# HG changeset patch
# User agpetit
# Date 1655818763 0
# Node ID 066606280457b6430787d611df57fa15b381b5e0
# Parent  a4097272ade09c2b0d6eca02263e29fb3b6627c7
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 39e6c57933401793343e38ebe55ad3cc52a3112d"

diff -r a4097272ade0 -r 066606280457 calculate_diameter.xml
--- a/calculate_diameter.xml	Tue Jun 14 13:26:07 2022 +0000
+++ b/calculate_diameter.xml	Tue Jun 21 13:39:23 2022 +0000
@@ -6,11 +6,13 @@
         <requirement type="package" version="2.1.0">mdanalysis</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
+        ln -s '$gro_file' '$gro_file.element_identifier' &&
+        ln -s '$xtc_file' '$xtc_file.element_identifier' &&
         python '$__tool_directory__/calculate_pore_diameter_aqp.py'
             --arr_one '$arr1'
             --arr_second '$arr2'
-            --gro_file '$gro_file'
-            --xtc_file '$xtc_file'
+            --gro_file '$gro_file.element_identifier'
+            --xtc_file '$xtc_file.element_identifier'
             --gro_file_ext '$gro_file.ext'
             --xtc_file_ext '$xtc_file.ext'
             --output '$table'
diff -r a4097272ade0 -r 066606280457 calculate_pore_diameter_aqp.py
--- a/calculate_pore_diameter_aqp.py	Tue Jun 14 13:26:07 2022 +0000
+++ b/calculate_pore_diameter_aqp.py	Tue Jun 21 13:39:23 2022 +0000
@@ -71,16 +71,16 @@
         help="""Information messages to stderr""",
     )
     parser.add_argument(
-        "-gro", "--gro_file", type=str, nargs=1, help="""My input .gro file"""
+        "-gro", "--gro_file", type=str, help="""My input .gro file"""
     )
     parser.add_argument(
-        "-xtc", "--xtc_file", type=str, nargs=1, help="""My input .xtc file"""
+        "-xtc", "--xtc_file", type=str, help="""My input .xtc file"""
     )
     parser.add_argument(
-        "--gro_file_ext", type=str, nargs=1, help="""My input .gro file"""
+        "--gro_file_ext", type=str, help="""My input .gro file"""
     )
     parser.add_argument(
-        "--xtc_file_ext", type=str, nargs=1, help="""My input .xtc file"""
+        "--xtc_file_ext", type=str, help="""My input .xtc file"""
     )
     parser.add_argument(
         "-w", "--work_directory", type=str, default="./",
@@ -89,7 +89,7 @@
     parser.add_argument(
         "-od",
         "--output_directory",
-        default="stdout",
+        default="out/",
         type=str,
         nargs=1,
         help="""It's output Directory""",
@@ -125,7 +125,9 @@
         help="""3-letter pattern of the 4 amino acids of second ArR on HE""",
     )
     parser.add_argument("-o", "--output", help="""Output for files""")
-    parser.add_argument("-log", "--log_output", help="""Output for files""")
+    parser.add_argument("-log", "--log_output",
+                        default="log/calculate_pore_diameter_aqp.log",
+                        help="""Output for files""")
     return parser.parse_args()
 
