Mercurial > repos > mingchen0919 > aurora_skewer

diff expose-outputs.sh @ 9:c0e57c994deb draft

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planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
author mingchen0919
date Thu, 26 Apr 2018 14:10:58 -0400
parents 7c9170b7d9f6
children
line wrap: on
line diff
--- a/expose-outputs.sh	Thu Apr 26 13:38:15 2018 -0400
+++ b/expose-outputs.sh	Thu Apr 26 14:10:58 2018 -0400
@@ -2,5 +2,16 @@
 cd ${REPORT_FILES_PATH}
 
 # copy outputs from tool outputs directory to corresponding galaxy output path
-cp star.html ${REPORT}
-cp Aligned.out.sorted.bam ${X_S}
\ No newline at end of file
+cp skewer.html ${REPORT}
+
+if [ -e trim-trimmed-pair1.fastq ]; then
+  cp trim-trimmed-pair1.fastq ${X_1}
+fi
+
+if [ -e trim-trimmed-pair2.fastq ]; then
+  cp trim-trimmed-pair2.fastq ${X_2}
+fi
+
+if [ -e trim-trimmed.fastq ]; then
+  cp trim-trimmed.fastq ${X_3}
+fi