/usr/share/mira/demoparam.prm is in mira-assembler 4.0.2-1+b1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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#
# MIRA genome and EST assembler
#
# Demo parameter file which just lists all possible parameters (or at least
# tries to), but does _not_ form a sensible parameter set on its own.
#
# $Id$
#
#############################################################################################
#
# The parameter file contains several sections (-GENERAL, -ASSEMBLY
# etc.) with each section containing certain options.
# The sections need not to be in a certain order and can be mixed,
# e.g. after some -ASSEMBLY parameteres some -GENERAL can be given
# and then again some -ASSEMBLY
#
#############################################################################################
#
# These parameters can be taken verbatim to the command line (in
# verbose form or using the aliases) by putting a colon between
# different options of a section.
#
# E.g.
# -ASSEMBLY
# mrl = 40
# -CLIPPING
# possible_vector_clip = yes
# quality_clip = yes
#
# could become: -AS:mrl=40 -CO:pvc=yes:qc=yes
# or even: -AS:mrl=40 -CO:pvc=yes -CO:qc=yes
#
#
# Please note: when using the parameters on the command line, then
# spaces are NOT allowed between sections and parameters or between
# parameters and values
# That is:
# -AS:mrl=40 is ok on the commandline
# -AS mrl=40 is NOT ok on the commandline
# -AS:mrl = 40 is NOT ok on the commandline
# Here we go
#
# General options control a few fundamental behaviours
#
-GENERAL
projectname = demo # project name; aliases: 'project', 'pro'
load_job = fofnexp # load data from; alias: 'lj'
filecheck_only = no # only check files by load; alias: 'fo'
external_quality = SCF # load ext. qual. from; alias: 'eq'
external_quality_override = yes # overide with ext. qualities alias: 'eqo'
readnaming_scheme = sanger # naming scheme of reads alias: 'rns'
merge_xmltraceinfo = yes # merge ancillary XML data? alias: 'mxti'
use_template_information = yes # Use templ. info in assembly alias: 'uti'
discard_read_on_eq_error = no # discard or use default qual alias: 'droeqe'
print_date = yes # print date in ouput log alias: 'pd'
#
# This options taking effect only for the EST assembly
#
est_startstep = 1 # start in step 1, 2 or 3 alias: 'ess'
#
# Options that control usage / loading of straindata and backbone data
# in assembly
#
-STRAIN/BACKBONE
load_straindata = no # load organism data file alias: 'lsd'
load_backbone = no # load backbone for assembly alias: 'lb'
backbone_filetype = caf # file type of backbone alias: 'bft'
backbone_raillength = 2500 # raillengths for backbone alias: 'brl'
backbone_strainname = mystrain # strain name for backbone alias: 'bsn'
backbone_basequals = 30 # default quals for backbone alias: 'bbq'
alsobuildnewcontigs = yes # not only map on backbone alias: 'abnc'
startbackboneusage_inpass = 3 # only use backbones then alias: 'sbuil'
#
# Assembly options control basic behaviour
# (number of iterations, resolve repeats etc.)
#
-ASSEMBLY
minimum_read_length = 40 # minimum read len. for ass. alias: 'mrl'
num_of_passes = 2 # number of assembly passes; alias: 'nop'
skim_each_pass = yes # run skim alg. each pass? alias: 'sep'
rmb_break_loops = 5 # max. num. of loops in prmb; alias: 'pbl'
spoiler_detection = yes # detect reads preven. joins; alias: 'sd'
sd_last_pass_only = yes # only last pass or anytime?; alias: 'sdlpo'
use_emergency_search_stop = yes # for high coverage searches; alias: 'uess'
ess_partnerdepth = 500 # enable on this # of partn. alias: 'esspd'
use_emergency_blacklist = no # blacklisting for hc search; alias: 'uebl'
use_max_contig_buildtime = no # use time restr. to build c. alias: 'umcbt'
buildtime_in_seconds = 10000 # seconds alloted to 1 cont. alias: 'bts'
#
# Special options for 454 assembly (testing)
#
#
#-454DATA
#main_data_is_454 = yes # defines reads to be 454 of type; alias: 'mdis454'.
