changeset 2:350afb9412fc draft default tip

planemo upload

--- a/build-and-run-job-scripts.sh	Mon May 14 16:17:19 2018 -0400
+++ b/build-and-run-job-scripts.sh	Mon May 14 16:58:24 2018 -0400
@@ -3,7 +3,8 @@
 
 #========== build and run job 1 script ============
 cat >curl-download.sh <<EOF
-curl -O output.$X_n $X_u > curl-log.txt 2>&1
+curl $X_u > output.$X_n
+cp output.$X_n ${JOB_WORKING_DIR}
 EOF
 
 # run job 1 script

--- a/command-line-arguments.csv	Mon May 14 16:17:19 2018 -0400
+++ b/command-line-arguments.csv	Mon May 14 16:58:24 2018 -0400
@@ -1,3 +1,5 @@
-short flag,argument mask,data type,variable name
-o,1,character,report
-d,1,character,report.files_path
\ No newline at end of file
+short flag,argument mask,data type,variable name
+o,1,character,report
+d,1,character,report.files_path
+n,1,character,output_ext
+u,1,character,url

--- a/rmarkdown_report.Rmd	Mon May 14 16:17:19 2018 -0400
+++ b/rmarkdown_report.Rmd	Mon May 14 16:58:24 2018 -0400
@@ -65,9 +65,3 @@
 cat('\n```')
 ```
 
-```{bash, echo=FALSE}
-# create a directory in current working directory and copy the downloaded file into that directory
-mkdir -p output_dir
-cp output.$X_n output_dir
-```
-

--- a/rmarkdown_report.xml	Mon May 14 16:17:19 2018 -0400
+++ b/rmarkdown_report.xml	Mon May 14 16:58:24 2018 -0400
@@ -41,7 +41,7 @@
         <param type="text" name="url" label="dataset url"/>
     </inputs>
     <outputs>
-        <data format="html" name="report" label="${tool_name} report on ${on_string}">
+        <data format="html" name="report" label="${tool.name} report on ${on_string}">
             <discover_datasets pattern="__designation_and_ext__" directory="output_dir" visible="true"/>
         </data>
     </outputs>

--- a/rmarkdown_report_render.R	Mon May 14 16:17:19 2018 -0400
+++ b/rmarkdown_report_render.R	Mon May 14 16:58:24 2018 -0400
@@ -16,6 +16,11 @@
 #------------------------------------------------------------------
 options(stringsAsFactors = FALSE)
 
+#------------------------------------------------
+# create a folder within working directory
+dir.create('output_dir')
+job_working_dir = getwd()
+Sys.setenv(JOB_WORKING_DIR=paste0(job_working_dir, '/output_dir/'))
 
 # define two helper functions
 #-----: helper function 1
@@ -149,6 +154,7 @@
 
 #============== expose outputs to galaxy history ===============
 system(command = 'sh ${TOOL_INSTALL_DIR}/expose-outputs-to-galaxy-history.sh')
+file.copy()
 #===============================================================