 
@@ -982,43 +984,59 @@
 
 if __name__ == "__main__":
     args = parse_arguments()
-    out_file_name = "test"
-    file_name_log = out_file_name + ".log"
     if args.verbose:
-        if args.log_output:
-            if os.path.isfile(args.log_output):
-                os.remove(args.log_output)
-            logging.basicConfig(
-                filename=args.log_output,
-                format="%(levelname)s - %(message)s",
-                level=logging.INFO,
-            )
+        if len(os.path.dirname(args.log_output)) > 1:
+            log_dir = os.path.dirname(args.log_output)
         else:
-            if os.path.isfile(file_name_log):
-                os.remove(file_name_log)
-            logging.basicConfig(
-                filename=file_name_log,
-                format="%(levelname)s - %(message)s",
-                level=logging.INFO,
-            )
+            log_dir = "log/"
+        try:
+            os.makedirs(log_dir, exist_ok=True)
+        except OSError:
+            print("Directory '%s' can not be created")
+        if os.path.isfile(args.log_output):
+            os.remove(args.log_output)
+        logging.basicConfig(
+            filename=args.log_output,
+            format="%(levelname)s - %(message)s",
+            level=logging.INFO,
+        )
         logging.info("verbose mode on")
     gro_file = ''
     xtc_file = ''
     if args.gro_file:
-        gro_file = os.path.basename(args.gro_file[0])
-    else:
-        logging.critical("A .gro file must be provided")
-    if args.xtc_file:
-        xtc_file = os.path.basename(args.xtc_file[0])
+        gro_file = os.path.basename(args.gro_file)
+        if ".gro" not in gro_file:
+            if args.verbose:
+                logging.critical("-gro error: input is not .gro file")
+            print("-gro error: input is not .gro file")
+            sys.exit(1)
     else:
-        logging.critical("A .xtc file must be provided")
-    if args.work_directory:
-        work_directory = args.work_directory[0]
+        if args.verbose:
+            logging.critical("A .gro file must be provided")
+        print("A .gro file must be provided")
+        sys.exit(1)
+    if args.xtc_file:
+        xtc_file = os.path.basename(args.xtc_file)
+        if ".xtc" not in xtc_file:
+            if args.xtc_file_ext == "xtc":
+                xtc_file = xtc_file + ".xtc"
+            else:
+                if args.verbose:
+                    logging.critical("-xtc error: input is not .xtc file")
+                print("-xtc error: input is not .xtc file")
+                sys.exit(1)
     else:
-        work_directory = os.path.dirname(args.gro_file[0])
-        if not work_directory.endswith("/"):
-            work_directory += "/"
-    output_directory = args.output_directory[0]
+        if args.verbose:
+            logging.critical("A .xtc file must be provided")
+        print("A .xtc file must be provided")
+        sys.exit(1)
+    if len(os.path.dirname(args.gro_file)) > 1:
+        work_directory = os.path.dirname(args.gro_file)
+    else:
+        work_directory = args.work_directory
+    if not work_directory.endswith("/"):
+        work_directory += "/"
+    output_directory = args.output_directory
     if args.output:
         output = args.output
     else:
@@ -1026,31 +1044,27 @@
     os.chdir(work_directory)
     if args.gro_file_ext and args.xtc_file_ext:
         u = Mda.Universe(
-            args.gro_file[0],
-            args.xtc_file[0],
-            topology_format=args.gro_file_ext[0],
-            format=args.xtc_file_ext[0],
+            args.gro_file,
+            args.xtc_file,
+            topology_format=args.gro_file_ext,
+            format=args.xtc_file_ext,
         )
     else:
-        u = Mda.Universe(args.gro_file[0], args.xtc_file[0])
+        u = Mda.Universe(args.gro_file, args.xtc_file)
     if args.verbose:
         logging.info("Load universe : " + str(u))
+    resid_npa1 = None
+    resid_npa2 = None
+    resid_arr1 = None
+    resid_arr2 = None
     if args.npa_one:
         resid_npa1 = args.npa_one[0].split()
-    else:
-        resid_npa1 = args.npa_one
     if args.npa_second:
         resid_npa2 = args.npa_second[0].split()
-    else:
-        resid_npa2 = args.npa_second
     if args.arr_one:
         resid_arr1 = args.arr_one[0].split()
-    else:
-        resid_arr1 = args.arr_one
     if args.arr_second:
         resid_arr2 = args.arr_second[0].split()
-    else:
-        resid_arr2 = args.arr_second
     df_final = create_final_dataframe(resid_arr1, resid_arr2,
                                       resid_npa1, resid_npa2, u)
     if len(output_directory) > 2:
@@ -1062,5 +1076,5 @@
     if len(output) > 2:
         df_final.to_csv(output, sep="\t", index=False)
     else:
-        file_name_tabular = out_file_name + "PairDist.tabular"
+        file_name_tabular = "Calculate_pair_dist_aqp.tabular"
         df_final.to_csv(file_name_tabular, sep="\t", index=False)
diff -r a4097272ade0 -r 066606280457 test-data/.PIP2.1_test.xtc_offsets.npz
Binary file test-data/.PIP2.1_test.xtc_offsets.npz has changed
diff -r a4097272ade0 -r 066606280457 test-data/.XIP3.1_5_frames.xtc_offsets.npz
Binary file test-data/.XIP3.1_5_frames.xtc_offsets.npz has changed