#UNIVERSAL VARIABLES
#where the programs are called from
#use the following unless otherwise appropriate
BIN=./bin

#unique prefix for your analysis
# it can not be a folder name only
# it can include a path which exists where you want to put it.
#example of what I want: /scratch/spacocha/tmp/unique
UNIQUE=./output_dir/unique

#filter out the low abundance seqeunces because they don't have statistical power
#this will increase the speed of the error calling program
#consider how many sequences you will need to find statistical power across your sample
#0 and 1 are the same, since it keeps things that are less than or equal to the number
# if you want to remove singletons use 2
FNUMBER=0

#RUNQIIME_RAWDATA variables
#define your file paths
#where is the fastq file you want to process
SOLFILEF=./test_data/raw_data.fastq

#What is the name of your barcode or indexing read file to be used with QIIME's split_libraries_fastq.py
BARFILE=./test_data/test_data.barfile

#Where it the assoicated mapping file
MAPFILE=./test_data/test_data.mapping

#the oligo file
OLIGO=./accessory_files/oligos.tab

#last_bar_character for quality for filtering
#use Q unless there is reason to use otherwise
QUAL=Q

#max_bad_run_length
#use 0 unless there is a reason to use otherwise
BADRUN=0

#min_per_read_length variable of QIIME split_libraries_fastq.py
#use the full length of your read unless this filters too many sequences
MINLEN=99

#how long is your barcode?
BARLEN=7

#Any other split_libraries_fastq.py variables
#such as to reverse_comp barcode or sequence
SLV=

#the length of the primers that are removed in trim.seqs
PRILEN=23

#EOTU_parallel specific variables
#the forward reference seqeunce to align to
#this is ok only for 76 bps in length from the end of the U515 primer
#remake this file from the silva alignment following the mothur protocol for trimming an alignment to specific lengths
#you can use pcr.seqs with start and stop, or trim.seqs and possibly filter.seqs as well
FALIGN=./accessory_files/new_silva_short_unique_1_149.fa

#file with 2 columns, first with the unique library name as in mapping file
#second column with a new lib name, use the same name in the second column to merge replicates
#this field can be blank if you don't want to use a different name for each lib
COMBREPS=

#the variable string you want to include with the error program
VARSTRING=

#DISTRIBUTION-CLUSTERING VARIABLES
#Include a sequence cutoff distance filter
# must range from 0 -1 with 0.2 being a good cut-off for 0.90 clustering
#this is different from the ProgressiveClustering, but can be made to be similar
#this is a distance, ProgressiveClustering UPPER and LOWER are percent identity
CUTOFF=0.1

#PROGRESSIVE CLUSTERING VARIABLES
TRIM=`expr $MINLEN - $PRILEN`
#The file that was cleaned and done with RunQiime_rawdata.csh
QIIMEFILE=${UNIQUE}_output/seqs.trim.names.${TRIM}.fa
#The upper starting point for progressive clustering
#should be a percent id (i.e. 99 or 98)
UPPER=98

#Thi lower limit of the clustering
#should be a percent id (i.e. 92 or 90)
LOWER=90

#EVALUATE_RESULTS varables

#what is after the process number that was put into the distribution-based clustering algorithm
#this should include periods, but not the .err or .log which was added by the program
AFTER=process.f0

#CLEAN_PARALLEL_PROCESSES variables
#the start and stop positions of your filter
ALIGNSTART=1

ALIGNEND=149