Mercurial > repos > galaxyp > msconvert

annotate msconvert_wrapper.py @ 4:158a71ee5733 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
author galaxyp
date Wed, 07 Dec 2016 17:43:19 -0500
parents ab59b1826345
children 637e309295cf
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
1 #!/usr/bin/env python
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
2 import optparse
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
3 import os
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
4 import sys
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
5 import tempfile
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
6 import shutil
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
7 import subprocess
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
8 import re
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
9 import logging
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
10
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
11 assert sys.version_info[:2] >= (2, 6)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
12
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
13 log = logging.getLogger(__name__)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
14 working_directory = os.getcwd()
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
15 tmp_stderr_name = tempfile.NamedTemporaryFile(dir=working_directory, suffix='.stderr').name
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
16 tmp_stdout_name = tempfile.NamedTemporaryFile(dir=working_directory, suffix='.stdout').name
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
17
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
18
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
19 def stop_err(msg):
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
20 sys.stderr.write("%s\n" % msg)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
21 sys.exit()
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
22
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
23
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
24 def read_stderr():
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
25 stderr = ''
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
26 if(os.path.exists(tmp_stderr_name)):
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
27 with open(tmp_stderr_name, 'rb') as tmp_stderr:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
28 buffsize = 1048576
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
29 try:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
30 while True:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
31 stderr += tmp_stderr.read(buffsize)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
32 if not stderr or len(stderr) % buffsize != 0:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
33 break
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
34 except OverflowError:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
35 pass
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
36 return stderr
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
37
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
38
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
39 def execute(command, stdin=None):
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
40 try:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
41 with open(tmp_stderr_name, 'wb') as tmp_stderr:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
42 with open(tmp_stdout_name, 'wb') as tmp_stdout:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
43 proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
44 returncode = proc.wait()
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
45 if returncode != 0:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
46 raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr()))
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
47 finally:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
48 print(( open(tmp_stderr_name, "r").read() ))
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
49 print(( open(tmp_stdout_name, "r").read() ))
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
50
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
51
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
52 def delete_file(path):
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
53 if os.path.exists(path):
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
54 try:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
55 os.remove(path)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
56 except:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
57 pass
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
58
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
59
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
60 def delete_directory(directory):
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
61 if os.path.exists(directory):
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
62 try:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
63 shutil.rmtree(directory)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
64 except:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
65 pass
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
66
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
67
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
68 def symlink(source, link_name):
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
69 import platform
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
70 if platform.system() == 'Windows':
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
71 try:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
72 import win32file
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
73 win32file.CreateSymbolicLink(source, link_name, 1)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
74 except:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
75 shutil.copy(source, link_name)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
76 else:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
77 os.symlink(source, link_name)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
78
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
79
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
80 def copy_to_working_directory(data_file, relative_path):
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
81 if os.path.abspath(data_file) != os.path.abspath(relative_path):
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
82 symlink(data_file, relative_path)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
83 return relative_path
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
84
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
85
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
86 def __main__():
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
87 run_script()
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
88
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
89 #ENDTEMPLATE
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
90
4
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents: 0
diff changeset
91 to_extensions = ['mzML', 'mzXML', 'unindexed_mzML', 'unindexed_mzXML', 'mgf', 'mz5', 'txt', 'ms2', 'cms2']
0
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
92
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
93
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
94 def str_to_bool(v):
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
95 """ From http://stackoverflow.com/questions/715417/converting-from-a-string-to-boolean-in-python """
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
96 return v.lower() in ["yes", "true", "t", "1"]
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
97
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
98
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
99 def _add_filter(filters_file, contents):
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
100 filters_file.write("filter=%s\n" % contents)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
101
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
102
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
103 def _skip_line(options, file_num, line_parts):
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
104 file_num_column = options.filter_table_file_column
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
105 if not file_num_column:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
106 return False
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
107 else:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
108 target_file_num_val = str(file_num).strip()
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
109 query_file_num_val = line_parts[int(file_num_column) - 1].strip()
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
110 #print "target %s, query %s" % (target_file_num_val, query_file_num_val)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
