(strsplit(tblout_files[1], '/')[[1]], 1) +colnames(pfams_df)[3] = first_file_name +for (f in tblout_files[-1]) { + df = read.csv(f, stringsAsFactors = FALSE) + df = df[df$target_name %in% common_pfams, c('target_name', 'accession', 'query_name')] + df = df %>% group_by(target_name) %>% + mutate(query_name = paste0(unique(query_name), collapse = ',')) %>% + distinct() %>% + arrange(target_name) + df = df[, c("target_name", "query_name"), drop=FALSE] + header = c("target_name", tail(strsplit(f, '/')[[1]], 1)) + colnames(df) = header + pfams_df = merge(pfams_df, df[, header], by = "target_name") +} + + + +add_links = function(features) { + items = strsplit(features, ',')[[1]] + res = tags$ul( + lapply(strsplit(items, ','), function(item) { + item_adj = gsub('_', '', item) + a(paste0(item, ';'), href=paste0('https://www.hardwoodgenomics.org/feature/', item_adj)) + }) + ) + list(res) +} + + +table_list = list() +table_list[[1]] = tags$tr(lapply(colnames(pfams_df), tags$th)) +for (i in 1:nrow(pfams_df)) { + row = c(pfams_df[i, c('target_name', 'accession')], + lapply(pfams_df[i, -c(1:2)], add_links)) + table_list[[i+1]] = tags$tr(lapply(row, tags$td)) +} +tags$table(table_list) +``` + + + + +
--- a/rmarkdown_report.sh Sun Sep 16 13:28:55 2018 -0400 +++ b/rmarkdown_report.sh Sun Sep 16 17:39:54 2018 -0400 @@ -17,4 +17,6 @@ -o $report -d $report.files_path - -p $hmmscan_pfam_tblouts \ No newline at end of file + -p $hmmscan_pfam_tblouts + + \ No newline at end of file
--- a/rmarkdown_report.xml Sun Sep 16 13:28:55 2018 -0400 +++ b/rmarkdown_report.xml Sun Sep 16 17:39:54 2018 -0400 @@ -1,4 +1,4 @@ -<tool name="aurora_tool" id="tool_1" version="1.0.0"> +<tool name="aurora_statonlab_hmmscan_merger" id="aurora_statonlab_hmmscan_merger" version="1.0.0"> <description>Merge results from the aurora_statonlab_hmmscan tool and group differentially expressed genes across multiple organims by pfam</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="1.1.1">r-tidyverse</requirement></requirements> @@ -21,9 +21,10 @@ -o $report -d $report.files_path - -p $hmmscan_pfam_tblouts]]></command> + -p $hmmscan_pfam_tblouts + ]]></command> <inputs> - <param type="data" name="hmmscan_pfam_tblouts" label="Table outputs from hmmscan" help="Table outputs in CSV format from the <code>aurora_statonlab_hmmscan</code> tool" optional="False" format="csv" multiple="True"/></inputs> + <param type="data" name="hmmscan_pfam_tblouts" label="Table outputs from aurora_statonlab_hmmscan" help="Table outputs in CSV format from the <code>aurora_statonlab_hmmscan</code> tool" optional="False" format="csv" multiple="True"/></inputs> <outputs> <data format="html" name="report" label="${tool.name} report on ${on_string}"/></outputs> <citations>
--- a/rmarkdown_report_render.R Sun Sep 16 13:28:55 2018 -0400 +++ b/rmarkdown_report_render.R Sun Sep 16 17:39:54 2018 -0400 @@ -137,7 +137,7 @@ ## Outputs ```{r, echo=FALSE} -tags$div(id="jstree", file_tree(Sys.getenv(\'REPORT_FILES_PATH\'))) +# tags$div(id="jstree", file_tree(Sys.getenv(\'REPORT_FILES_PATH\'))) ```' write( x = jstree_lines,