diff hardklor.py @ 0:d796e6613d19 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hardklor.py	Mon May 23 11:12:40 2016 -0400
@@ -0,0 +1,62 @@
+"""
+Usage:
+python hardklor.py ms1extenstion ms2extension ms1file
+ms2file outputfile
+"""
+import sys
+import os
+import subprocess
+
+
+CONFIG_FILE = 'hk.conf'
+extension_lookup = {
+    'mzml'  :   'mzML',
+    'mzxml' :   'mzXML',
+    'ms1'   :   'MS1',
+    }
+
+# input:
+ms1_ext = sys.argv[1]
+ms1_file = sys.argv[2]
+output_file = sys.argv[3]
+config_load = os.path.join(os.path.split(sys.argv[0])[0], 'hardklor.conf')
+
+# parse options
+options = {}
+for arg in [x.split('=') for x in sys.argv[4:]]:
+    if arg[1] != '':
+        options[arg[0].replace('-', '')] = arg[1]
+
+
+# create softlinks since hardklor needs "proper" extensions for input files
+if ms1_ext in extension_lookup:
+    ms1_ext = extension_lookup[ms1_ext]
+    linkname = 'ms1_dsetlink.{0}'.format(ms1_ext)
+    os.symlink(ms1_file, linkname)
+    ms1_file = linkname 
+
+# load template and dump to config file
+with open(config_load) as fp:
+    config_str = fp.read()
+config_to_dump = config_str.format(
+    instrument=options['instrument'],
+    resolution=options['resolution'],
+    centroided=options['centroided'],
+    mslvl=options['mslvl'],
+    depth=options['depth'],
+    algorithm=options['algorithm'],
+    charge_algo=options['charge_algo'],
+    mincharge=options['mincharge'],
+    maxcharge=options['maxcharge'],
+    correlation=options['correlation'],
+    sensitivity=options['sensitivity'],
+    maxfeat=options['maxfeat'],
+    inputfile=ms1_file,
+    outputfile=output_file,
+    )
+with open(CONFIG_FILE, 'w') as fp:
+    fp.write(config_to_dump)
+
+# Run hardklor
+err = subprocess.call(['hardklor', CONFIG_FILE])
+sys.exit(err)