Mercurial > repos > youngkim > ezbamqc
view BAMqc.sh @ 11:5bfcc6c131ed
Uploaded
author | cshl-bsr |
---|---|
date | Wed, 30 Mar 2016 12:14:21 -0400 |
parents | b4ff32b63fcd |
children |
line wrap: on
line source
#!/bin/sh ### Galaxy Wrapper for BAMqc ### alignment_files="" refgene="" attrID="" rRNA="" outputHTML="" stranded="" mapq="30" lowBound="-250" upperBound="250" stepSize="5" labels="" cores="1" ARGS=$(getopt -o "r:f:R:o:s:p:q:" -- "$@") if [ $? -ne 0 ]; then echo "Invalid command-line parameters. Do not use this script outside of Galaxy" >&2 exit 1 fi eval set -- "$ARGS" while [ $# -gt 0 ]; do case "$1" in -r) refgene="$2" shift 2 ;; -f) attrID="$2" shift 2 ;; -R) rRNA="$2" shift 2 ;; -o) outputHTML=$2 shift 2 ;; -s) stranded=$2 shift 2 ;; -q) mapq=$2 shift 2 ;; -p) cores=$2 shift 2 ;; --) shift break ;; esac done if [ "$cores" -gt 10 ];then cores="10" fi outputDir=`echo $outputHTML | sed 's/\.dat$/_files/'` if [ ! -d "$outputDir" ]; then mkdir $outputDir fi touch bamqc.log while [ "$#" -ne 0 ]; do FILE="$1" LABEL=`echo $2 | sed 's/ /-/g; s/\[//; s/\]//;'` shift 2 QNAME_SORTED=`samtools view -H ${FILE} | grep "SO:queryname"` if [ $? -ne 0 ]; then BASE=`basename ${FILE} \.dat` echo "Sorting BAM file (${LABEL}." >>samtools.log samtools sort -@ 5 -n ${FILE} ${BASE} 2>>samtools.log if [ $? -ne 0 ]; then echo "Error with samtools sorting for BAM file (${LABEL})." >&2 cat samtools.log >&2 exit 1 fi echo "BAM file (${LABEL}) was re-sorted by query name." >>bamqc.log FILELIST="$FILELIST ${BASE}.bam" else FILELIST="$FILELIST $FILE" fi LABELLIST="$LABELLIST $LABEL" done CMD="ezBAMQC -i $FILELIST -l $LABELLIST -f $attrID -r $refgene -o Galaxy_BAMqc_output --stranded $stranded -q $mapq --rRNA $rRNA -t $cores" echo "BAMqc command: $CMD" >> bamqc.log echo >> bamqc.log $CMD 2>> bamqc.log if [ $? -ne 0 ]; then echo "BAMqc ran with errors" >&2 cat bamqc.log >&2 exit 1 fi sed -i "s/\.\.\/Galaxy_BAMqc_output\///g;" Galaxy_BAMqc_output/bamqc_output.html cp -r Galaxy_BAMqc_output/data "$outputDir" cp -r Galaxy_BAMqc_output/figs "$outputDir" cp Galaxy_BAMqc_output/bamqc_output.html "$outputHTML" if [ $? -ne 0 ]; then echo "Copying BAMqc results failed" >&2 fi echo "BAMqc results copied to $outputDir" >>bamqc.log