Mercurial > repos > jbrayet > peaksplitter_1_0_docker
changeset 0:ba7684ab5009 draft
Uploaded
| author | jbrayet |
|---|---|
| date | Thu, 21 Jan 2016 05:30:29 -0500 |
| parents | |
| children | f2b22de83c6c |
| files | peakSplitter_wrapper.sh |
| diffstat | 1 files changed, 31 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/peakSplitter_wrapper.sh Thu Jan 21 05:30:29 2016 -0500 @@ -0,0 +1,31 @@ +#!/bin/bash + + +while getopts "p:w:o:h:" optionName; do +case "$optionName" in + +p) PEAKS_FILE="$OPTARG";; +w) WIG_FILE="$OPTARG";; +o) SUB_PEAKS_FILE="$OPTARG";; +h) GALAXY_HOME="$OPTARG";; + +esac +done + +ROOT_NAME=`basename $PEAKS_FILE .dat` +SUB_PEAKS_FILENAME=${ROOT_NAME}.subpeaks.dat +TMP_DIR=`mktemp -d` + +trackNumber=$(grep -c "track" $WIG_FILE) +if [[ trackNumber > 1 ]]; then + cp $WIG_FILE $WIG_FILE.tmp + sed -i "/track/d" $WIG_FILE.tmp + line=$(head -n 1 $WIG_FILE) + sed -i "1s/^/$line\n/" $WIG_FILE.tmp + /usr/bin/peaksplitter/PeakSplitter_v1/PeakSplitter -p $PEAKS_FILE -w $WIG_FILE.tmp -o $TMP_DIR -f + rm -f $WIG_FILE.tmp +else + /usr/bin/peaksplitter/PeakSplitter_v1/PeakSplitter -p $PEAKS_FILE -w $WIG_FILE -o $TMP_DIR -f +fi + +mv $TMP_DIR/$SUB_PEAKS_FILENAME $SUB_PEAKS_FILE