# HG changeset patch
# User earlhaminst
# Date 1631286486 0
# Node ID 07f5b2c5ac1090b726706aafebe8f05723055c72
# Parent  02d73e6ca86919a17877ef911e921b2be5b4f54e
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e015ac3e0d8c1bc62b1301527241ee5e377b91db"

diff -r 02d73e6ca869 -r 07f5b2c5ac10 hcluster_sg_parser.py
--- a/hcluster_sg_parser.py	Fri Jul 19 11:44:07 2019 -0400
+++ b/hcluster_sg_parser.py	Fri Sep 10 15:08:06 2021 +0000
@@ -5,9 +5,10 @@
 
 Usage:
 
-python hcluster_sg_parser.py [-m <N>] [-M <N>] <file> <discarded_out>
+python hcluster_sg_parser.py [-m <N>] [-M <N>] <file> <discarded_min_out> <discarded_max_out>
 """
 import optparse
+import os
 import sys
 
 
@@ -15,8 +16,11 @@
     parser = optparse.OptionParser()
     parser.add_option('-m', '--min', type='int', default=0, help='Minimum number of cluster elements')
     parser.add_option('-M', '--max', type='int', default=sys.maxsize, help='Maximum number of cluster elements')
+    parser.add_option('-d', '--dir', type='string', help="Absolute or relative path to output directory. If the directory does not exist, it will be created")
     options, args = parser.parse_args()
 
+    if options.dir and not os.path.exists(options.dir):
+        os.mkdir(options.dir)
     with open(args[2], 'w') as discarded_max_out:
         with open(args[1], 'w') as discarded_min_out:
             with open(args[0]) as fh:
@@ -32,6 +36,8 @@
                         discarded_max_out.write(id_list)
                     else:
                         outfile = cluster_id + '_output.txt'
+                        if options.dir:
+                            outfile = os.path.join(options.dir, outfile)
                         with open(outfile, 'w') as f:
                             f.write(id_list)