# HG changeset patch
# User mingchen0919
# Date 1528810523 14400
# Node ID bd236d81187be7fab338cbc19eda6382ebce24c5
# Parent  759232961286eed37d3603dd0b548490d87bc7a8
planemo upload for repository https://github.com/feltus/BDSS

diff -r 759232961286 -r bd236d81187b rmarkdown_report.Rmd
--- 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 != '']
diff -r 759232961286 -r bd236d81187b rmarkdown_report.xml
--- 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>