# HG changeset patch
# User galaxyp
# Date 1355895145 18000
# Node ID ba86fd127f5af8d10647fad4f616c170a6cce12e
Uploaded
diff -r 000000000000 -r ba86fd127f5a LICENSE
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE Wed Dec 19 00:32:25 2012 -0500
@@ -0,0 +1,202 @@
+
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diff -r 000000000000 -r ba86fd127f5a README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md Wed Dec 19 00:32:25 2012 -0500
@@ -0,0 +1,23 @@
+TODO: Document this tool repository.
+# Obtaining Tools
+
+Repositories for all Galaxy-P tools can be found at
+https:/bitbucket.org/galaxyp/.
+
+# Contact
+
+Please send suggestions for improvements and bug reports to
+jmchilton@gmail.com.
+
+# License
+
+All Galaxy-P tools are licensed under the Apache License Version 2.0
+unless otherwise documented.
+
+# Tool Versioning
+
+Galaxy-P tools will have versions of the form X.Y.Z. Versions
+differing only after the second decimal should be completely
+compatible with each other. Breaking changes should result in an
+increment of the number before and/or after the first decimal. All
+tools of version less than 1.0.0 should be considered beta.
diff -r 000000000000 -r ba86fd127f5a README_GALAXYP.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README_GALAXYP.md Wed Dec 19 00:32:25 2012 -0500
@@ -0,0 +1,22 @@
+# Obtaining Tools
+
+Repositories for all Galaxy-P tools can be found at
+https:/bitbucket.org/galaxyp/.
+
+# Contact
+
+Please send suggestions for improvements and bug reports to
+jmchilton@gmail.com.
+
+# License
+
+All Galaxy-P tools are licensed under the Apache License Version 2.0
+unless otherwise documented.
+
+# Tool Versioning
+
+Galaxy-P tools will have versions of the form X.Y.Z. Versions
+differing only after the second decimal should be completely
+compatible with each other. Breaking changes should result in an
+increment of the number before and/or after the first decimal. All
+tools of version less than 1.0.0 should be considered beta.
diff -r 000000000000 -r ba86fd127f5a README_REPO.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README_REPO.md Wed Dec 19 00:32:25 2012 -0500
@@ -0,0 +1,25 @@
+# OpenMS
+
+This repository is in an early alpha state and many OpenMS tools are
+not yet available or are largely untested. If there is a tool that is
+part of OpenMS but not available here, let John Chilton
+(jmchilton@gmail.com) and he will try to add it.
+
+These tools require Galaxy to be equipped with common proteomic
+datatypes. These can be obtained by installing Ira Cooke's ProtK via
+the tool shed or merging the changesets from the following repository
+into your Galaxy instance:
+
+ https://bitbucket.org/galaxyp/galaxy-dist-proteomics
+
+# Installing
+
+These tools all require OpenMS and may require other dependencies
+(such as PepNovo for instance).
+
+For Galaxy-P we are installing this tool via CloudBioLinux
+(https://github.com/jmchilton/cloudbiolinux/blob/proteomics/cloudbio/custom/bio\
+_proteomics.py). While
+this fabric script may not be exactly appropriate for your environment
+it may serve as a template for how to install this software.
+
diff -r 000000000000 -r ba86fd127f5a baseline_filter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/baseline_filter.xml Wed Dec 19 00:32:25 2012 -0500
@@ -0,0 +1,37 @@
+
+
+ Executes the top-hat filter to remove the baseline of an MS experiment.
+
+
+ openms
+
+
+ openms_wrapper.py --executable 'BaselineFilter' --config $config
+
+
+ [simple_options]
+in=${in}
+out=${out}
+
+
+
+
+
+
+
+
+
+**What it does**
+
+This nonlinear filter, known as the top-hat operator in morphological mathematics (see Soille, ''Morphological Image Analysis''), is independent of the underlying baseline shape. It is able to detect an over brightness even if the environment is not uniform. The principle is based on the subtraction of a signal from its opening (erosion followed by a dilation). The size the structuring element (here a flat line) being conditioned by the width of the lineament (in our case the maximum width of a mass spectrometric peak) to be detected.
+
+http://ftp.mi.fu-berlin.de/OpenMS/doc-1.9-official/html/TOPP_BaselineFilter.html
+http://ftp.mi.fu-berlin.de/OpenMS/doc-1.9-official/html/TOPP_example_signalprocessing.html#TOPP_example_signalprocessing_parameters
+
+**Citation**
+
+For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.``
+
+If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
+
+
diff -r 000000000000 -r ba86fd127f5a file_info.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/file_info.xml Wed Dec 19 00:32:25 2012 -0500
@@ -0,0 +1,44 @@
+
+
+ Shows basic information about the file, such as data ranges and file type.