111 return target_file_num_val != query_file_num_val
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
112
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
113
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
114 def _read_table_numbers(path, options, file_num=None):
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
115 unique_numbers = set([])
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
116 column_num = options.filter_table_column
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
117 input = open(path, "r")
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
118 first_line = True
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
119 for line in input:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
120 if not line:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
121 continue
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
122 line = line.strip()
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
123 if line.startswith("#"):
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
124 first_line = False
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
125 continue
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
126 if column_num == None:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
127 column = line
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
128 else:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
129 line_parts = line.split("\t")
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
130 if _skip_line(options, file_num, line_parts):
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
131 continue
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
132 column = line_parts[int(column_num) - 1]
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
133 match = re.match("\d+", column)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
134 if match:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
135 unique_numbers.add(int(match.group()))
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
136 first_line = False
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
137 return unique_numbers
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
138
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
139
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
140 def shellquote(s):
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
141 return '"' + s.replace('"', '\\"') + '"'
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
142
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
143
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
144 def _add_filter_line_from_file(filter_file, options, file_num=None):
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
145 file = options.filter_table
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
146 if not file:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
147 return
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
148 numbers = _read_table_numbers(file, options, file_num)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
149 msconvert_int_set = " ".join([str(number) for number in numbers])
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
150 filter_type = options.filter_table_type
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
151 if filter_type == 'number':
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
152 filter_prefix = 'scanNumber'
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
153 else:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
154 filter_prefix = 'index'
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
155 _add_filter(filter_file, "%s %s" % (filter_prefix, msconvert_int_set))
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
156
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
157
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
158 def _create_filters_file(options, file_num=None, debug=False):
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
159 suffix = "" if not file_num else str(file_num)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
160 filters_file_path = "filters%s" % suffix
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
161 filters_file = open(filters_file_path, "w")
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
162 if options.filters_file:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
163 filters_file.write(open(options.filters_file, "r").read())
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
164 for filter in options.filter:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
165 _add_filter(filters_file, filter)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
166 _add_filter_line_from_file(filters_file, options, file_num=file_num)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
167
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
168 filters_file.close()
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
169 if debug:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
170 print(( open(filters_file_path, "r").read() ))
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
171 return filters_file_path
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
172
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
173
4
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents: 0
diff changeset
174 def _build_base_cmd(options,args=None):
0
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
175 to_extension = options.toextension
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
176 if to_extension.startswith("unindexed_"):
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
177 to_extension = to_extension[len("unindexed_"):]
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
178 to_params = "--noindex"
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
179 else:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
180 to_params = ""
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
181 cmd = "msconvert --%s %s" % (to_extension, to_params)
4
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents: 0
diff changeset
182 if args:
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents: 0
diff changeset
183 cmd = "%s %s" % (cmd, ' '.join(args))
0
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
184 if str_to_bool(options.zlib):
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
185 cmd = "%s %s" % (cmd, "--zlib")
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
186 if options.binaryencoding:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
187 cmd = "%s --%s" % (cmd, options.binaryencoding)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
188 if options.mzencoding:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
189 cmd = "%s --mz%s" % (cmd, options.mzencoding)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
190 if options.intensityencoding:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
191 cmd = "%s --inten%s" % (cmd, options.intensityencoding)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
192 return cmd
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
193
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
194
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
195 def _run(base_cmd, output_dir='output', inputs=[], debug=False):
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
196 inputs_as_str = " ".join(['%s' % shellquote(input) for input in inputs])
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
197 os.mkdir(output_dir)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
198 cmd = "%s -o %s %s" % (base_cmd, shellquote(output_dir), inputs_as_str)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
199 if debug:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
200 print(cmd)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
201 execute(cmd)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
202 output_files = os.listdir(output_dir)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
203 assert len(output_files) == 1
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
204 output_file = output_files[0]
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
205 return os.path.join(output_dir, output_file)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
206
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
207
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
208 def run_script():
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
209 parser = optparse.OptionParser()
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
210 parser.add_option('--input', dest='inputs', action='append', default=[])
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
211 parser.add_option('--input_name', dest='input_names', action='append', default=[])
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
212 parser.add_option('--implicit', dest='implicits', action='append', default=[], help='input files that should NOT be on the msconvert command line.')
