# HG changeset patch
# User mingchen0919
# Date 1528779264 14400
# Node ID 86f38533b2ab3d255f704615217fe9ccc5bd3e99
# Parent  af2e4c66261fe6edc86d8bbebdd0a639ba0bf607
planemo upload for repository https://github.com/feltus/BDSS

diff -r af2e4c66261f -r 86f38533b2ab build-and-run-job-scripts.sh
--- a/build-and-run-job-scripts.sh	Tue Jun 12 00:15:20 2018 -0400
+++ b/build-and-run-job-scripts.sh	Tue Jun 12 00:54:24 2018 -0400
@@ -1,6 +1,3 @@
-# create a download_dir in current job working directory
-JOB_WORKING_DIR=$(pwd)
-
 # run job scripts within the tool outputs directory
 cd ${REPORT_FILES_PATH}
 mkdir download_dir
@@ -11,7 +8,8 @@
 echo 'do' >> bdss-download.sh
 echo '  bdss transfer --destination download_dir -u $u' >> bdss-download.sh
 echo 'done' >> bdss-download.sh
+echo 'echo $(pwd)' >> bdss-download.sh
 
 sh bdss-download.sh
-
-cp -r download_dir ${JOB_WORKING_DIR}/download_dir
\ No newline at end of file
+# copy data from REPORT_FILES_PATHS to JOB_WORKING_DIR so that files can be discovered automatically.
+cp -r download_dir ${JOB_WORKING_DIR}
\ No newline at end of file
diff -r af2e4c66261f -r 86f38533b2ab rmarkdown_report.xml
--- a/rmarkdown_report.xml	Tue Jun 12 00:15:20 2018 -0400
+++ b/rmarkdown_report.xml	Tue Jun 12 00:54:24 2018 -0400
@@ -38,7 +38,7 @@
                help="Multiple URLs should be separated with comma or space"/>
     </inputs>
     <outputs>
-        <data format="html" name="report" label="${tool.name} report on ${on_string}"/>
+        <data format="html" name="report" label="${tool.name} report"/>
         <data name="output" label="BDSS downloaded data">
             <discover_datasets pattern="__name_and_ext__" directory="download_dir" visible="true"/>
         </data>
diff -r af2e4c66261f -r 86f38533b2ab rmarkdown_report_render.R
--- a/rmarkdown_report_render.R	Tue Jun 12 00:15:20 2018 -0400
+++ b/rmarkdown_report_render.R	Tue Jun 12 00:54:24 2018 -0400
@@ -109,6 +109,8 @@
 # define environment variables for all input values. this is useful when we
 # want to use input values by other programming language in r markdown
 do.call(Sys.setenv, opt[-1])
+# add current job working directory
+Sys.setenv(JOB_WORKING_DIR=getwd())
 #===============================================================