+
+
+ openms
+
+
+ openms_wrapper.py --executable 'FileInfo' --config $config
+
+
+ [simple_options]
+m=${m}
+p=${p}
+s=${s}
+d=${d}
+in=${in}
+in_type=${in.ext}
+out=${out}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+
+Shows basic information about the file, such as data ranges and file type.
+
+**Citation**
+
+For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.``
+
+If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
+
+
diff -r 000000000000 -r ba86fd127f5a high_res_precursosr_mass_corrector.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/high_res_precursosr_mass_corrector.xml Wed Dec 19 00:32:25 2012 -0500
@@ -0,0 +1,34 @@
+
+
+precursor m/z correction on picked (centroided) high resolution data.
+
+
+ openms
+
+
+ [simple_options]
+in=${input}
+out=${out}
+
+
+
+ openms_wrapper.py -executable 'HighResPrecursorMassCorrector' -config $config
+
+
+
+
+
+
+
+
+**What it does**
+
+This tool performs precursor mz correction on picked (=centroided) high resolution data.
+
+**Citation**
+
+For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.``
+
+If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
+
+
diff -r 000000000000 -r ba86fd127f5a id_file_converter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/id_file_converter.xml Wed Dec 19 00:32:25 2012 -0500
@@ -0,0 +1,48 @@
+
+
+ Converts identification engine file formats.
+
+
+ openms
+
+
+ openms_wrapper.py --executable 'IDFileConverter' --config $config
+
+
+ [simple_options]
+in=${in}
+in_type=${in.ext}
+out=${out}
+out_type=${output_type}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+
+Shows basic information about the file, such as data ranges and file type.
+
+**Citation**
+
+For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.``
+
+If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
+
+
diff -r 000000000000 -r ba86fd127f5a id_merger.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/id_merger.xml Wed Dec 19 00:32:25 2012 -0500
@@ -0,0 +1,44 @@
+
+
+ Merges several idXML files into one idXML file.
+
+
+ openms
+
+
+ openms_wrapper.py --executable 'IDMerger' --config $config
+
+
+ [simple_options]
+#set $in_str = ""
+#for $input in $inputs
+#set $in_str = $input.input + " " $in_str
+#end for
+in="${in_str}"
+out=${out}
+annotate_file_origin=${annotate_file_origin}
+
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+
+The peptide hits and protein hits of the input files will be written into the single output file. In general, the number of idXML files that can be merged into one file is not limited.
+
+The combination of search engine and processing date/time should be unique for every identification run over all input files. If this is not the case, the date/time of a conflicting run will be increased in steps of seconds until the combination is unique.
+
+**Citation**
+
+For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.``
+
+If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
+
+
diff -r 000000000000 -r ba86fd127f5a idxml_exporter.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/idxml_exporter.py Wed Dec 19 00:32:25 2012 -0500
@@ -0,0 +1,68 @@
+from xml.sax import make_parser, ContentHandler
+from optparse import OptionParser
+
+
+def main():
+ (options, _) = _parse_args()
+ with open(options.output, "w") as out:
+ parser = make_parser()
+ handler = _get_handler(options, out)
+ parser.setContentHandler(handler)
+ parser.parse(open(options.input, "r"))
+
+
+def _get_handler(option, out):
+ return PeptideHandler(out)
+
+
+class PeptideHandler(ContentHandler):
+ record_values = {
+ "IdentificationRun": ["search_engine"],
+ "PeptideIdentification": ["score_type", "significance_threshold", "MZ", "RT"],
+ "PeptideHit": ["score", "sequence", "charge"],
+ }
+
+ def __init__(self, output):
+ self.output = output
+
+ def __record_values(self, keys, attrs):
+ for key in keys:
+ setattr(self, key, attrs.get(key, None))
+
+ def startElement(self, name, attrs):
+ self._set_attributes(name, attrs)
+
+ def endElement(self, name):
+ if name == "PeptideHit":
+ self._write_peptide()
+ # reset values for element
+ self._set_attributes(name, {})
+
+ def _write_peptide(self):
+ col_keys = ["score", "peptide", "score_type", "charge", "MZ", "RT"]
+ row_values = self._get_values(col_keys)
+ row = "\t".join(row_values)
+ self._write_line(row)
+
+ def _write_line(self, line):
+ self.output.write(line)
+ self.output.write("\n")
+
+ def _get_values(self, keys):
+ return [getattr(self, key, "") for key in keys]
+
+ def _set_attributes(self, name, attrs):
+ for element_name, element_attributes in self.record_values.iteritems():
+ if name == element_name:
+ self.__record_values(element_attributes, attrs)
+
+
+def _parse_args():
+ parser = OptionParser()
+ parser.add_option("--input", dest="input")
+ parser.add_option("--output", dest="output")
+ parser.add_option("--type", dest="type", choices=["peptide"])
+ return parser.parse_args()
+
+if __name__ == "__main__":
+ main()
diff -r 000000000000 -r ba86fd127f5a idxml_to_peptides.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/idxml_to_peptides.xml Wed Dec 19 00:32:25 2012 -0500
@@ -0,0 +1,26 @@
+
+
+
+
+ openms
+
+
+ idxml_exporter.py --type peptide --in ${in} --out ${out}
+
+
+
+
+
+
+
+
+
+**What it does**
+
+Extracts a peptide-level tabular report from an idXML file. The "Export idXML to Tabular" tool provides similar functionality and wraps the OpenMS program TextExporter. However the output of that program may be difficult to utilize in Galaxy and it fails under under certain conditions (e.g. on idXML files coming from PepNovo). This tool was designed for Galaxy and its output is easier to process with other tools in Galaxy.