4
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents: 0
diff changeset
213 parser.add_option('--ident', dest='idents', action='append', default=[])
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents: 0
diff changeset
214 parser.add_option('--ident_name', dest='ident_names', action='append', default=[])
0
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
215 parser.add_option('--output', dest='output')
4
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents: 0
diff changeset
216 parser.add_option('--refinement', dest='refinement')
0
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
217 parser.add_option('--fromextension', dest='fromextension')
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
218 parser.add_option('--toextension', dest='toextension', default='mzML', choices=to_extensions)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
219 parser.add_option('--binaryencoding', dest='binaryencoding', choices=['32', '64'])
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
220 parser.add_option('--mzencoding', dest='mzencoding', choices=['32', '64'])
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
221 parser.add_option('--intensityencoding', dest='intensityencoding', choices=['32', '64'])
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
222 parser.add_option('--zlib', dest='zlib', default="false")
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
223 parser.add_option('--filter', dest='filter', action='append', default=[])
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
224 parser.add_option('--filters_file', dest='filters_file', default=None)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
225 parser.add_option('--filter_table', default=None)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
226 parser.add_option('--filter_table_type', default='index', choices=['index', 'number'])
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
227 parser.add_option('--filter_table_column', default=None)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
228 parser.add_option('--filter_table_file_column', default=None)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
229 parser.add_option('--debug', dest='debug', action='store_true', default=False)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
230
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
231 (options, args) = parser.parse_args()
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
232 if len(options.inputs) < 1:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
233 stop_err("No input files to msconvert specified")
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
234 if len(options.input_names) > 0 and len(options.input_names) != len(options.inputs):
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
235 stop_err("Number(s) of supplied input names and input files do not match")
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
236 if not options.output:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
237 stop_err("Must specify output location")
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
238 input_files = []
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
239 for i, input in enumerate(options.inputs):
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
240 input_base = None
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
241 if len(options.input_names) > i:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
242 input_base = options.input_names[i]
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
243 input_base = input_base.replace("'", "").replace("\"", "")
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
244 print("1- input_base: %s" % input_base)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
245 if not input_base:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
246 input_base = 'input%s' % i
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
247 print("2- input_base: %s" % input_base)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
248 if not input_base.lower().endswith('.%s' % options.fromextension.lower()) and input not in options.implicits:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
249 input_file = '%s.%s' % (input_base, options.fromextension)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
250 print("3- input_base: %s" % input_base)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
251 print("3- input_file: %s" % input_file)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
252 else:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
253 input_file = input_base
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
254 print("4- input_base: %s" % input_base)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
255 print("4- input_file: %s" % input_file)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
256 input_file = input_file
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
257 copy_to_working_directory(input, input_file)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
258 if input in options.implicits:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
259 continue
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
260 input_files.append(input_file)
4
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents: 0
diff changeset
261 for i, ident in enumerate(options.idents):
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents: 0
diff changeset
262 ident_file = options.ident_names[i]
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents: 0
diff changeset
263 copy_to_working_directory(ident, ident_file)
0
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
264
4
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents: 0
diff changeset
265 cmd = _build_base_cmd(options,args=args)
0
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
266 file_column = options.filter_table_file_column
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
267 if not file_column:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
268 # Apply same filters to all files, just create a unviersal filter files
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
269 # and run msconvert once.
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
270 filters_file_path = _create_filters_file(options, debug=options.debug)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
271 cmd = "%s -c %s" % (cmd, filters_file_path)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
272 else:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
273 # Dispatching on a column to filter different files differently, need to filter
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
274 # each input once with msconvert and then merge once.
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
275 filtered_files = []
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
276 for index, input_file in enumerate(input_files):
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
277 filters_file_path = _create_filters_file(options, index + 1, debug=options.debug)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
278 filter_cmd = "%s -c %s" % (cmd, filters_file_path)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
279 filtered_output_file = _run(filter_cmd, output_dir='output%d' % index, inputs=[input_file], debug=options.debug)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
280 filtered_files.append(filtered_output_file)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
281 input_files = filtered_files
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
282 if len(input_files) > 1:
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
283 cmd = "%s --merge" % cmd
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
284 output_file = _run(cmd, output_dir='output', inputs=input_files, debug=options.debug)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
285 shutil.copy(output_file, options.output)
4
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents: 0
diff changeset
286 if options.refinement:
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents: 0
diff changeset
287 # .mzRefinement.tsv
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents: 0
diff changeset
288 files = os.listdir(os.getcwd())
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents: 0
diff changeset
289 for fname in files:
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents: 0
diff changeset
290 if fname.endswith('.mzRefinement.tsv'):
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents: 0
diff changeset
291 shutil.copy(fname, options.refinement)
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents: 0
diff changeset
292 break
0
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
293
4
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents: 0
diff changeset
294 def __main__():
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents: 0
diff changeset
295 run_script()
0
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
296
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
297 if __name__ == '__main__':
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff changeset
298 __main__()