staden-common 2.0.0+b11-2 / usr / share / staden / etc / pregap4rc

#
# Copyright (c) Medical Research Council, Laboratory of Molecular Biology,
# 1998. All rights reserved.
#
# This file is part of the Staden Package. See the Staden Package copyright
# notice for information on the restrictions for usage and distribution, and
# for a disclaimer of all warranties.
#

# The menu state bit enable/disable patterns are as follows
# Bit 0: Startup (and no database open)         (on)
# Bit 1: Busy mode                              (off)

set_menu pregap4_menu
add_menu File           1 0 left
add_menu Modules        1 0 left
add_menu {Information source} 1 0 left
add_menu Options        1 0 left
add_menu Help           1 0 right

add_command     {File.Set Files to Process}       1   0 {file_panel}
add_command {File.Load New Config File}   1   2 {load_new_config}
add_command     {File.Load Naming Scheme}         1   2 {add_template_gui 1}
add_command     {File.Include Config Component}   1   2 {add_template_gui 0}
add_separator   {File.S1}
add_command     {File.Save All Parameters (in all modules)}     \
                                                  1   2 {save_all_params}
add_command     {File.Save All Parameters (in all modules) to:}     \
                                                  1   2 {save_all_params_to}
add_command     {File.Save Module List}           1   0 {save_module_list}
add_separator   {File.S2}
add_command     {File.Exit}                       1   0 {exit}

add_command     {Modules.Add/Remove Modules}      1   2 {select_modules}
add_command     {Modules.Configure Modules}       1   2 {config_panel}
add_separator   {Modules.S1}
add_command     {Modules.Select all modules}      1   2 {select_all_modules 1}
add_command     {Modules.Deselect all modules}    1   2 {select_all_modules 0}
add_separator   {Modules.S2}
add_command     {Modules.Run}                        1   0 {run_gui}


add_command     {Information source.Simple Text Database} \
                          1   2 {unix_database}
add_command     {Information source.Experiment File Line Types} \
                              1   2 {edit_exp_types}

add_command     {Options.Set Fonts}               1   2 {SetFonts}
if { $tcl_platform(platform) != "windows" } {
  add_command     {Options.Set Colours}             1   2 {ConfigureColours}
}
#add_command     {Options.Compact Window Style}   1   2 {set_window_style compact}
#add_command     {Options.Separate Windows Style}  1   2 {set_window_style separate}

add_command     {Help.Contents}     1   0 \
    {show_help pregap4 {Contents}}
add_command     {Help.Index}    1   0 \
    {show_help pregap4 {General Index}}
add_separator   {Help.S1}
add_command     {Help.Introduction} 1   0 \
    {show_help pregap4 {Pregap4-Introduction}}
add_command     {Help.Files}        1   0 \
    {show_help pregap4 {Pregap4-Files}}
add_command     {Help.Configuring Modules}  1   0 \
    {show_help pregap4 {Pregap4-Modules}}
add_separator   {Help.S2}
add_command {Help.Show Licence} 1 0 {show_help pregap4 Copyright}

set_def WINDOW_STYLE compact

set line_types "CN CV SV SF CF WT DR DT MC MN MT OP TN ST PN PR SC SP SI
        SS EX AP CH"

# -----------------------------------------------------------------------------
# Where to find modules, and which ones to use

#[module_list]
set MODULE_PATH {$env(STADTCL)/pregap4/modules}
if { $tcl_platform(platform) != "windows" } {
    set MODULES {
    phred
    atqa
    eba
    convert_trace
    compress_trace
    init_exp
    augment_exp
    quality_clip
    sequence_vector_clip
    cross_match_svec
    screen_vector
    polyA
    cloning_vector_clip
    screen_seq
    blast
    interactive_clip
    repeat_masker
    hetins
    reference
    mutscan
    gap4_assemble
    cap3_assemble
    fakii_assemble
    phrap_assemble
    enter_assembly
    email
    }
} else {
    set MODULES {
    phred
    atqa
    eba
    convert_trace
    init_exp
    augment_exp
    quality_clip
    sequence_vector_clip
    cross_match_svec
    screen_vector
    polyA
    cloning_vector_clip
    screen_seq
    interactive_clip
    hetins
    reference
    mutscan
    gap4_assemble
    phrap_assemble
    enter_assembly
    }
}

# -----------------------------------------------------------------------------
# Global variables

#[global_variables]

# -----------------------------------------------------------------------------
# Module default parameters
#
# The following parameters are the defaults defined in the module files
# themselves. They do not need to be defined here, but this list is a handy
# location to edit site-wide defaults for Pregap4.

