Mercurial > repos > agpetit > cut_trajectory
changeset 7:763261d4720d draft
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 9167288bf44ec486f68dade6f4fca41728690dd6-dirty"
| author | agpetit |
|---|---|
| date | Tue, 14 Jun 2022 13:23:26 +0000 |
| parents | d58e59d262cb |
| children | ccd03d6e7c49 |
| files | calculate_pore_diameter_aqp.py cut_trajectory.xml |
| diffstat | 2 files changed, 6 insertions(+), 4 deletions(-) [+] |
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--- a/calculate_pore_diameter_aqp.py Tue Jun 07 12:02:36 2022 +0000 +++ b/calculate_pore_diameter_aqp.py Tue Jun 14 13:23:26 2022 +0000 @@ -83,7 +83,7 @@ "--xtc_file_ext", type=str, nargs=1, help="""My input .xtc file""" ) parser.add_argument( - "-w", "--work_directory", type=str, nargs=1, + "-w", "--work_directory", type=str, default="./", help="""It's work Directory""" ) parser.add_argument( @@ -1054,8 +1054,10 @@ df_final = create_final_dataframe(resid_arr1, resid_arr2, resid_npa1, resid_npa2, u) if len(output_directory) > 2: - if not os.path.exists(output_directory): - os.makedirs(output_directory) + try: + os.makedirs(output_directory, exist_ok=True) + except OSError: + print("Directory '%s' can not be created") os.chdir(output_directory) if len(output) > 2: df_final.to_csv(output, sep="\t", index=False)
--- a/cut_trajectory.xml Tue Jun 07 12:02:36 2022 +0000 +++ b/cut_trajectory.xml Tue Jun 14 13:23:26 2022 +0000 @@ -33,7 +33,7 @@ --number_cpus "\${GALAXY_SLOTS:-1}" ]]></command> <inputs> - <param name="gro_file" type="data" format="gro" help="Put your .gro file"/> + <param name="gro_file" type="data" format="gro" help="Put your .gro file"/> <param name="xtc_file" type="data" format="xtc" help="Put your .xtc file"/> <conditional name="sub_traj"> <param name="number_sub_traj" type="select" label="Number of sub-trajectories">