Mercurial > repos > mingchen0919 > rmarkdown_mirdeep2
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit a23e23222252167ef7c3338a4872e84706df8f83-dirty
author | mingchen0919 |
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date | Tue, 08 Aug 2017 15:06:46 -0400 |
parents | 963905bcb754 |
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--- title: 'Mirdeep2 Mapper' output: html_document: number_sections: true toc: true theme: cosmo highlight: tango --- ```{r setup, include=FALSE, warning=FALSE, message=FALSE} knitr::opts_chunk$set( echo = ECHO ) ``` # Job command line ## View arguments from command line. ```{r 'view arguments'} str(opt) ``` ```{r 'build PATH', echo=FALSE} # set PATH environment. PATH = system('pwd', intern = TRUE) %>% (function(x) { paste0('/home/galaxy/mirdeep2/bin:', x) }) %>% paste0(':$PATH') ``` ## Build job command line. ```{r 'build command line'} command_line = paste0('export PATH=', PATH, ' && ') %>% # index reference genome paste0(' bowtie-build REFERENCE_GENOME ref_genome &&') %>% paste0(' mapper.pl ') %>% # reads (function(x) { paste0(x, 'FASTQ_READS -c ') }) %>% # reference genome (function(x) { paste0(x, '-p ref_genome ') }) %>% # # parse to fasta # (function(x) { # ifelse(PARSE_TO_FASTA, paste0(x, '-h '), x) # }) %>% # clean entries (function(x) { ifelse(CLEAN_ENTRIES, paste0(x, '-j '), x) }) %>% # clip 3 adapter (function(x) { ifelse('CLIP_3_ADAPTER' == '', x, paste0(x, '-k CLIP_3_ADAPTER ')) }) %>% # discard shorter reads (function(x) { paste0(x, '-l DISCARD_SHORTER_READS ') }) %>% # collapse reads (function(x) { # ifelse(COLLAPSE_READS, paste0(x, '-m '), x) paste0(x, '-m ') }) %>% # map with one mismatch (function(x) { ifelse(MAP_WITH_ONE_MISMATCH, paste0(x, '-q '), x) }) %>% # map up to position (function(x) { paste0(x, '-r MAP_UP_TO_POSITION ') }) %>% # overwrite existing files(-n), outputs (function(x) { paste0(x, '-s reads_collapsed.fa -t reads_collapsed_vs_genome.arf -v -n ') }) %>% # write stdout to reprot.log (function(x) { paste0(x, ' 2>report.log') }) command_line ``` ## Run command line ```{r} system(command_line) ```