Mercurial > repos > mingchen0919 > rmarkdown_fastq_dump
changeset 18:dcd0e0b6fcaf draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit e6035405141d63626702084eacd02089f816cdc7-dirty
| author | mingchen0919 |
|---|---|
| date | Wed, 27 Sep 2017 20:43:32 -0400 |
| parents | cf1233051a9b |
| children | 42e154ba2d35 |
| files | fastq_dump_pe.Rmd fastq_dump_pe.xml |
| diffstat | 2 files changed, 3 insertions(+), 3 deletions(-) [+] |
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--- a/fastq_dump_pe.Rmd Wed Sep 27 17:12:39 2017 -0400 +++ b/fastq_dump_pe.Rmd Wed Sep 27 20:43:32 2017 -0400 @@ -33,7 +33,7 @@ if('FORMAT' == 'fasta') { command = paste0('fastq-dump --fasta --split_files ', '-O read_files_directory ') } else { - command = paste0('fastq-dump --fastq --split_files ', '-O read_files_directory ') + command = paste0('fastq-dump --split_files ', '-O read_files_directory ') } print(command) @@ -47,6 +47,6 @@ old_files = paste0('./read_files_directory/', list.files('./read_files_directory')) new_files = gsub('_1', '_forward', old_files) new_files = gsub('_2', '_reverse', new_files) -file.copy('./read_files_directory/') +file.rename(old_files, new_files) ```
--- a/fastq_dump_pe.xml Wed Sep 27 17:12:39 2017 -0400 +++ b/fastq_dump_pe.xml Wed Sep 27 20:43:32 2017 -0400 @@ -36,7 +36,7 @@ <param type="text" name="sra_accession" label="SRR/DRR/ERR accessions" optional="false" 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="true" - label="output files in fastq (true) or fasta (false)?"/> + 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>