Mercurial > repos > mingchen0919 > rmarkdown_fastq_dump
changeset 4:c9b56151f112 draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit c9517f0b061cdca3b79678d9a2620e1e43115d42-dirty
| author | mingchen0919 |
|---|---|
| date | Wed, 27 Sep 2017 11:10:59 -0400 |
| parents | dce9200ef1b7 |
| children | a2ba5619f51b |
| files | fastq_dump_se.xml fastq_dump_se_render.R |
| diffstat | 2 files changed, 2 insertions(+), 2 deletions(-) [+] |
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--- a/fastq_dump_se.xml Wed Sep 27 10:36:39 2017 -0400 +++ b/fastq_dump_se.xml Wed Sep 27 11:10:59 2017 -0400 @@ -39,7 +39,7 @@ ]]> </command> <inputs> - <param type="text" name="sra_accession" label="SRR/DRR/ERR accessions" optional="false" + <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 (true) or fasta (false)?"/> <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
--- a/fastq_dump_se_render.R Wed Sep 27 10:36:39 2017 -0400 +++ b/fastq_dump_se_render.R Wed Sep 27 11:10:59 2017 -0400 @@ -59,7 +59,7 @@ #----- 01 fastq_dump_se.Rmd ----------------------- readLines(opt$fastq_dump_se_rmd) %>% (function(x) { - gsub('SRA_ACCESSION', opt$file_list, x) + gsub('SRA_ACCESSION', opt$sra_accession, x) }) %>% (function(x) { gsub('ECHO', opt$echo, x)