--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ms_data_converter.py	Wed Mar 11 11:36:26 2015 -0400
@@ -0,0 +1,157 @@
+#!/usr/bin/env python
+import optparse
+import os
+import sys
+import tempfile
+import shutil
+import subprocess
+import re
+import logging
+
+assert sys.version_info[:2] >= (2, 6)
+
+log = logging.getLogger(__name__)
+working_directory = os.getcwd()
+tmp_stderr_name = tempfile.NamedTemporaryFile(dir=working_directory, suffix='.stderr').name
+tmp_stdout_name = tempfile.NamedTemporaryFile(dir=working_directory, suffix='.stdout').name
+
+
+def stop_err(msg):
+    sys.stderr.write("%s\n" % msg)
+    sys.exit()
+
+
+def read_stderr():
+    stderr = ''
+    if(os.path.exists(tmp_stderr_name)):
+        with open(tmp_stderr_name, 'rb') as tmp_stderr:
+            buffsize = 1048576
+            try:
+                while True:
+                    stderr += tmp_stderr.read(buffsize)
+                    if not stderr or len(stderr) % buffsize != 0:
+                        break
+            except OverflowError:
+                pass
+    return stderr
+
+
+def execute(command, stdin=None):
+    try:
+        with open(tmp_stderr_name, 'wb') as tmp_stderr:
+            with open(tmp_stdout_name, 'wb') as tmp_stdout:
+                proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ)
+                returncode = proc.wait()
+                if returncode != 0:
+                    raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr()))
+    finally:
+        print(( open(tmp_stderr_name, "r").read() ))
+        print(( open(tmp_stdout_name, "r").read() ))
+
+
+def delete_file(path):
+    if os.path.exists(path):
+        try:
+            os.remove(path)
+        except:
+            pass
+
+
+def delete_directory(directory):
+    if os.path.exists(directory):
+        try:
+            shutil.rmtree(directory)
+        except:
+            pass
+
+
+def symlink(source, link_name):
+    import platform
+    if platform.system() == 'Windows':
+        try:
+            import win32file
+            win32file.CreateSymbolicLink(source, link_name, 1)
+        except:
+            shutil.copy(source, link_name)
+    else:
+        os.symlink(source, link_name)
+
+
+def copy_to_working_directory(data_file, relative_path):
+    if os.path.abspath(data_file) != os.path.abspath(relative_path):
+        symlink(data_file, relative_path)
+    return relative_path
+
+
+def __main__():
+    run_script()
+
+#ENDTEMPLATE
+
+def str_to_bool(v):
+    """ From http://stackoverflow.com/questions/715417/converting-from-a-string-to-boolean-in-python """
+    return v.lower() in ["yes", "true", "t", "1"]
+
+def shellquote(s):
+    return '"' + s.replace('"', '\\"') + '"'
+
+def run_script():
+    parser = optparse.OptionParser()
+    parser.add_option('--input', dest='inputs', action='append', default=[])
+    parser.add_option('--input_name', dest='input_names', action='append', default=[])
+    parser.add_option('--implicit', dest='implicits', action='append', default=[], help='input files that should NOT be on the AB SCIEX MS Data Converter command line.')
+    parser.add_option('--output', dest='output')
+    parser.add_option('--fromextension', dest='fromextension')
+    parser.add_option('--toextension', dest='toextension', default='mzML', choices=['mzML', 'mgf'])
+    parser.add_option('--content_type', dest='content_type', default='centroid', choices=['profile', 'centroid', 'proteinpilot'])
+    parser.add_option('--binaryencoding', dest='binaryencoding', choices=['32', '64'])
+    parser.add_option('--zlib', dest='zlib', default="false")
+    parser.add_option('--index', dest='index', default="false")
+    parser.add_option('--debug', dest='debug', action='store_true', default=False)
+
+    (options, args) = parser.parse_args()
+    if len(options.inputs) < 1:
+        stop_err("No input files to ms_data_convert specified")
+    if len(options.input_names) > 0 and len(options.input_names) != len(options.inputs):
+        stop_err("Number(s) of supplied input names and input files do not match")
+    if not options.output:
+        stop_err("Must specify output location")
+    input_files = []
+    for i, input in enumerate(options.inputs):
+        input_base = None
+        if len(options.input_names) > i:
+            input_base = options.input_names[i]
+            input_base = input_base.replace("'", "").replace("\"", "")
+            print("1- input_base: %s" % input_base)
+        if not input_base:
+            input_base = 'input%s' % i
+            print("2- input_base: %s" % input_base)
+        if not input_base.lower().endswith(options.fromextension.lower()) and input not in options.implicits:
+            input_file = '%s.%s' % (input_base, options.fromextension)
+            print("3- input_base: %s" % input_base)
+            print("3- input_file: %s" % input_file)
+        else:
+            input_file = input_base
