#!/usr/bin/perl
use strict;

my $fld="lefse_results";
mkdir $fld if !-e $fld;
my $meta="lefse_L7.txt";
my $lefse="lefse";
my $title="Significantly Represented Taxa";
open(OUT,">lefse.sh")||die;
print OUT "format_input.py $meta $fld/$lefse.in -f c -c 2 -u 1 -o 1000000\n";
print OUT "run_lefse.py $fld/$lefse.in $fld/$lefse.res > $fld/run_$lefse.log\n";
print OUT "plot_res.py $fld/$lefse.res $fld/$lefse.plot.png --format png --title '$title'\n";
print OUT "plot_res.py $fld/$lefse.res $fld/$lefse.plot.svg --format svg --title '$title'\n";
print OUT "plot_res.py $fld/$lefse.res $fld/$lefse.plot.pdf --format pdf --title '$title'\n";

print OUT "plot_cladogram.py $fld/$lefse.res $fld/$lefse.cladogram.species.png --format png --title '$title'\n";
print OUT "plot_cladogram.py $fld/$lefse.res $fld/$lefse.cladogram.species.svg --format svg --title '$title'\n";
print OUT "plot_cladogram.py $fld/$lefse.res $fld/$lefse.cladogram.species.pdf --format pdf --title '$title'\n";

print OUT "plot_cladogram.py $fld/$lefse.res $fld/$lefse.cladogram.genus.png --max_lev 6 --format png --title '$title'\n";
print OUT "plot_cladogram.py $fld/$lefse.res $fld/$lefse.cladogram.genus.svg --max_lev 6 --format svg --title '$title'\n";
print OUT "plot_cladogram.py $fld/$lefse.res $fld/$lefse.cladogram.genus.pdf --max_lev 6 --format pdf --title '$title'\n";
mkdir "$fld/all_diff_features" if !-e "$fld/all_diff_features";

print OUT "plot_features.py $fld/$lefse.in $fld/$lefse.res $fld/all_diff_features/ -f diff --format png\n";
print OUT "plot_features.py $fld/$lefse.in $fld/$lefse.res $fld/all_diff_features/ -f diff --format svg\n";
print OUT "plot_features.py $fld/$lefse.in $fld/$lefse.res $fld/all_diff_features/ -f diff --format pdf\n";

close OUT;