Mercurial > repos > mingchen0919 > rmarkdown_collection_builder
changeset 46:8dacd341b8b7 draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit b15eec6b208c8a41b8ad8969ab9c6046d7f0b73c-dirty
| author | mingchen0919 |
|---|---|
| date | Tue, 26 Sep 2017 12:10:20 -0400 |
| parents | 335e9eb25532 |
| children | fb05ca474127 |
| files | collection_list.xml collection_list_paired.xml collection_paired.Rmd collection_paired.xml collection_paired_render.R |
| diffstat | 5 files changed, 13 insertions(+), 10 deletions(-) [+] |
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--- a/collection_list.xml Tue Sep 26 12:04:54 2017 -0400 +++ b/collection_list.xml Tue Sep 26 12:10:20 2017 -0400 @@ -7,7 +7,7 @@ <requirement type="package" version="0.5.0">r-dplyr</requirement> </requirements> <description> - Create a 'list' dataset collection from a set of files in Galaxy history. + Create a list of datasets collection from files in history. </description> <stdio> <regex match="Execution halted"
--- a/collection_list_paired.xml Tue Sep 26 12:04:54 2017 -0400 +++ b/collection_list_paired.xml Tue Sep 26 12:10:20 2017 -0400 @@ -7,7 +7,7 @@ <requirement type="package" version="0.5.0">r-dplyr</requirement> </requirements> <description> - Create a 'list:paired' dataset collection from a set of files in Galaxy history. + Create a list of paired dataset collection from files in history. </description> <stdio> <regex match="Execution halted"
--- a/collection_paired.Rmd Tue Sep 26 12:04:54 2017 -0400 +++ b/collection_paired.Rmd Tue Sep 26 12:10:20 2017 -0400 @@ -23,7 +23,7 @@ # Rename files ```{r} -file.copy("FORWARD_INPUT", './files_directory/forward.FORMAT') -file.copy("REVERSE_INPUT", './files_directory/reverse.FORMAT') +file.copy("FORWARD_INPUT", './OUTPUT_DIR/forward.FORMAT') +file.copy("REVERSE_INPUT", './OUTPUT_DIR/reverse.FORMAT') ```
--- a/collection_paired.xml Tue Sep 26 12:04:54 2017 -0400 +++ b/collection_paired.xml Tue Sep 26 12:10:20 2017 -0400 @@ -7,7 +7,7 @@ <requirement type="package" version="0.5.0">r-dplyr</requirement> </requirements> <description> - Create a 'paired' dataset collection from a set of files in Galaxy history. + Create a paired dataset collection from files in history. </description> <stdio> <regex match="Execution halted"
--- a/collection_paired_render.R Tue Sep 26 12:04:54 2017 -0400 +++ b/collection_paired_render.R Tue Sep 26 12:10:20 2017 -0400 @@ -35,8 +35,8 @@ spec_list$ECHO = c('echo', 'e', '1', 'character') spec_list$FORMAT = c('format', 'f', '1', 'character') ##--------2. output report and outputs -------------- -spec_list$OUTPUT_HTML = c('list_paired_collection_html', 'r', '1', 'character') -spec_list$OUTPUT_DIR = c('list_paired_collection_dir', 'd', '1', 'character') +spec_list$OUTPUT_HTML = c('paired_collection_html', 'r', '1', 'character') +spec_list$OUTPUT_DIR = c('paired_collection_dir', 'd', '1', 'character') ##--------3. Rmd templates in the tool directory ---------- spec_list$LIST_COLLECTION_RMD = c('list_collection_rmd', 't', '1', 'character') @@ -50,7 +50,7 @@ library(dplyr) #----- 1. create the report directory ------------------------ -system(paste0('mkdir -p ', opt$list_paired_collection_dir)) +system(paste0('mkdir -p ', opt$paired_collection_dir)) #----- 2. generate Rmd files with Rmd templates -------------- # a. templates without placeholder variables: @@ -73,13 +73,16 @@ gsub('REVERSE_INPUT', opt$reverse_forward_input, x) }) %>% (function(x) { - fileConn = file('list_paired_collection.Rmd') + gsub('OUTPUT_DIR', opt$reverse_forward_input, x) + }) %>% + (function(x) { + fileConn = file('paired_collection.Rmd') writeLines(x, con=fileConn) close(fileConn) }) #------ 3. render all Rmd files -------- -render('list_paired_collection.Rmd', output_file = opt$list_paired_collection_html) +render('paired_collection.Rmd', output_file = opt$paired_collection_html) #-------4. manipulate outputs -----------------------------