#
# Special options for data preprocessing (if wanted)
#
-DATAPROCESSING
use_read_extension = yes # extend reads if possible; alias: 'ure'
read_extension_window_len = 30 # window len for ext.routines;alias: 'rewl'
read_extension_window_maxerrors = 2 # max errors for ext.routines;alias: '0'
first_extension_in_pass = 0 # start extending after pass;alias: 'feip'
last_extension_in_pass = 0 # stop extending after pass ;alias: 'leip'
tag_polyat_at_ends = no # tag polyAT stretches? alias: 'tpae'
polybase_window_len = 7 # window for tagging; alias: 'pbwl'
polybase_window_maxerrors = 2 # max non-AT in window; alias: 'pbwme'
polybase_window_gracedistance = 9 # distance before stoping; alias: 'pbwgc'
#
# SKIM is the fast all-against-all read comparison
#
-SKIM
bases_per_hash = 16 # wordsize (8-30); alias: 'bph'
hash_save_stepping = 4 # ratio of hashes saved; alias: 'hss'
percent_required = 50 # skim percent identity required; alias: 'pr'
max_hashes_in_memory = 15000000 # hashes generated in mem.; alias: 'mhim'
maxhits_perread = 200 # max. num. of hits per read; alias: 'mhpr'
#
# Clipping options control if and how sequences should be clipped
#
-CLIPPING
possible_vector_clip = yes # clip possible seq. vectors; alias: 'pvc'
pvc_maxlenallowed = 12 # but only if <= num bases; alias: 'pvcmla'
quality_clip = yes # perform quality clip; alias: 'qc'
qc_minimum_quality = 20 # min. qual. for clip; alias: 'qcmq'
qc_window_length = 30 # window len. for qual. clip; alias: 'qcwl'
maskedbase_clip = yes # clip masked bases (X); alias: 'mbc'
mbc_gap_size = 15 # mb clip max. internal gap; alias: 'mbcgs'
mbc_max_front_gap = 30 # mb clip max. front gap; alias: 'mbcmfg'
mbc_max_end_gap = 60 # mb clip max. end gap; alias: 'mbcmeg'
ensure_minimum_left_clip = Yes # clip minimum number left? alias: 'emlc'
minimum_left_clip_required = 25 # minimum number left req. alias: 'mlcr'
set_minimum_left_clip_to = 30 # set to this, if num<'mlcr' alias: 'smlc'
#
# Align options for controlling the Smith-Waterman (banded) alignment
# and the alignment post-processing
#
-ALIGN
bandwidth_in_percent = 15 # SW bandwidth in percent alias: 'bip'
bandwidth_max = 100 # but max bandwidth alias: 'bx'
bandwidth_min = 10 # but min bandwidth alias: 'bn'
min_score = 15 # Min. SW score alias: 'ms'
min_overlap = 15 # Min. overlap length alias: 'mo'
min_relative_score = 65 # Min. relative score alias: 'mrs'
extra_gap_penalty = yes # Use an extra gap penalty alias: 'egp'
egp_level = low # Extra gap penalty level alias: 'egpl'
