[General]
ref = /home/galaxydev/galaxy/tools/SouthGreen/scaffremodler/test-data/Ref_for_SV_detection.fasta
chr = /home/galaxydev/galaxy/tools/SouthGreen/scaffremodler/test-data/chromosome_information.txt
mini = 2500
maxi = 7500
thread = 1
tool = bowtie2_single
q1 = /home/galaxydev/galaxy/tools/SouthGreen/scaffremodler/test-data/reads_mate1_SV.fq
q2 = /home/galaxydev/galaxy/tools/SouthGreen/scaffremodler/test-data/reads_mate2_SV.fq
qual = 33
orient = rf
index = n
rmindex = n
sd_multiplicator = 3.0
restimate = y
mini_dis = 10000
mult_max_cov = 10.0
mult_min_cov = 0.25
min_zone = 500
min_gap = 300
max_dist_merge = 1000.0
yis = 0.0
mis = 0.5
yic = 0.0
mic = 0.25
min_score = 70
ploid = 0.66
fai_file = /home/galaxydev/galaxy/tools/SouthGreen/scaffremodler/test-data/Ref_for_SV_detection.fasta.fai
exclude_chrom = no_exclude

[Mapping]
out = /home/galaxydev/galaxy/tools/SouthGreen/scaffremodler/test-data/alignment.sam

[Single_filter]
rminput = n
filter_multi = y
asxs = 1
qual = not_filled
out = /home/galaxydev/galaxy/tools/SouthGreen/scaffremodler/test-data/quality_threshold.sam
type = sam

[Remove_dup]
rminput = n
sort = coordinate
out = /home/galaxydev/galaxy/tools/SouthGreen/scaffremodler/test-data/bam_remove_redundancy.bam
type = bam

[Calc_coverage]
out = /home/galaxydev/galaxy/tools/SouthGreen/scaffremodler/test-data/coverage.txt
median_insert = 5199
mean_insert = 5200.10472232
standard_deviation_insert = 501.815580589
mean_coverage = 4.85657925724
median_coverage = 5.0
mini = 3693.55325823
maxi = 6704.44674177

[Trie_discord]
rminput = n 
type = bam

[Score_discord]
mis = 2599.5
mic = 1.25

[Ident_discord] 

