Mercurial > repos > mingchen0919 > rmarkdown_i_adhore
changeset 13:d41a3115e470 draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit 377565cfe72b3455320ea04b7c58191bf4428d79-dirty
| author | mingchen0919 |
|---|---|
| date | Tue, 29 Aug 2017 21:48:28 -0400 |
| parents | fcd72af3f41e |
| children | e10d998b078d |
| files | i_adhore_configure.Rmd |
| diffstat | 1 files changed, 5 insertions(+), 15 deletions(-) [+] |
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--- a/i_adhore_configure.Rmd Tue Aug 29 17:57:47 2017 -0400 +++ b/i_adhore_configure.Rmd Tue Aug 29 21:48:28 2017 -0400 @@ -12,20 +12,10 @@ knitr::opts_chunk$set(echo = ECHO) ``` +```{r echo=FALSE} # Genomes and analysis files - -```{r} g_analysis_files_set = strsplit(opt$g_analysis_file, ';')[[1]] g_analysis_files_list = list() -# for(i in g_analysis_files_set) { -# genome = strsplit(i, ':')[[1]][1] -# analysis_files = strsplit(i, ':')[[1]][2] %>% -# strsplit(',') %>% `[[`(1) %>% -# (function(x){ -# paste0(1:length(x),' ', x) -# }) -# g_analysis_files_list[[genome]] = analysis_files -# } for(i in g_analysis_files_set) { genome = strsplit(i, ':')[[1]][1] analysis_files = strsplit(i, ':')[[1]][2] %>% @@ -39,12 +29,12 @@ 'name' = paste0('genome=', strsplit(i, ':')[[1]][1]), 'analysis_files' = analysis_files ) - print(paste0('genome=', strsplit(i, ':')[[1]][1])) - print(analysis_files) + #print(paste0('genome=', strsplit(i, ':')[[1]][1])) + #print(analysis_files) } ``` -# Other parameters +# Tool parameters ```{r} output_dir = tail(strsplit(opt$i_adhore_configure_dir, '/')[[1]], 1) @@ -85,7 +75,7 @@ ```{bash} # run i-adhore analysis -i-adhore I_ADHORE_CONFIGURE_TXT +i-adhore I_ADHORE_CONFIGURE_TXT > /dev/null 2>&1 ``` Links to outputs