changeset 0:ba86fd127f5a draft

Uploaded

--- /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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--- /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
[e-mail].
+
+# 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.

--- /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
[e-mail].
+
+# 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.

--- /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
+([e-mail]) 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.
+

--- /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 @@
+<tool id="openms_baseline_filter" version="0.1.0" name="Baseline Filter">
+  <description>
+    Executes the top-hat filter to remove the baseline of an MS experiment.
+  </description>
+  <requirements>
+    <requirement type="package">openms</requirement>
+  </requirements>
+  <command interpreter="python">
+    openms_wrapper.py --executable 'BaselineFilter' --config $config
+  </command>
+  <configfiles>
+    <configfile name="config">[simple_options]
+in=${in}
+out=${out}
+</configfile>
+  </configfiles>
+  <inputs>
+    <param format="mzml" name="in" type="data" label="Input mzML"/>
+  </inputs>
+  <outputs>
+    <data format="mzml" name="out" />
+  </outputs>
+  <help>
+**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
+  </help>
+</tool>

--- /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 @@
+<tool id="openms_file_info" version="0.1.0" name="File Info">
+  <description>
+    Shows basic information about the file, such as data ranges and file type.
+  </description>
+  <requirements>
+    <requirement type="package">openms</requirement>
+  </requirements>
+  <command interpreter="python">
+    openms_wrapper.py --executable 'FileInfo' --config $config
+  </command>
+  <configfiles>
+    <configfile name="config">[simple_options]
+m=${m}
+p=${p}
+s=${s}
+d=${d}
+in=${in}
+in_type=${in.ext}
+out=${out}
+</configfile>
+  </configfiles>
+  <inputs>
+    <param format="mzxml,mzml,mgf,pepxml,idxml" name="in" type="data" label="Input Mass Spec Related File"/>
+    <param type="boolean" name="m" label="Show meta information about the whole experiment" />
+    <param type="boolean" name="p" label="Shows data processing information" />
+    <param type="boolean" name="s" label="Computes a five-number statistics of intensities, qualities, and widths" />
+    <param type="boolean" name="d" label="Show detailed listing of all spectra and chromatograms (peak files only)" />
+    <param type="boolean" name="c" label="Check for corrupt data in the file (peak files only)" />
+  </inputs>
+  <outputs>
+    <data format="txt" name="out" />
+  </outputs>
+  <help>
+**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
+  </help>
+</tool>

--- /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 @@
+<tool id="openms_high_res_precursor_mass_corrector" version="0.1" name="Precursor Mass Corrector (Hi Res)">
+  <description>
+precursor m/z correction on picked (centroided) high resolution data.
+  </description>
+  <requirements>
+    <requirement type="package">openms</requirement>
+  </requirements>
+  <configfiles>
+    <configfile name="config">[simple_options]
+in=${input}
+out=${out}
+</configfile>
+  </configfiles>  
+  <command interpreter="python">
+    openms_wrapper.py -executable 'HighResPrecursorMassCorrector' -config $config
+  </command>
+  <inputs>
+    <param format="mzML" name="input" type="data" label="Input picked peak list"/>
+  </inputs>
+  <outputs>
+    <data format="mzML" name="output" />
+  </outputs>
+  <help>
+**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    
+  </help>
+</tool>

--- /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 @@
+<tool id="openms_id_file_converter" version="0.1.0" name="ID File Converter">
+  <description>
+    Converts identification engine file formats.
+  </description>
+  <requirements>
+    <requirement type="package">openms</requirement>
+  </requirements>
+  <command interpreter="python">
+    openms_wrapper.py --executable 'IDFileConverter' --config $config
+  </command>
+  <configfiles>
+    <configfile name="config">[simple_options]
+in=${in}
+in_type=${in.ext}
+out=${out}
+out_type=${output_type}
+</configfile>
+  </configfiles>
+  <inputs>
+    <param format="pepxml,protxml,idxml" name="in" type="data" label="Input Identification File"/>
+    <param name="output_type" type="select" label="Output Type">
+      <option value="idxml">idXML</option>
+      <option value="pepxml">pepXM</option>
+      <option value="mzid">mzIdentML</option>
+      <option value="fasta">FASTA</option>
+    </param>    
+  </inputs>
+  <outputs>
+    <data format="idxml" name="out">
+      <change_format>
+        <when input="output_type" value="pepxml" format="pepxml" />
+        <when input="output_type" value="mzid" format="mzid" />
+        <when input="output_type" value="fasta" format="fasta" />
+      </change_format>
+    </data>
+  </outputs>
+  <help>
+**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
+  </help>
+</tool>

