# HG changeset patch
# User mingchen0919
# Date 1507736619 14400
# Node ID 04100e773314276203598dc2c787b56e8bec5ba3
# Parent  206c59e498e780dab168ea91b4c41b7c12ca3e1e
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty

diff -r 206c59e498e7 -r 04100e773314 bdss_client_sra_pe.Rmd
--- 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)
diff -r 206c59e498e7 -r 04100e773314 bdss_client_sra_pe.xml
--- 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?"/>
diff -r 206c59e498e7 -r 04100e773314 bdss_client_sra_se.xml
--- 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?"/>