Mercurial > repos > mingchen0919 > aurora_htseq

diff htseq_count.xml @ 6:7c54fd452b8e draft

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add kableExtra package
author mingchen0919
date Wed, 18 Apr 2018 15:59:38 -0400
parents aacd5f53ac99
children 63cde8d7f89c
line wrap: on
line diff
--- a/htseq_count.xml	Wed Apr 18 13:17:28 2018 -0400
+++ b/htseq_count.xml	Wed Apr 18 15:59:38 2018 -0400
@@ -5,7 +5,7 @@
         <requirement type="package" version="1.20.0">r-getopt</requirement>
         <requirement type="package" version="1.6">r-rmarkdown</requirement>
         <requirement type="package" version="0.9.1">htseq</requirement>
-        <requirement type="package" version="0.2">r-dt</requirement>
+        <requirement type="package" version="0.8.0">r-kableextra</requirement>
     </requirements>
     <stdio>
         <regex match="XXX" source="stderr" level="warning"
@@ -27,8 +27,6 @@
         ############ create a hidden file to store r markdown rendering log
         echo '------ Rmd rendering log -------\n' > $report.files_path/.r_rendering.log.txt &&
 
-    echo echo 'R markdown rendering started.' &&
-
     Rscript '${__tool_directory__}/htseq_count_render.R'
 
 			-o $report
@@ -45,9 +43,7 @@
 			-i $idattr
 			-m $mode
 			-c $count
-			-O $count_rdata &&
-
-	echo 'R markdown rendering finished.'
+			-O $count_rdata
 
     ]]></command>
     <inputs>