Minor fixes to new ccat-format script. Updated yaml for new arguments.

chipathlon/jobs/params/ccat_format_bed.yaml

@@ -10,13 +10,13 @@ ccat_format_bed:
       file_type: bed
   command: chip-job-ccat-format-bed
   arguments:
-    - "-c":
+    - "--input":
         type: file
         changeable: false
         required: true
         has_value: true
         default: $inputs.0
-    - "-b":
+    - "--output":
         type: file
         changeable: false
         required: true

scripts/chip-job-ccat-format-bed

@@ -12,7 +12,7 @@ import argparse
 # chr1    3318040 3318245 ccat_1  4   .   5.483551    0.577000    0.001
 # chr1    3372210 3372465 ccat_2  5   .   6.854439    0.462000    0.001
 
-parser = argpasre.ArgumentParser(description = "Format ccat result files.")
+parser = argparse.ArgumentParser(description = "Format ccat result files.")
 parser.add_argument("--input", "-i", dest="input", required=True, help="Path to input ccat file.")
 parser.add_argument("--output", "-o", dest="output", required=True, help="Output file to write formatted results.")
 args = parser.parse_args()
@@ -30,4 +30,4 @@ with open(args.output, "w") as wh:
 	for i, line in enumerate(sorted_data):
 		# Fix the peak numbers
 		line[3] = "ccat_%s" % (i,)
-		wh.write(line + "\n")
+		wh.write("\t".join(line) + "\n")