Mercurial > repos > mingchen0919 > rmarkdown_fastq_dump
changeset 13:66bc1016ec2a draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
| author | mingchen0919 |
|---|---|
| date | Wed, 27 Sep 2017 16:54:07 -0400 |
| parents | d330ce2d4663 |
| children | 61ab2acf0205 |
| files | fastq_dump_pe.Rmd fastq_dump_pe.xml fastq_dump_pe_render.R fastq_dump_se_render.R |
| diffstat | 4 files changed, 5 insertions(+), 18 deletions(-) [+] |
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--- a/fastq_dump_pe.Rmd Wed Sep 27 16:49:22 2017 -0400 +++ b/fastq_dump_pe.Rmd Wed Sep 27 16:54:07 2017 -0400 @@ -31,16 +31,11 @@ # loop through SRA accessions to download and extract reads. for(id in sra_accessions) { if('FORMAT' == 'fasta') { - command = paste0('fastq-dump --fasta ', '-O read_files_directory ') + command = paste0('fastq-dump --fasta --split_files ', '-O read_files_directory ') } else { - command = paste0('fastq-dump ', '-O read_files_directory ') + command = paste0('fastq-dump --fastq --split_files ', '-O read_files_directory ') } - if('SPLIT_FILES' == TRUE) { - command = paste0(command, '--split_files ', id) - } else { - command = paste0(command, id) - } print(command) system(command = command) }
--- a/fastq_dump_pe.xml Wed Sep 27 16:49:22 2017 -0400 +++ b/fastq_dump_pe.xml Wed Sep 27 16:54:07 2017 -0400 @@ -8,7 +8,7 @@ <requirement type="package" version="0.5.4">parallel-fastq-dump</requirement> </requirements> <description> - Download and extract single end reads in fastq or fasta format from NCBI SRA. The output is a list of datasets + Download and extract paired end reads in fastq or fasta format from NCBI SRA. The output is a list of paired datasets collection. </description> <stdio> @@ -27,7 +27,6 @@ -p $split_files -r $report - -d $report.files_path -s $sink_message -t '${__tool_directory__}/fastq_dump_pe.Rmd' @@ -38,9 +37,6 @@ help="A list of SRR/DRR/ERR accessions separated by comma or space. e.g. SRR6077558,ERR343809"/> <param type="boolean" name="format" truevalue="fastq" falsevalue="fasta" checked="false" label="output files in fastq (true) or fasta (false)?"/> - <param type="boolean" name="split_files" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Split files" - help="Dump each read into separate file. Files will receive suffix corresponding to read number"/> - <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?"/> </inputs>
--- a/fastq_dump_pe_render.R Wed Sep 27 16:49:22 2017 -0400 +++ b/fastq_dump_pe_render.R Wed Sep 27 16:54:07 2017 -0400 @@ -38,11 +38,10 @@ spec_list$SRA_ACCESSION = c('sra_accession', 'i', '1', 'character') spec_list$FORMAT = c('format', 'f', '1', 'character') spec_list$ECHO = c('echo', 'e', '1', 'character') -spec_list$SPLIT_FILES = c('split_files', 'p', '1', 'character') ##--------2. output report and outputs -------------- spec_list$REPORT_HTML = c('report_html', 'r', '1', 'character') spec_list$OUTPUT_DIR = c('output_dir', 'd', '1', 'character') -spec_list$SINK_OUTPUT = c('sink_output', 's', '1', 'character') +spec_list$SINK_OUTPUT = c('sink_message', 's', '1', 'character') ##--------3. Rmd templates in the tool directory ---------- spec_list$FASTQ_DUMP_SE_RMD = c('fastq_dump_pe_rmd', 't', '1', 'character') @@ -75,9 +74,6 @@ gsub('ECHO', opt$echo, x) }) %>% (function(x) { - gsub('SPLIT_FILES', opt$split_files, x) - }) %>% - (function(x) { gsub('OUTPUT_DIR', opt$output_dir, x) }) %>% (function(x) {
--- a/fastq_dump_se_render.R Wed Sep 27 16:49:22 2017 -0400 +++ b/fastq_dump_se_render.R Wed Sep 27 16:54:07 2017 -0400 @@ -41,7 +41,7 @@ ##--------2. output report and outputs -------------- spec_list$REPORT_HTML = c('report_html', 'r', '1', 'character') spec_list$OUTPUT_DIR = c('output_dir', 'd', '1', 'character') -spec_list$SINK_OUTPUT = c('sink_output', 's', '1', 'character') +spec_list$SINK_OUTPUT = c('sink_message', 's', '1', 'character') ##--------3. Rmd templates in the tool directory ---------- spec_list$FASTQ_DUMP_SE_RMD = c('fastq_dump_se_rmd', 't', '1', 'character')