--- /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 @@
+<tool id="openms_id_merger" version="0.1.0" name="ID Merger">
+  <description>
+    Merges several idXML files into one idXML file.
+  </description>
+  <requirements>
+    <requirement type="package">openms</requirement>
+  </requirements>
+  <command interpreter="python">
+    openms_wrapper.py --executable 'IDMerger' --config $config
+  </command>
+  <configfiles>
+    <configfile name="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}
+</configfile>
+  </configfiles>
+  <inputs>
+    <repeat name="inputs">
+      <param format="idxml" name="input" type="data" label="idXML Input"/>
+    </repeat>
+    <param type="boolean" name="annotate_file_origin" label="Annotate file origin" help="Store the original filename in each protein/peptide identification (MetaValue: file_origin)." />
+  </inputs>
+  <outputs>
+    <data format="idxml" name="out" />
+  </outputs>
+  <help>
+**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
+  </help>
+</tool>

--- /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()

--- /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 @@
+<tool id="openms_idxml_to_peptides" version="0.1.0" name="Export peptide report from idXML ">
+  <description>
+  </description>
+  <requirements>
+    <requirement type="package">openms</requirement>
+  </requirements>
+  <command interpreter="python">
+    idxml_exporter.py --type peptide --in ${in} --out ${out}
+  </command>
+  <inputs>
+    <param format="idxml" name="in" type="data" label="Input Identification File"/>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="out">
+    </data>
+  </outputs>
+  <help>
+**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
+  </help>
+</tool>

--- /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 @@
+<tool id="openms_idxml_to_tabular" version="0.1.0" name="Export idXML to Tabular">
+  <description>
+    Converts identification engine file formats.
+  </description>
+  <requirements>
+    <requirement type="package">openms</requirement>
+  </requirements>
+  <command interpreter="python">
+    openms_wrapper.py --executable 'TextExporter' --config $config
+  </command>
+  <configfiles>
+    <configfile name="config">[simple_options]
+in=${in}
+out=${out}
+#if $dump_type == "protein"
+proteins_only=true
+#end if
+#if $dump_type == "pepetide"
+peptides_only=true
+#end if
+$extra_rt
+</configfile>
+  </configfiles>
+  <inputs>
+    <param format="idxml" name="in" type="data" label="Input Identification File"/>
+    <param name="dump_type" type="select" label="Export type">
+      <option value="all">Run, peptide, and protein information</option>
+      <option value="protein">Run and protein information only</option>
+      <option value="peptide">Peptide information only</option>
+    </param>
+    <param name="extra_rt" type="boolean" truevalue="first_dim_rt=true" falsevalue="" label="Include RT information (if present)" />
+  </inputs>
+  <outputs>
+    <data format="tabular" name="out">
+    </data>
+  </outputs>
+  <help>
+**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
+  </help>
+</tool>

--- /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 @@
+<tool id="openms_noise_filter" version="0.1.0" name="Noise Filter">
+  <description>
+    Utilize a filter to reduce the noise in an MS experiment.
+  </description>
+  <requirements>
+    <requirement type="package">openms</requirement>
+  </requirements>
+  <command interpreter="python">
+    #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 $config
+  </command>
+  <configfiles>
+    <configfile name="config">[simple_options]
+in=${in}
+out=${out}
+</configfile>
+  </configfiles>
+  <inputs>
+    <param format="mzml" name="in" type="data" label="Input mzML"/>
+    <conditional name="filter">
+      <param type="select" name="type" label="Filter Type">
+        <option value="gaussian">Gaussian</option>
+        <option value="sgolay">Savitzky Golay</option>
+      </param>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data format="mzml" name="out" />
+  </outputs>
+  <help>
+**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
+  </help>
+</tool>

--- /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()

