varname,input,default,options,description
host,,coli,[coli | yeast | sapiens],Host name for assigning codon table
Ni_cutoff,,8,,Lower cut off for frequency per mutant
Q_cutoff,,30,,Lower cut off for Phred score quality
transform_type,,log,[log: log2  |  plog: log2 with pseudocount | rlog: regularised log2 (needs deseq)| vst: variance stabilizing transformation (needs DESeq2)],Type of transformation of frequecies of mutants
norm_type,,none,[GLM: by generalized linear modelling (needs DESeq2) | none : use raw fold changes | MLE: wrt MLE of synonymous mutations ],Type of normalization of fold changes
alignment_type,,loc,[loc:local | glob:global],Alignment type
cores,,2,,Number of cores to be used
mut_type,,single,[single: double],Whether input data is of single mutation or double mutations
rescaling,,FALSE,[FALSE | TRUE],Optional: Position wise rescaling the fold changes by fold changes of synonymous (wild type) mutations
mut_subset,,N,[N: Non-synonymous | S: Synonymous | A: All],Optional: Subset of mutations to be used for down-stream analysis
ml_input,,Fi,[FC: Preferential enrichments| Fi: Fitness scores ],Optional: Whether to use Preferential enrichments or Fitness scores for identification of molecular constraints
clips,,,,Optional: Clip upstream UPTO and downstream FROM codons (space delimited) rg. 10<SPACE>167
fsta_fh,,found in project directory,,Optional: Path to reference fasta file
pdb_fh,,found in project directory,,Optional: Path to pdb file
active_sites,,,,Optional: residue numbers of active sites (space delimited) eg. 68<SPACE>192
cctmr,,,,Optional: if reference sequence is concatamer (space delimited) eg. 1<SPACE>265<SPACE>268<SPACE>532
trimmomatic_com,,,,Optional: additional commands to pass to trmmomatic
bowtie2_com,,,,Optional: additional commands to pass to bowtie2
dssp_fh,,,,Optional: path to dssp module (dependencies)
trimmomatic_fh,,,,Optional: path to trimmomatic source (.jar) file (dependencies)
bowtie2_fh,,,,Optional: path to bowtie2 source file
samtools_fh,,,,Optional: path to samtools source file
clustalo_fh,,,,Optional: path to clustal omega source file
msms_fh,,,,Optional: path to MSMS source file (for calculation of residue depths)
rate4site_fh,,,,Optional: path to rate4site source file (for calculation of conservation scores)
rscript_fh,~/anaconda/envs/dms2dfe/bin/Rscript,/usr/bin/Rscript,,Optional: path to Rscript (for use of Deseq2) can be identified by executing command 'which Rscript'
