Mercurial > repos > mingchen0919 > rmarkdown_fastq_dump
changeset 15:627c487d22e3 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 17:05:22 -0400 |
| parents | 61ab2acf0205 |
| children | 883f102eb227 |
| files | fastq_dump_pe.xml fastq_dump_pe_render.R |
| diffstat | 2 files changed, 3 insertions(+), 3 deletions(-) [+] |
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--- a/fastq_dump_pe.xml Wed Sep 27 17:00:42 2017 -0400 +++ b/fastq_dump_pe.xml Wed Sep 27 17:05:22 2017 -0400 @@ -34,9 +34,9 @@ <inputs> <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="false" + <param type="boolean" name="format" truevalue="fastq" falsevalue="fasta" checked="true" label="output files in fastq (true) or fasta (false)?"/> - <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="true" + <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?"/> </inputs> <outputs>
--- a/fastq_dump_pe_render.R Wed Sep 27 17:00:42 2017 -0400 +++ b/fastq_dump_pe_render.R Wed Sep 27 17:05:22 2017 -0400 @@ -43,7 +43,7 @@ spec_list$OUTPUT_DIR = c('output_dir', 'd', '1', 'character') spec_list$SINK_OUTPUT = c('sink_message', 's', '1', 'character') ##--------3. Rmd templates in the tool directory ---------- -spec_list$FASTQ_DUMP_SE_RMD = c('fastq_dump_pe_rmd', 't', '1', 'character') +spec_list$FASTQ_DUMP_PE_RMD = c('fastq_dump_pe_rmd', 't', '1', 'character') spec = t(as.data.frame(spec_list)) opt = getopt(spec)