--- /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 @@
+<tool id="openms_peak_file_convert" version="0.1.0" name="Peak List File Converter">
+  <description>
+    Converts between different MS file formats.
+  </description>
+  <requirements>
+    <requirement type="package">openms</requirement>
+  </requirements>
+  <command interpreter="python">
+    openms_wrapper.py --executable 'FileConverter' --config $config
+  </command>
+  <configfiles>
+    <configfile name="config">[simple_options]
+in=${in}
+in_type=${in.ext}
+out=${out}
+out_type=${out_format}
+</configfile>
+  </configfiles>
+  <inputs>
+    <param format="mzml,mgf,mzxml,ms2" name="in" type="data" label="Input mzML File"/>
+    <param type="select" name="out_format" label="Output Type">
+      <option value="mzml">mzML</option>
+      <option value="mzxml">mzXML</option>
+      <option value="mgf">MGF</option>
+      <option value="ms2">MS2</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="mzml" name="out">
+      <change_format>
+        <when input="out_format" value="mzxml" format="mzxml" />
+        <when input="out_format" value="mgf" format="mgf" />
+        <when input="out_format" value="ms2" format="ms2" />
+      </change_format>
+    </data>
+  </outputs>
+  <help>
+**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
+  </help>
+</tool>

--- /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 @@
+<tool id="openms_peak_file_filter" version="0.1.0" name="mzML File Filter">
+  <description>
+    Extract portions of peak lists.
+  </description>
+  <requirements>
+    <requirement type="package">openms</requirement>
+  </requirements>
+  <command interpreter="python">
+    openms_wrapper.py --executable 'FileFilter' --config $config
+  </command>
+  <configfiles>
+    <configfile name="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
+</configfile>
+  </configfiles>
+  <inputs>
+    <param format="mzml" name="in" type="data" label="Input mzML File"/>
+    <param type="float" name="signal_to_noise" label="Minimum signal-to-noise ratio" value="0" />
+    <conditional name="mz">
+      <param type="boolean" name="specify" label="Filter by m/z" />
+      <when value="true">
+        <param type="float" name="min" label="Minimum m/z (optional)" optional="true" value="" />
+        <param type="float" name="max" label="Maximum m/z (optional)" optional="true" value="" />
+      </when>
+    </conditional>
+    <conditional name="rt">
+      <param type="boolean" name="specify" label="Filter by retention time" />
+      <when value="true">
+        <param type="float" name="min" label="Minimum retention time (optional)" optional="true" value="" />
+        <param type="float" name="max" label="Maximum retention (optional)" optional="true" value="" />
+      </when>
+    </conditional>
+    <conditional name="intensity">
+      <param type="boolean" name="specify" label="Filter by intensity" />
+      <when value="true">
+        <param type="float" name="min" label="Minimum intensity (optional)" optional="true" value="" />
+        <param type="float" name="max" label="Maximum intensity (optional)" optional="true" value="" />
+      </when>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data format="mzml" name="out" />
+  </outputs>
+  <help>
+**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
+  </help>
+</tool>

--- /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 @@
+<tool id="openms_peak_picker_hi_res" version="0.1" name="Peak Peaker (Hi Res)">
+  <description>
+  </description>
+  <requirements>
+    <requirement type="package">openms</requirement>
+  </requirements>
+  <command>
+    openms_wrapper.py --executable 'PeakPickerHiRes' --config $config
+  </command>
+  <configfiles>
+    <configfile name="config">[simple_options]
+in=${input}
+out=${out}
+algorithm!signal_to_noise=${signal_to_noise}
+algorithm!ms1_only=${ms1_only}
+</configfile>
+  </configfiles>  
+  <inputs>
+    <param format="mzML" name="input" type="data" label="Input profile peak list"/>
+    <param type="float" name="signal_to_noise" value="1" label="Signal-to-noise ratio" help="Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)" />
+    <param type="boolean" name="ms1_only" label="MS1 Only" help="If checked, peak picking is only applied to MS1 scans. Other scans are copied to the output without changes." />
+  </inputs>
+  <outputs>
+    <data format="mzML" name="out" />
+  </outputs>
+  <help>
+**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    
+  </help>
+</tool>