+
+**Citation**
+
+If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
+
+
diff -r 000000000000 -r ba86fd127f5a idxml_to_tabular.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/idxml_to_tabular.xml Wed Dec 19 00:32:25 2012 -0500
@@ -0,0 +1,48 @@
+
+
+ Converts identification engine file formats.
+
+
+ openms
+
+
+ openms_wrapper.py --executable 'TextExporter' --config $config
+
+
+ [simple_options]
+in=${in}
+out=${out}
+#if $dump_type == "protein"
+proteins_only=true
+#end if
+#if $dump_type == "pepetide"
+peptides_only=true
+#end if
+$extra_rt
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+
+Converts idXML files to tabular.
+
+**Citation**
+
+For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.``
+
+If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
+
+
diff -r 000000000000 -r ba86fd127f5a noise_filter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/noise_filter.xml Wed Dec 19 00:32:25 2012 -0500
@@ -0,0 +1,48 @@
+
+
+ Utilize a filter to reduce the noise in an MS experiment.
+
+
+ openms
+
+
+ #if $filter.type == "gaussian"
+ #set $filter_exec = "NoiseFilterGaussian"
+ #elif $filter.type == "sgolay"
+ #set $filter_exec = "NoiseFilterSGolay"
+ #end if
+ openms_wrapper.py --executable '$filter_exec' --config $config
+
+
+ [simple_options]
+in=${in}
+out=${out}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+
+TODO: Document
+
+http://ftp.mi.fu-berlin.de/OpenMS/doc-1.9-official/html/TOPP_NoiseFilterSGolay.html
+http://ftp.mi.fu-berlin.de/OpenMS/doc-1.9-official/html/TOPP_NoiseFilterGaussian.html
+
+**Citation**
+
+For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.``
+
+If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
+
+
diff -r 000000000000 -r ba86fd127f5a openms_wrapper.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/openms_wrapper.py Wed Dec 19 00:32:25 2012 -0500
@@ -0,0 +1,118 @@
+import os
+import sys
+from optparse import OptionParser
+from ConfigParser import SafeConfigParser
+from xml.etree import ElementTree
+import subprocess
+
+DEBUG = False
+
+
+def main():
+ (options, args) = _parse_args()
+ for executable, config_path in zip(options.executables, options.configs):
+ _run_openms(executable, config_path)
+
+
+def _run_openms(executable, config_path):
+ _exec("%s -write_ini openms.ini" % executable)
+ tree = ElementTree.parse("openms.ini")
+ options = _load_options(config_path)
+ _set_options(tree, executable, options)
+ tree.write("openms.ini")
+ if DEBUG:
+ print 'With openms.ini as:\n%s\n, calling: %s -ini openms.ini' % (open("openms.ini", "r").read(), executable)
+ _exec("%s -ini openms.ini" % executable)
+
+
+def _exec(command):
+ proc = subprocess.Popen(args=command, shell=True)
+ return_code = proc.wait()
+ if return_code != 0:
+ sys.exit(return_code)
+
+
+def _set_options(tree, executable, options):
+ executable_node = tree.find("./NODE[@name='%s']" % executable)
+ options_node = executable_node.find("./NODE[@name='1']")
+ for key, raw_value in options.items("simple_options"):
+ value = _parse_value(raw_value)
+ _set_option(options_node, key.split("!"), value)
+ _set_option(options_node, ["no_progress"], "true", required=False)
+
+
+def _set_option(node, key_parts, value, required=True):
+ key = key_parts[0]
+ if len(key_parts) == 1:
+ item = node.find("./ITEM[@name='%s']" % key)
+ if item is not None:
+ item.set("value", value)
+ elif required:
+ raise Exception("Failed to find specific OpenMS option [%s] in node [%s]" % (key, node))
+ else:
+ sub_node = node.find("./NODE[@name='%s']" % key)
+ _set_option(sub_node, key_parts[1:], value, required)
+
+
+def _parse_value(raw_value):
+ value = raw_value
+ if raw_value in VALUE_FUNCTIONS:
+ value = VALUE_FUNCTIONS[raw_value](raw_value)
+ return value
+
+
+## Special value parser for various OpenMS components