##[::init]
module init {
set enabled 1
set use_sample_name 0
}
#
##[::convert_trace]
module convert_trace {
set enabled 1
#set down_scale 0
#set down_scale_range 255
#set output_format ztr
#set subtract_background 0
#set normalise 0
}
##[::compress_trace]
module compress_trace {
set enabled 0
#set keep_names 0
#set compression none
}
#
##[::eba]
module eba {
set enabled 1
set scale logarithmic
}
#
##[::phred]
module phred {
set enabled 0
}
#
##[::atqa]
module atqa {
set enabled 0
}
#
##[::init_exp]
module init_exp {
set enabled 1
}
#
##[::augment_exp]
module augment_exp {
set enabled 1
}
#
##[::uncalled_clip]
module uncalled_clip {
set enabled 0
#set offset 70
#set min_extent 0
#set max_extent 999999
#set right_win_length 100
#set right_num_uncalled 5
#set left_win_length 100
#set left_num_uncalled 5
}
#
##[::quality_clip]
module quality_clip {
set enabled 1
set clip_mode confidence
set conf_val 15
set window_length 50
#set offset 70
#set min_extent 0
#set max_extent 999999
#set right_win_length 100
#set right_num_uncalled 5
#set left_win_length 100
#set left_num_uncalled 5
}
#
##[::sequence_vector_clip]
module sequence_vector_clip {
set enabled 1
#set min_5_match 60
#set min_3_match 80
#set def_5_pos -1
}
#
##[::cloning_vector_clip]
module cloning_vector_clip {
set enabled 1
#set word_length 4
#set probability 0.000001
}
##[::polyA]
module polyA {
set enabled 0
}
#
#
##[::old_cloning_vector_clip]
module old_cloning_vector_clip {
set enabled 1
#set word_length 4
#set num_diags 7
#set diag_score 0.3
}
#
##[::screen_vector]
module screen_vector {
set enabled 1
#set min_match 30
}
#
##[::screen_seq]
module screen_seq {
set enabled 0
#set min_match 25
#set max_length 250000
#set screen_mode fofn
#set screen_file $env(STADENROOT)/userdata/ecoli.files
}
#
##[::blast]
module blast {
set enabled 0
#set database $env(STADTABL)/blast_data/ecoli
#set match_fraction 0.5
}
#
##[::interactive_clip]
module interactive_clip {
set enabled 0
}
#
##[::hetins]
module hetins {
set enabled 0
}
#
##[::reference]
module reference {
set enabled 0
}
#
##[::mutscan]
module mutscan {
set enabled 0
}
#
##[::gap4_assemble]
module gap4_assemble {
set enabled 0
#set database_name {}
#set database_version 0
#set create 0
#set min_match 15
#set max_pads 25
#set max_pmismatch 5.0
#set enter_all 0
}
#
##[::cap2_assemble]
module cap2_assemble {
set enabled 0
}
#
##[::cap3_assemble]
module cap3_assemble {
set enabled 0
#set generate_constraints 0
}
#
##[::fakii_assemble]
module fakii_assemble {
set enabled 0
#set graph_e_limit .099
#set graph_d_limit 0.0001
#set graph_o_threshold 10.0
#set assem_o_threshold 20.0
#set assem_d_threshold 0.0001
#set assem_number 1
#set generate_constraints 0
}
#
##[::phrap_assemble]
module phrap_assemble {
set enabled 0
#set minmatch 12
#set minscore 30
}
#
##[::enter_assembly]
module enter_assembly {
set enabled 0
#set database_name {}
#set database_version 0
#set create 0
#set quality_clip 0
#set difference_clip 1
}
#
##[::email]
module email {
set enabled 0
#set email_address {}
#set email_program Mail
#set email_args {-s "Pregap4 has finished"}
}
#
##[::shutdown]
module shutdown {
set enabled 1
}
#
##[::cross_match_svec]
module cross_match_svec {
set enabled 0
#set vector_file {}
#set minmatch 12
#set minscore 20
}
#
##[::repeat_masker]
module repeat_masker {
set enabled 0
#set tag_type REPT
#set alu_only 0
#set simple_only 0
#set no_primate_rodent 0
#set rodent_only 0
#set no_low_complexity 0
#set library "<default>"
#set cutoff 200
}