Mercurial > repos > mingchen0919 > rmarkdown_bdss_client
changeset 5:04100e773314 draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
| author | mingchen0919 |
|---|---|
| date | Wed, 11 Oct 2017 11:43:39 -0400 |
| parents | 206c59e498e7 |
| children | 415ebc9016da |
| files | bdss_client_sra_pe.Rmd bdss_client_sra_pe.xml bdss_client_sra_se.xml |
| diffstat | 3 files changed, 3 insertions(+), 4 deletions(-) [+] |
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--- a/bdss_client_sra_pe.Rmd Wed Oct 11 11:31:48 2017 -0400 +++ b/bdss_client_sra_pe.Rmd Wed Oct 11 11:43:39 2017 -0400 @@ -55,14 +55,13 @@ if (length(all_fastq_files) == 1) { # this is a single end SRA file. build url to download fastq print(paste0('only one fastq file found for this SRA accession: ', id)) - print('Downloading skipped for ', id) + print(paste0('Downloading skipped for ', id)) # url = paste0(url_base, '/', all_fastq_files) # bdss_command = paste0('/tool_deps/_conda/bin/bdss transfer -u ', url) # run_bdss = system(bdss_command, intern = TRUE) # print(run_bdss) } else { print(paste0('Two fastq files found for this SRA accession: ', id)) - print('Downloading skipped for ', id) url_1 = paste0(url_base, '/', all_fastq_files[1]) bdss_command_1 = paste0('/tool_deps/_conda/bin/bdss transfer -u ', url_1) run_bdss_1 = system(bdss_command, intern = TRUE)
--- a/bdss_client_sra_pe.xml Wed Oct 11 11:31:48 2017 -0400 +++ b/bdss_client_sra_pe.xml Wed Oct 11 11:43:39 2017 -0400 @@ -40,7 +40,7 @@ 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 (Yes) or fasta (No)?"/> - <param type="boolean" name="sra" truevalue="TRUE" falsevalue="FALSE" checked="false" + <param type="boolean" name="sra" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Download SRA or Fastq"/> <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?"/>
--- a/bdss_client_sra_se.xml Wed Oct 11 11:31:48 2017 -0400 +++ b/bdss_client_sra_se.xml Wed Oct 11 11:43:39 2017 -0400 @@ -39,7 +39,7 @@ 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 (Yes) or fasta (No)?"/> - <param type="boolean" name="sra" truevalue="TRUE" falsevalue="FALSE" checked="false" + <param type="boolean" name="sra" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Download SRA or Fastq"/> <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?"/>