+def _get_pepnovo_models_path(_):
+ pepnovo_path = _get_pepnovo_executable_path(None)
+ pepnovo_dir = os.path.split(pepnovo_path)[0]
+ guesses = [os.path.join(pepnovo_dir, 'Models'),
+ os.path.join(pepnovo_dir, '..', 'Models'),
+ os.path.join(pepnovo_dir, '..', 'share', 'pepnovo', 'Models')]
+ models_dir = None
+ for guess in guesses:
+ if os.path.isdir(guess):
+ models_dir = guess
+ break
+ return models_dir
+
+
+def _get_pepnovo_executable_path(_):
+ return _which("PepNovo")
+
+VALUE_FUNCTIONS = {"@PEPNOVO_MODELS_PATH@": _get_pepnovo_models_path,
+ "@PEPNOVO_EXECUTABLE_PATH@": _get_pepnovo_executable_path}
+
+
+# http://stackoverflow.com/questions/377017/test-if-executable-exists-in-python
+def _which(program):
+
+ def is_exe(fpath):
+ return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
+
+ fpath, fname = os.path.split(program)
+ if fpath:
+ if is_exe(program):
+ return program
+ else:
+ for path in os.environ["PATH"].split(os.pathsep):
+ exe_file = os.path.join(path, program)
+ if is_exe(exe_file):
+ return exe_file
+
+ return None
+
+
+def _parse_args():
+ parser = OptionParser()
+ parser.add_option("-e", "--executable", dest="executables", default=[], action="append")
+ parser.add_option("-c", "--config", dest="configs", default=[], action="append")
+ return parser.parse_args()
+
+
+def _load_options(config_path):
+ config_parser = SafeConfigParser()
+ config_parser.read(config_path)
+ return config_parser
+
+if __name__ == "__main__":
+ main()
diff -r 000000000000 -r ba86fd127f5a peak_file_converter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/peak_file_converter.xml Wed Dec 19 00:32:25 2012 -0500
@@ -0,0 +1,48 @@
+
+
+ Converts between different MS file formats.
+
+
+ openms
+
+
+ openms_wrapper.py --executable 'FileConverter' --config $config
+
+
+ [simple_options]
+in=${in}
+in_type=${in.ext}
+out=${out}
+out_type=${out_format}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+
+Extracts portions of the data from an mzML.
+
+**Citation**
+
+For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.``
+
+If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
+
+
diff -r 000000000000 -r ba86fd127f5a peak_file_filter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/peak_file_filter.xml Wed Dec 19 00:32:25 2012 -0500
@@ -0,0 +1,68 @@
+
+
+ Extract portions of peak lists.
+
+
+ openms
+
+
+ openms_wrapper.py --executable 'FileFilter' --config $config
+
+
+ [simple_options]
+#if $mz.specify
+mz=${mz.min}:${mz.max}
+#end if
+#if $rt.specify
+rt=${rt.min}:${rt.max}
+#end if
+#if $intensity.specify
+int=${intensity.min}:${intensity.max}
+#end if
+sn=${signal_to_noise}
+in=${in}
+in_type=mzML
+out=${out}
+out_type=mzML
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+
+Extracts portions of the data from an mzML.
+
+**Citation**
+
+For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.``
+
+If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
+
+
diff -r 000000000000 -r ba86fd127f5a peak_picker_hi_res.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/peak_picker_hi_res.xml Wed Dec 19 00:32:25 2012 -0500
@@ -0,0 +1,39 @@
+
+
+
+
+ openms
+
+
+ openms_wrapper.py --executable 'PeakPickerHiRes' --config $config
+
+
+ [simple_options]
+in=${input}
+out=${out}
+algorithm!signal_to_noise=${signal_to_noise}
+algorithm!ms1_only=${ms1_only}
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+
+This peak-picking algorithm detects ion signals in raw data and reconstructs the corresponding peak shape by cubic spline interpolation. Signal detection depends on the signal-to-noise ratio which is adjustable by the user (see parameter signal_to_noise). A picked peak's m/z and intensity value is given by the maximum of the underlying peak spline. Please notice that this method is still experimental since it has not been tested thoroughly yet.
