--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/collectorcurve/collectorcurve.sh	Fri May 30 03:16:03 2014 -0400
@@ -0,0 +1,73 @@
+#!/bin/bash
+
+echo $@
+
+command=''
+filetype=$1
+input=$2
+label=$3
+echo label is $label
+if [ $label != 'None' ]; then
+ labelformatted=${label//,/-}
+ command+=', 'label=$labelformatted
+fi
+output=$4
+outputid=$5
+outputpath=$6
+calc=$7
+advanced=$8
+if [ $advanced == True ]; then
+     cabund=$9
+     abund=${10}
+     if [ $cabund == True ]; then
+     	command+=', 'abund=$abund
+     fi
+     csize=${11}
+     size=${12}
+     if [ $csize == True ]; then
+        if [ $size != 0 ]; then
+           command+=', 'size=$size
+       fi 
+     fi
+     cfreq=${13}
+     freq=${14}
+     if [ $cfreq == True ]; then
+        command+=', 'freq=$freq
+        echo $command
+     fi
+fi
+
+
+echo path: $outputpath id: $outputid
+## get filename only remove the extension
+file="${input%.*}"
+echo `cp $input $file'.'$filetype`
+inputfile=$file'.'$filetype
+calculator=${calc//,/-}
+IFS=',' read -a sum_calc <<< "$calc"
+for element in "${sum_calc[@]}"
+do
+    if [[ "$element" != "nseqs" ]] && [[ "$element" != "coverage" ]] && [[ "$element" != "sobs" ]]
+    then
+      sum_calculator+='-'$element
+    fi
+done
+#echo "collect.single($filetype=$inputfile, calc=$calc)"
+## use Mothur collect.single to calculate collector's curve - alpha diversity
+#mothur "#summary.single($filetype=$inputfile, calc=$calculator$command)"
+mothur "#summary.single($filetype=$inputfile, calc=nseqs-coverage-sobs$sum_calculator$command)"
+mothur "#collect.single($filetype=$inputfile, calc=$calculator$command)" 
+IFS=, read -a calcs <<< "${calc}"
+count=0
+##copy summary as main output
+echo `cp $file'.summary' $output`
+#copy calc files into directory
+for i in "${calcs[@]}"
+do
+   #if [ $count == 0 ]; then
+   #   echo `cp $file'.'$i $output`
+   #else
+      echo `cp $file'.'$i $outputpath'/primary_'$outputid'_'$i'_visible_tabular'`
+   #fi
+   let count+=1
+done