diff expose-outputs.sh @ 7:c5c297020c36 draft

planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311

--- a/expose-outputs.sh	Wed Apr 25 17:20:11 2018 -0400
+++ b/expose-outputs.sh	Thu Apr 26 12:49:35 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