+
+The algorithm used by this tool is best suited for high-resolution MS data (FT-ICR-MS, Orbitrap). In high-resolution data, the signals of ions with similar mass-to-charge ratios (m/z) exhibit little or no overlapping and therefore allow for a clear separation. Furthermore, ion signals tend to show well-defined peak shapes with narrow peak width. These properties faciliate a fast computation of picked peaks so that even large data sets can be processed very quickly.
+
+**Citation**
+
+For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.``
+
+If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
+
+
diff -r 000000000000 -r ba86fd127f5a pepnovo_adapter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/pepnovo_adapter.xml Wed Dec 19 00:32:25 2012 -0500
@@ -0,0 +1,117 @@
+
+
+
+
+
+ openms
+ pepnovo
+
+
+ openms_wrapper.py
+#if $input_block.do_clean
+ --executable 'FileConverter' --config $inputConfig
+#end if
+ --executable 'PepNovoAdapter' --config $config
+
+
+ [simple_options]
+#if $input_block.do_clean
+in=input.mzXML
+#else
+in=${input_block.input1}
+#end if
+out=${out}
+model_directory=@PEPNOVO_MODELS_PATH@
+pepnovo_executable=@PEPNOVO_EXECUTABLE_PATH@
+temp_data_directory=.
+model=${model}
+digest=${digest}
+#if $corrections != "none"
+correct_pm=true
+#end if
+#if $corrections == "mass"
+use_spectrum_charge=true
+#end if
+#if $corrections == "mz"
+use_spectrum_mz=true
+#end if
+$quality_filter
+#if $override_pm.do_override
+pm_tolerance=${override_pm.percursor_tolerance}
+#end if
+#if $override_fragment.do_override
+fragment_tolerance=${override_fragment.fragment_tolerance}
+#end if
+
+ [simple_options]
+in=${input_block.input1}
+in_type=${input_block.input1.ext}
+out=input.mzXML
+out_type=mzXML
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+
+De novo peptide sequencing of mass spectrometry data.
+
+More information and publications on PepNovo can be found at the following site: http://proteomics.ucsd.edu/Software/PepNovo.html.
+
+**Citation**
+
+For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.`` and ``PepNovo: De Novo Peptide Sequencing via Probabilistic Network Modeling. Frank, A. and Pevzner, P. Analytical Chemistry 77:964-973, 2005.``.
+
+If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
+
+
diff -r 000000000000 -r ba86fd127f5a pepxml_protxml_merger.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/pepxml_protxml_merger.xml Wed Dec 19 00:32:25 2012 -0500
@@ -0,0 +1,37 @@
+
+
+
+
+ openms
+
+
+ openms_wrapper.py --executable 'IDMerger' --config $config
+
+
+ [simple_options]
+in="${pepxml} ${protxml}"
+out=${out}
+annotate_file_origin=${annotate_file_origin}
+pepxml_protxml=true
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+
+Merge idXML files derived from a pepXML and corresponding protXML file.
+
+**Citation**
+
+For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.``
+
+If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
+
+
diff -r 000000000000 -r ba86fd127f5a update.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/update.sh Wed Dec 19 00:32:25 2012 -0500
@@ -0,0 +1,35 @@
+#!/bin/bash
+
+LICENSE_FILE=LICENSE
+# Ensure repository contains license file.
+if [ ! -e "$LICENSE_FILE" ];
+then
+ wget http://www.apache.org/licenses/LICENSE-2.0.txt -O "$LICENSE_FILE"
+fi
+
+# Run repository specific update actions.
+if [ -f update_repo.sh ];
+then
+ ./update_repo.sh
+fi
+
+wget https://raw.github.com/gist/3749747/README_GALAXYP.md -O README_GALAXYP.md
+
+# Create repository README
+if [ ! -e README_REPO.md ];
+then
+ echo "TODO: Document this tool repository." > README_REPO.md
+fi
+cat README_REPO.md README_GALAXYP.md > README.md
+
+
+# If version file exists, update all tools to this version
+VERSION_FILE=version
+if [ -e "$VERSION_FILE" ];
+then
+ VERSION=`cat $VERSION_FILE`
+
+ # Replace tool version in each tool XML file `
+ find -iname "*xml" -exec sed -i'' -e '0,/version="\(.\+\)"/s/version="\(.\+\)"/version="'$VERSION'"/1g' {} \;
+
+fi