Mercurial > repos > bgruening > bismark

diff bismark_methylation_extractor.py @ 22:8c191acde702 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 3005cec91ca52f9d28aa2fe0bd4190555abafc35
author: bgruening
date: Tue, 01 Aug 2023 11:42:10 +0000
parents: 120b7b35e442
--- a/bismark_methylation_extractor.py	Thu Apr 22 17:05:46 2021 +0000
+++ b/bismark_methylation_extractor.py	Tue Aug 01 11:42:10 2023 +0000
@@ -69,6 +69,8 @@
     parser.add_argument("--splitting_report", dest="splitting_report")
     parser.add_argument("--mbias_report", dest="mbias_report")
     parser.add_argument("--cytosine_report", dest="cytosine_report")
+    parser.add_argument("--coverage_file", dest="coverage_file")
+
     parser.add_argument("--genome_file", dest="genome_file")
     parser.add_argument("--cx_context", action="store_true")
 
@@ -133,7 +135,6 @@
                     "--bedGraph",
                     "--CX_context",
                     "--cytosine_report",
-                    "--CX_context",
                     "--genome_folder",
                     tmp_genome_dir,
                 ]
@@ -175,11 +176,20 @@
                 glob(os.path.join(output_dir, "*CX_report.txt"))[0],
                 args.cytosine_report,
             )
+
         else:
             shutil.move(
                 glob(os.path.join(output_dir, "*CpG_report.txt"))[0],
                 args.cytosine_report,
             )
+
+    # coverage file
+    if args.coverage_file:
+        shutil.move(
+            glob(os.path.join(output_dir, "*datbismark.cov.gz"))[0],
+            args.coverage_file,
+        )
+
     # splitting report
     if args.splitting_report:
         logger.debug("Collecting splitting report.")