+            print("4- input_base: %s" % input_base)
+            print("4- input_file: %s" % input_file)
+        input_file = input_file
+        copy_to_working_directory(input, input_file)
+        if input not in options.implicits:
+            input_files.append(input_file)
+    ## AB_SCIEX_MS_Converter <input format> <input data> <output content type> <output format> <output file> [data compression setting] [data precision setting] [create index flag]
+    inputs_as_str = " ".join(['%s' % shellquote(input) for input in input_files])
+    output_file = re.sub('(%s)?$' % options.fromextension.lower(), options.toextension, input_files[0].lower())
+    cmd = "AB_SCIEX_MS_Converter %s %s %s %s %s" % (options.fromextension.upper(), inputs_as_str, options.content_type, options.toextension.upper(), output_file )
+    if str_to_bool(options.zlib):
+        cmd = "%s %s" % (cmd, "/zlib")
+    if options.binaryencoding:
+        cmd = "%s %s" % (cmd, "/singleprecision" if options.binaryencoding == '32' else "/doubleprecision")
+    if str_to_bool(options.zlib):
+        cmd = "%s %s" % (cmd, "/index")
+    if options.debug:
+        print(cmd)
+    execute(cmd)
+    shutil.copy(output_file, options.output)
+
+if __name__ == '__main__':
+    __main__()

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ms_data_converter.xml	Wed Mar 11 11:36:26 2015 -0400
@@ -0,0 +1,91 @@
+<tool id="ms_data_converter" name="MS Data Converter" version="1.3.0">
+  <!-- BEGIN_VERSION_DEFAULT -->
+  <description>for WIFF format using AB SCIEX MS Data Converter</description>
+  <!-- END_VERSION_DEFAULT -->
+  <!--
+  <requirements>
+    <requirement type="package" version="1.3beta">ab_sciex_ms_data_converter</requirement>
+  </requirements>
+-->
+  <command interpreter="python">
+    #import re
+    #import os.path
+    #set $ext = $input.ext
+    ms_data_converter.py
+    #set basename = 'absciex'
+    #if hasattr($input, 'display_name')
+        #set basename = $re.sub('\W','_',$input.display_name)
+    #end if
+    --input="${input.extra_files_path}/wiff"
+    --input_name="${basename}.wiff"
+    #if $os.path.exists($os.path.join($input.extra_files_path,'wiff_scan')):
+      --implicit="${input.extra_files_path}/wiff_scan"
+      --input="${input.extra_files_path}/wiff_scan"
+      --input_name="${basename}.wiff.scan"
+    #end if
+    #if $os.path.exists($os.path.join($input.extra_files_path,'wiff_mtd')):
+      --implicit="${input.extra_files_path}/wiff_mtd"
+      --input="${input.extra_files_path}/wiff_mtd"
+      --input_name="${basename}.wiff.mtd"
+    #end if
+    --output=${output}
+    ## BEGIN_VERSION_DEFAULT
+    --fromextension=$ext
+    --content_type=$content_type
+    ## END_VERSION_DEFAULT
+    --toextension=${result.output_format}
+    #if $result.output_format == "mzML"
+    --zlib=${result.zlib}
+    --binaryencoding=${result.precision}
+    --index=${result.index}
+    #end if
+  </command>
+
+  <inputs>
+
+    <!-- BEGIN_VERSION_DEFAULT -->
+    <param format="wiff" name="input" type="data" label="Input wiff"/>
+    <!-- END_VERSION_DEFAULT -->
+    <conditional name="result">
+        <param name="output_format" type="select" label="Output Format">
+            <option value="mzML">mzML</option>
+            <option value="mgf">mgf</option>
+        </param>
+        <when value="mzML">
+            <param type="boolean" name="index" truevalue="true" falsevalue="false" checked="true" label="Index the mzML output"/>
+            <param type="boolean" name="zlib" truevalue="true" falsevalue="false" checked="true" label="Binary zlib array compression"/>
+            <param type="select" name="precision" label="Precision">
+                <option value="32">32</option>
+                <option value="64" selected="true">64</option>
+            </param>
+        </when>
+        <when value="mgf"/>
+    </conditional>
+    <param name="content_type" type="select" label="Output Content Type">
+      <option value="profile">profile</option>
+      <option value="centroid">centroid</option>
+      <option value="proteinpilot">proteinpilot</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="mzml" name="output">
+      <change_format>
+        <when input="output_format" value="mgf" format="mgf" />
+      </change_format>
+    </data>
+  </outputs>
+  <help>
+**What it does**
+
+AB SCIEX MS Data Converter to convert mass spectral data from any AB SCIEX instrument into open data formats. Data can be converted into two different formats - mzML or mgf. You can also control what kind of information is written. You can choose to get an exact translation of what the instrument recorded or choose to convert to a processed version, reducing the data down to peak lists.
+
+http://www.absciex.com/Documents/Downloads/Software/ABSCIEX-MS%20Data-Converter-User-Guide.pdf
+
+------
+
+**Citation**
+
+If you use this tool in Galaxy, please cite Chilton J, et al. https://github.com/galaxyproteomics/
+
+  </help>
+</tool>