Mercurial > repos > qfab > rdp_multiclassifier

diff 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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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rdpmulticlassifier/rdpmulticlassifier.sh	Thu May 29 02:27:56 2014 -0400
@@ -0,0 +1,19 @@
+#!/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