--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BAMqc.sh	Tue Mar 29 15:25:51 2016 -0400
@@ -0,0 +1,122 @@
+#!/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