Mercurial > repos > qfab > rdp_multiclassifier
annotate rdpmulticlassifier/rdpmulticlassifier.sh @ 0:a73ae72b47aa draft default tip
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| author | qfab |
|---|---|
| date | Thu, 29 May 2014 02:27:56 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| 0 | 1 #!/bash/bin |
| 2 #echo $@ | |
| 3 | |
| 4 gene=$1 | |
| 5 addotutable=$2 | |
| 6 input_file=$3 | |
| 7 otu_input_file=$4 | |
| 8 conf=$5 | |
| 9 output_hier=$6 | |
| 10 output_assign=$7 | |
| 11 output_otutable=$8 | |
| 12 format=$9 | |
| 13 full_path=$(echo "`dirname $0`";) | |
| 14 | |
| 15 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`; | |
| 16 if [ $addotutable == True ] | |
| 17 then | |
| 18 echo `python $full_path\/scripts\/generateOTUtable.py $output_otutable $otu_input_file $output_assign`; | |
| 19 fi |