#
# Contig options
# Contigs are implemented as intelligent objects who fully control which
# sequences they choose to add and which they reject.
# They also have routines to recognize misassemblies due to possible
# repeats and mark important repeat discerning bases (PRMB = Possible
# Repeat Marker Base) or SNPs when running in EST assembly mode
#
-CONTIG
analysis = signal # perform error analysis alias: 'an'
rej_on_dropinrelscore = 10 # max.drop in relscore allowed alias: 'rodirs'
danger_max_error_rate = 1 # Max. error rate in d. zone alias: 'dmer'
mark_repeats = yes # mark repeats; alias: 'mr'
min_reads_per_group = 2 # Min. reads in a group to tag alias: 'mrpg'
min_rmb_neighbor_qual = 20 # Min. qual of neigh. to tag; alias: 'mnq'
min_groupqual_for_rmb_tagging = 30 # Min. groupqual for tagging alias: 'mgqpt
endread_mark_exclusion_area = 15 # Exclude num. bases at ends alias: 'emea'
also_mark_gap_bases = yes # Mark columns with gap bases alias: 'amgb'
also_mark_gap_bases_even_multicolumn = yes #:even with neighbouring gaps alias: 'amgbemc'
also_mark_gap_bases_needbothstrands = yes #:only if gaps in both strands alias: 'amgbnbs'
defaultinsertsizeminimum = 500 # Min. insert size of template alias: 'ismin'
defaultinsertsizemaximum = 5000 # Max. insert size of template alias: 'ismax'
#
# EdIt parameters for controling the integrated automatic editor
# which uses available SCF data to resolve conflicts
#
-EDIT
automatic_contig_editing = yes # edit contigs using scf data? alias: 'ace'
confirmation_threshold = 80 # editing confirmation thresh. alias: 'ct'
strict_editing_mode = yes # use strict editing mode? alias: 'sem'
#
# Directory names where to find or where to write data
# Note: log directory will have the project name prepended
#
-DIRECTORY
gap4da = gap4da # Dir. for gapda output
exp = exp # Dir. for input of exp files
scf = scf # Dir. for input of scf files
fasta = fasta # Dir. for input of fast files
log = miralog # Dir. for output temp. log
#
# File names
#
-FILE
fofnexpin = demofe.fofn # name of fofn of exp files alias: 'fei'
fofnphdin = demoph.fofn # name of fofn of phd file alias: 'fpi'
phdin = demoin.phd # name of phd infile alias: 'pi'
fastain = demoin.fasta # name of fasta infile alias: 'fai'
fastaqualin = demoin.fasta.qual # name of fasta qual. infile alias: 'fqi'
straindatain = straindata.txt # name of straindata infile alias: 'sdi'
cafin = demoin.caf # name of caf infile alias: 'ci'
cafout = demores.caf # name of caf outfile alias: 'co'
xmltraceinfoin = demo_t_in.xml # name of trace info file alias: 'xtii'
#
# Options for controling which results to write and to which type of files
#
-OUTPUT
output_result_caf = yes # output in caf format; alias: 'orc'
output_result_gap4da = yes # output as gap4 dir.ass.for. alias: 'orf'
output_result_fasta = yes # output in fasta format alias: 'org'
output_result_ace = yes # output in ace format alias: 'ora'
output_result_text = yes # output in text format alias: 'ort'
output_result_html = no # output in html format alias: 'orh'
output_tmpresult_caf = no # temporary results are alias: 'otc'
output_tmpresult_gap4da = no # results after each alias: 'otg'
output_tmpresult_fasta = no # main pass. alias: 'otf'
output_tmpresult_ace = no # alias: 'ota'
output_tmpresult_text = no # alias: 'ott'
output_tmpresult_html = no # alias: 'oth'
output_exttmpresult_caf = no # extra temporary results alias: 'oetc'
output_exttmpresult_gap4da = no # can happen inbetween a alias: 'oetg'
output_exttmpresult_fasta = no # pass if, e.g., a contig alias: 'oetf'
output_exttmpresult_ace = no # must be rebuilt because alias: 'oeta'
output_exttmpresult_html = no # of clashes in repeats alias: 'oeth'
oetas = no # also singlets? alias: 'output_exttmpresult_alsosinglets'
text_chars_per_line = 60 # number of bases in a text alignment line alias: 'tcpl'
html_chars_per_line = 60 # number of bases in a HTML alignment line alias: 'hcpl'
text_endgap_fillchar = " " # endgap character for text alignment line alias: 'tegfc'
html_endgap_fillchar = " " # endgap character for text alignment line alias: 'hegfc'
#
# Quick mode switches
# These switches set default parameters considered useful when
# assembling projects having a certain file input type
#
-fasta
-phd
-caf
#
# These modes also have a version where the filename of the input data
# can be given
#
-fasta = demoin.fasta
-phd = demoin.phd
-caf = demoin.caf
#
# Setting the project name (via this switch or via the -GENERAL one)
# automatically sets a lot of different default input and output file
# and directory names to reflect the name of the project.
#
-projectname = demoproject # aliases: '-project', '--project', '--projectname'
# other quickswitches
-borg
-horrid
-estmode
#
# Loading parameters from other files is also possible
#
#
#--params = somefile.prm
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