--- /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 @@
+<tool id="pepnovo_adapter" version="0.1.0" name="PepNovo (OpenMS)">
+  <description>
+
+  </description>
+  <requirements>
+    <requirement type="package">openms</requirement>
+    <requirement type="package">pepnovo</requirement>
+  </requirements>
+  <command interpreter="python">
+    openms_wrapper.py 
+#if $input_block.do_clean
+    --executable 'FileConverter' --config $inputConfig
+#end if
+    --executable 'PepNovoAdapter' --config $config
+  </command>
+  <configfiles>
+    <configfile name="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
+</configfile>
+    <configfile name="inputConfig">[simple_options]
+in=${input_block.input1}
+in_type=${input_block.input1.ext}
+out=input.mzXML
+out_type=mzXML
+</configfile>
+  </configfiles>
+  <inputs>
+    <conditional name="input_block">
+      <param name="do_clean" type="boolean" label="Process input peak list" description="The version of PepNovo used by this tool takes only mzXML files and even then fails to parse many valid such files. Enabling this option will run the input peak list (mzXML or otherwise) through the OpenMS FileConverter application to hopefully produce an mzXML file suiteable for PepNovo." />
+      <when value="true">
+        <param name="input1" type="data" format="mzxml,mzml,mgf,ms2" label="Input peak list" />
+      </when>
+      <when value="false">
+        <param name="input1" type="data" format="mzxml" label="Input peak list" />
+      </when>
+    </conditional>
+    <param name="model" type="select" label="Model">
+      <options from_file="pepnovo_models.loc">
+        <column name="name" index="0" />
+        <column name="value" index="0" />
+      </options>
+    </param>
+    <param name="digest" type="select" label="Digest"> 
+      <option value="TRYPSIN">Trypsin</option>
+      <option value="NON_SPECIFIC">Non-specific</option>
+    </param>
+    <param name="corrections" type="select" label="Spectrum adjustments">
+      <option value="none">None.</option>
+      <option value="both">Find optimal precursor m/z and charge values.</option>
+      <option value="mz">Find optimal precursor m/z values.</option>
+      <option value="charge">Find optimal charge values.</option>
+    </param>
+    <param name="quality_filter" type="boolean" checked="true" label="Filter low quality spectra" truevalue="no_quality_filter=true" falsevalue=""/>
+    <conditional name="override_pm">
+      <param name="do_override" type="boolean" label="Override model's percursor mass tolerance" />
+      <when value="true">
+        <param name="percursor_tolerance" type="float" label="Precursor mass tolerance (Daltons)" help="Must between 0 and 5.0. Set to -1.0 to use model default." value="-1.0">
+          <validator type="in_range" min="-1.0" max="5.0" />
+        </param>
+      </when>
+      <when value="false">
+      </when>
+    </conditional>
+    <conditional name="override_fragment">
+      <param name="do_override" type="boolean" label="Override model's fragment tolerance" />
+      <when value="true">
+        <param name="fragment_tolerance" type="float" label="Fragment tolerance (Daltons)" help="Must between 0 and 0.75. Set to -1.0 to use model default." value="-1.0">
+          <validator type="in_range" min="-1.0" max="0.75" />
+        </param>
+      </when>
+      <when value="false">
+      </when>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data format="idxml" name="out" />
+  </outputs>
+  <help>
+**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
+  </help>
+</tool>

--- /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 @@
+<tool id="openms_pepxml_protxml_merger" version="0.1.0" name="Merge idXML from PepXML and ProtXML">
+  <description>
+  </description>
+  <requirements>
+    <requirement type="package">openms</requirement>
+  </requirements>
+  <command interpreter="python">
+    openms_wrapper.py --executable 'IDMerger' --config $config
+  </command>
+  <configfiles>
+    <configfile name="config">[simple_options]
+in="${pepxml} ${protxml}"
+out=${out}
+annotate_file_origin=${annotate_file_origin}
+pepxml_protxml=true
+</configfile>
+  </configfiles>
+  <inputs>
+    <param format="idxml" name="pepxml" type="data" label="idXML from PepXML"/>
+    <param format="idxml" name="protxml" type="data" label="idXML from ProtXML"/>
+    <param type="boolean" name="annotate_file_origin" label="Annotate file origin" help="Store the original filename in each protein/peptide identification (MetaValue: file_origin)." />
+  </inputs>
+  <outputs>
+    <data format="idxml" name="out" />
+  </outputs>
+  <help>
+**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
+  </help>
+</tool>

--- /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