Mercurial > repos > devteam > fastx_barcode_splitter
comparison fastx_barcode_splitter_galaxy_wrapper.sh @ 3:3b0cd3132ddc draft
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 12:40:38 -0400 |
| parents | 6cbe88c680bb |
| children |
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| 2:1a20fbb8bad8 | 3:3b0cd3132ddc |
|---|---|
| 60 BASEPATH="$OUTPUT_PATH/" | 60 BASEPATH="$OUTPUT_PATH/" |
| 61 #PREFIX="$BASEPATH"`date "+%Y-%m-%d_%H%M__"`"${LIBNAME}__" | 61 #PREFIX="$BASEPATH"`date "+%Y-%m-%d_%H%M__"`"${LIBNAME}__" |
| 62 PREFIX="$BASEPATH""${LIBNAME}__" | 62 PREFIX="$BASEPATH""${LIBNAME}__" |
| 63 SUFFIX=".txt" | 63 SUFFIX=".txt" |
| 64 | 64 |
| 65 RESULTS=`zcat -f "$FASTQ_FILE" | fastx_barcode_splitter.pl --bcfile "$BARCODE_FILE" --prefix "$PREFIX" --suffix "$SUFFIX" "$@"` | 65 RESULTS=`zcat -f < "$FASTQ_FILE" | fastx_barcode_splitter.pl --bcfile "$BARCODE_FILE" --prefix "$PREFIX" --suffix "$SUFFIX" "$@"` |
| 66 if [ $? != 0 ]; then | 66 if [ $? != 0 ]; then |
| 67 echo "error" | 67 echo "error" |
| 68 fi | 68 fi |
| 69 | 69 |
| 70 # | 70 # |