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planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
author rv43
date Thu, 23 Mar 2023 13:39:14 +0000
parents 1cf15b61cd83
children
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#!/bin/bash

# From workflow
#python -m workflow run_tomo -i sobhani-3249-A_reduce.nxs -c sobhani-3249-A_centers.yaml -o sobhani-3249-A_recon.nxs -n 48 -s 'only' --reconstruct_data
#python -m workflow run_tomo -i tenstom_1304r-1_one_stack_reduce.nxs -c tenstom_1304r-1_one_stack_centers.yaml -o tenstom_1304r-1_one_stack_recon.nxs -n 48 -s 'only' --reconstruct_data
#python -m workflow run_tomo -i tenstom_1304r-1_reduce.nxs -c tenstom_1304r-1_centers.yaml -o tenstom_1304r-1_recon.nxs -n 48 -s 'only' --reconstruct_data

# As Galaxy tool:
python tomo_reconstruct.py -i sobhani-3249-A_reduce.nxs -c sobhani-3249-A_centers.yaml -o sobhani-3249-A_recon.nxs --log_level INFO -l tomo.log --galaxy_flag --x_bounds 650 1050 --y_bounds 270 1430
python tomo_reconstruct.py -i tenstom_1304r-1_one_stack_reduce.nxs -c tenstom_1304r-1_one_stack_centers.yaml -o tenstom_1304r-1_one_stack_recon.nxs --log_level INFO -l tomo.log --galaxy_flag --x_bounds 629 1450 --y_bounds 606 1468
python tomo_reconstruct.py -i tenstom_1304r-1_reduce.nxs -c tenstom_1304r-1_centers.yaml -o tenstom_1304r-1_recon.nxs --log_level INFO -l tomo.log --galaxy_flag --x_bounds 629 1450 --y_bounds 606 1468