# HG changeset patch
# User mingchen0919
# Date 1524759873 14400
# Node ID ec906e72784d81161a8aa6d28ce18500c4e26e70
# Parent  578a96df86908527a6b736f9535f04e8c56a3c21
planemo upload commit e2f267840cded7ba17bb75a074796a4babbaab5b-dirty

diff -r 578a96df8690 -r ec906e72784d expose-outputs.sh
--- a/expose-outputs.sh	Wed Apr 25 14:22:32 2018 -0400
+++ b/expose-outputs.sh	Thu Apr 26 12:24:33 2018 -0400
@@ -3,5 +3,4 @@
 
 # copy files to corresponding tool output paths.
 cp htseq_count.html ${REPORT}
-cp counts.RData ${X_O}
-cp counts.txt ${X_c}
\ No newline at end of file
+cp count_data.csv ${X_c}
\ No newline at end of file
diff -r 578a96df8690 -r ec906e72784d getopt_specification.csv
--- a/getopt_specification.csv	Wed Apr 25 14:22:32 2018 -0400
+++ b/getopt_specification.csv	Thu Apr 26 12:24:33 2018 -0400
@@ -12,4 +12,3 @@
 i,1,character,idattr
 m,1,character,mode
 c,1,character,count
-O,1,character,count_rdata
\ No newline at end of file
diff -r 578a96df8690 -r ec906e72784d htseq_count.Rmd
--- a/htseq_count.Rmd	Wed Apr 25 14:22:32 2018 -0400
+++ b/htseq_count.Rmd	Thu Apr 26 12:24:33 2018 -0400
@@ -1,10 +1,20 @@
 ---
-title: 'htseq-count analysis'
+title: 'htseq-count analysis report'
 output:
     html_document:
       highlight: pygments
 ---
 
+```{css echo=FALSE}
+# code chunks scrollable
+pre code, pre, code {
+  white-space: pre !important;
+  overflow-x: scroll !important;
+  word-break: keep-all !important;
+  word-wrap: initial !important;
+}
+```
+
 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
 knitr::opts_knit$set(progress = FALSE)
 knitr::opts_chunk$set(error = TRUE, echo = FALSE)
@@ -44,26 +54,33 @@
 
 ## Job script
 
-* htseq-count analysis: [htseq-count.sh](htseq-count.sh)
-
 ```{bash, echo=FALSE}
 sh ${TOOL_INSTALL_DIR}/shell-script-template.sh
 ```
 
+```{r echo=FALSE, comment='', results='asis'}
+cat('```bash\n')
+cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/htseq-count.sh')), sep = '\n')
+cat('\n```')
+```
 
 ## Counts
 
+Only the first few rows are displayed. 
+
 ```{r, echo=FALSE}
 count_data = read.table(paste0(opt$X_d, '/counts.txt'), row.names = 1)
 sample_names = trimws(strsplit(opt$X_B, ',')[[1]])
 colnames(count_data) = rep(sample_names, length = ncol(count_data))
 kable(head(count_data))
+
+# modify column names
+count_data = data.frame(feature_id = rownames(count_data), count_data)
+write.csv(count_data, 
+          file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/count_data.csv'),
+          quote = FALSE, row.names = FALSE)
 ```
 
-```{r, echo=FALSE}
-# save count data as an R object
-save(count_data, file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/counts.RData'))
-```
 
 -----------------------------------------
 ## Output
diff -r 578a96df8690 -r ec906e72784d htseq_count.xml
--- a/htseq_count.xml	Wed Apr 25 14:22:32 2018 -0400
+++ b/htseq_count.xml	Thu Apr 26 12:24:33 2018 -0400
@@ -42,7 +42,6 @@
 			-i $idattr
 			-m $mode
 			-c $count
-			-O $count_rdata
 
     ]]></command>
     <inputs>
@@ -86,8 +85,7 @@
     </inputs>
     <outputs>
         <data name="report" format="html" label="${tool.name} report on ${on_string}" hidden="false"/>
-        <data name="count" format="txt" label="${tool.name} txt count on ${on_string}" hidden="false"/>
-        <data name="count_rdata" format="rdata" label="${tool.name} rdata count data on ${on_string}"/>
+        <data name="count" format="csv" label="${tool.name} txt count on ${on_string}" hidden="false"/>
     </outputs>
     <citations>
         <citation type="bibtex"><![CDATA[
diff -r 578a96df8690 -r ec906e72784d shell-script-template.sh
--- a/shell-script-template.sh	Wed Apr 25 14:22:32 2018 -0400
+++ b/shell-script-template.sh	Thu Apr 26 12:24:33 2018 -0400
@@ -6,7 +6,6 @@
 
 # build job-script.sh
 cat >${SHELL_SCRIPT} <<EOF
-#------------ BELOW IS WHERE YOU WRITE YOUR OWN SHELL SCRIPT --------------
 
   htseq-count \\
     $(echo ${X_A} | sed 's/,/ /g') \\
@@ -21,7 +20,6 @@
     
   grep -v '__no_feature\|__ambiguous\|__too_low_aQual\|__not_aligned\|__alignment_not_unique' htseq-counts-raw.txt > counts.txt
 
-#------------ END OF SHELL SCRIPT ------------------------------------------  
 EOF
 
 # run SHELL_SCRIPT