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view rdpmulticlassifier/rdpmulticlassifier.sh @ 0:a73ae72b47aa draft default tip

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author qfab
date Thu, 29 May 2014 02:27:56 -0400
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#!/bash/bin
#echo $@

gene=$1
addotutable=$2
input_file=$3
otu_input_file=$4
conf=$5
output_hier=$6
output_assign=$7
output_otutable=$8
format=$9
full_path=$(echo "`dirname $0`";)

echo `java -Xmx1g -jar $JAVA_JAR_PATH/MultiClassifier.jar --gene=$gene --conf=$conf --hier_outfile=$output_hier --assign_outfile=$output_assign --format=$format $input_file`;
if [ $addotutable == True ] 
then
  echo `python $full_path\/scripts\/generateOTUtable.py $output_otutable $otu_input_file $output_assign`;
fi