Mercurial > repos > mingchen0919 > rmarkdown_fastq_dump
changeset 9:233210d44681 draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 5d2a63708a8abf73432c1d6863d970146c6a38b2-dirty
| author | mingchen0919 |
|---|---|
| date | Wed, 27 Sep 2017 16:16:12 -0400 |
| parents | 86a31717730e |
| children | 057a6b742899 |
| files | fastq_dump_se.Rmd fastq_dump_se.xml fastq_dump_se_render.R |
| diffstat | 3 files changed, 8 insertions(+), 6 deletions(-) [+] |
line wrap: on
line diff
--- a/fastq_dump_se.Rmd Wed Sep 27 14:05:42 2017 -0400 +++ b/fastq_dump_se.Rmd Wed Sep 27 16:16:12 2017 -0400 @@ -30,7 +30,7 @@ sra_accessions = sra_accessions[sra_accessions != ''] # loop through SRA accessions to download and extract reads. for(id in sra_accessions) { - if(FORMAT == 'fasta') { + if('FORMAT' == 'fasta') { command = paste0('fastq-dump --fasta ', '-O read_files_directory ', id) } else { command = paste0('fastq-dump ', '-O read_files_directory ', id)
--- a/fastq_dump_se.xml Wed Sep 27 14:05:42 2017 -0400 +++ b/fastq_dump_se.xml Wed Sep 27 16:16:12 2017 -0400 @@ -34,7 +34,7 @@ -r $report -d $report.files_path - -s $sink_output + -s $sink_message -t '${__tool_directory__}/fastq_dump_se.Rmd' ]]> @@ -42,7 +42,7 @@ <inputs> <param type="text" name="sra_accession" label="SRR/DRR/ERR accessions" 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 (Yes) or fasta (No)?"/> + <param type="boolean" name="format" truevalue="fastq" falsevalue="fasta" checked="true" label="output files in fastq (Yes) or fasta (No)?"/> <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" /> </inputs> <outputs> @@ -50,6 +50,6 @@ <collection type="list" name="list_collection"> <discover_datasets pattern="__name_and_ext__" directory="read_files_directory" /> </collection> - <data format="txt" name="sink_output" label="sink output" from_work_dir="sink_output.txt" /> + <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt" /> </outputs> </tool> \ No newline at end of file
--- a/fastq_dump_se_render.R Wed Sep 27 14:05:42 2017 -0400 +++ b/fastq_dump_se_render.R Wed Sep 27 16:16:12 2017 -0400 @@ -20,8 +20,10 @@ library(tools) }) -#/////////////////////// SINK OUTPUTS TO A FILE FOR DEBUGGING /////////// -sink('sink_output.txt') +#/////////////////////// SINK WARNINGS AND ERRORS TO A FILE FOR DEBUGGING /////////// +zz = file('warnings_and_errors.txt') +sink(zz) +sink(zz, type = 'message') # column 1: the long flag name # column 2: the short flag alias. A SINGLE character string