diff bismark2report_wrapper.py @ 38:b2d0e92f81c2 draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"

--- a/bismark2report_wrapper.py	Fri Oct 04 11:33:01 2019 -0400
+++ b/bismark2report_wrapper.py	Thu Apr 22 17:05:07 2021 +0000
@@ -12,30 +12,68 @@
 
 
 def log_subprocess_output(logger, pipe):
-    for line in iter(pipe.readline, b''):
+    for line in iter(pipe.readline, b""):
         logger.debug(line.decode().rstrip())
 
 
 def get_arg():
     parser = argparse.ArgumentParser()
-    parser.add_argument('--alignment_report', dest='alignment_report', action='store', metavar='alignment_report',
-                        type=str)
-    parser.add_argument('--dedup_report', dest='dedup_report', action='store', metavar='dedup_report', type=str)
-    parser.add_argument('--splitting_report', dest='splitting_report', action='store', metavar='splitting_report',
-                        type=str)
-    parser.add_argument('--mbias_report', dest='mbias_report', action='store', metavar='mbias_report', type=str)
-    parser.add_argument('--nucleotide_report', dest='nucleotide_report', action='store', metavar='nucleotide_report',
-                        type=str)
-    parser.add_argument('--output_html_report', dest='output_html_report', action='store', metavar='output_html_report',
-                        type=str)
-    parser.add_argument('--log_report', dest='log_report', action='store', metavar='log_report', type=str)
+    parser.add_argument(
+        "--alignment_report",
+        dest="alignment_report",
+        action="store",
+        metavar="alignment_report",
+        type=str,
+    )
+    parser.add_argument(
+        "--dedup_report",
+        dest="dedup_report",
+        action="store",
+        metavar="dedup_report",
+        type=str,
+    )
+    parser.add_argument(
+        "--splitting_report",
+        dest="splitting_report",
+        action="store",
+        metavar="splitting_report",
+        type=str,
+    )
+    parser.add_argument(
+        "--mbias_report",
+        dest="mbias_report",
+        action="store",
+        metavar="mbias_report",
+        type=str,
+    )
+    parser.add_argument(
+        "--nucleotide_report",
+        dest="nucleotide_report",
+        action="store",
+        metavar="nucleotide_report",
+        type=str,
+    )
+    parser.add_argument(
+        "--output_html_report",
+        dest="output_html_report",
+        action="store",
+        metavar="output_html_report",
+        type=str,
+    )
+    parser.add_argument(
+        "--log_report",
+        dest="log_report",
+        action="store",
+        metavar="log_report",
+        type=str,
+    )
     args = parser.parse_args()
     return args
 
 
 def __main__():
     args = get_arg()
-    logger = logging.getLogger('bismark_deduplicate_wrapper')
+    logger = logging.getLogger("bismark_deduplicate_wrapper")
     logger.setLevel(logging.DEBUG)
     ch = logging.StreamHandler(sys.stdout)
     if args.log_report:
@@ -47,17 +85,23 @@
         ch.setLevel(logging.DEBUG)
     logger.addHandler(ch)
 
-    cmd = ['bismark2report', '--verbose', '--alignment_report', args.alignment_report,
-           '--output', args.output_html_report]
+    cmd = [
+        "bismark2report",
+        "--verbose",
+        "--alignment_report",
+        args.alignment_report,
+        "--output",
+        args.output_html_report,
+    ]
 
     if args.dedup_report:
-        cmd.extend(['--dedup_report', args.dedup_report])
+        cmd.extend(["--dedup_report", args.dedup_report])
     if args.splitting_report:
-        cmd.extend(['--splitting_report', args.splitting_report])
+        cmd.extend(["--splitting_report", args.splitting_report])
     if args.mbias_report:
-        cmd.extend(['--mbias_report', args.mbias_report])
+        cmd.extend(["--mbias_report", args.mbias_report])
     if args.nucleotide_report:
-        cmd.extend(['--nucleotide_report', args.nucleotide_report])
+        cmd.extend(["--nucleotide_report", args.nucleotide_report])
 
     logger.info("Generating report with: '%s'", " ".join(cmd))
     process = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
@@ -65,7 +109,12 @@
         log_subprocess_output(logger, process.stdout)
     exitcode = process.wait()
     if exitcode != 0:
-        stop_err(logger, "Bismark pretty report error (also check the log file if any)!\n%s" % process.stderr)
+        stop_err(
+            logger,
+            "Bismark pretty report error (also check the log file if any)!\n%s"
+            % process.stderr,
+        )
 
 
-if __name__ == "__main__": __main__()
+if __name__ == "__main__":
+    __main__()