Mercurial > repos > mingchen0919 > aurora_bdss_sra
changeset 1:bd236d81187b draft
planemo upload for repository https://github.com/feltus/BDSS
| author | mingchen0919 |
|---|---|
| date | Tue, 12 Jun 2018 09:35:23 -0400 |
| parents | 759232961286 |
| children | ad0bc5ffbd9d |
| files | rmarkdown_report.Rmd rmarkdown_report.xml |
| diffstat | 2 files changed, 7 insertions(+), 3 deletions(-) [+] |
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--- a/rmarkdown_report.Rmd Tue Jun 12 09:24:06 2018 -0400 +++ b/rmarkdown_report.Rmd Tue Jun 12 09:35:23 2018 -0400 @@ -61,7 +61,9 @@ pe_dir = paste0(Sys.getenv('JOB_WORKING_DIR'), '/pe_read_files_dir') ``` -```{r 'download and extract reads'} +```{r 'download and extract reads', echo=-1} +Sys.setenv(PATH=paste0('/main/sites/galaxy/galaxy/tools/_conda/bin:', Sys.getenv('PATH'))) + # download and extract reads (single end) sra_ids_se = strsplit(gsub(',', ' ', 'SRA_IDS_SE'), ' ')[[1]] sra_ids_se = sra_ids_se[sra_ids_se != '']
--- a/rmarkdown_report.xml Tue Jun 12 09:24:06 2018 -0400 +++ b/rmarkdown_report.xml Tue Jun 12 09:35:23 2018 -0400 @@ -37,9 +37,11 @@ ]]></command> <inputs> <param type="text" name="sra_ids_se" area="true" size="5x25" label="SRR/DRR/ERR accessions of single end SRA" - help="A list of SRR/DRR/ERR accessions separated by comma or space. e.g. SRR039885"/> + help="A list of SRR/DRR/ERR accessions separated by comma or space. e.g. SRR039885. Valid SRA IDs can be + obtained from ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/."/> <param type="text" name="sra_ids_pe" area="true" size="5x25" label="SRR/DRR/ERR accessions of paired end SRA" - help="A list of SRR/DRR/ERR accessions separated by comma or space. e.g. ERR1748507"/> + help="A list of SRR/DRR/ERR accessions separated by comma or space. e.g. ERR1748507. Valid SRA IDs can be + obtained from ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/."/> <param type="select" name="format" label="Output format"> <option value="fastq" selected="true">fastq</option> <option value="fasta">fasta</option>