--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE	Fri May 10 17:06:14 2013 -0400
@@ -0,0 +1,202 @@
+
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
+
+      "Derivative Works" shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
+      represent, as a whole, an original work of authorship. For the purposes
+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
+      the Work and Derivative Works thereof.
+
+      "Contribution" shall mean any work of authorship, including
+      the original version of the Work and any modifications or additions
+      to that Work or Derivative Works thereof, that is intentionally
+      submitted to Licensor for inclusion in the Work by the copyright owner
+      or by an individual or Legal Entity authorized to submit on behalf of
+      the copyright owner. For the purposes of this definition, "submitted"
+      means any form of electronic, verbal, or written communication sent
+      to the Licensor or its representatives, including but not limited to
+      communication on electronic mailing lists, source code control systems,
+      and issue tracking systems that are managed by, or on behalf of, the
+      Licensor for the purpose of discussing and improving the Work, but
+      excluding communication that is conspicuously marked or otherwise
+      designated in writing by the copyright owner as "Not a Contribution."
+
+      "Contributor" shall mean Licensor and any individual or Legal Entity
+      on behalf of whom a Contribution has been received by Licensor and
+      subsequently incorporated within the Work.
+
+   2. Grant of Copyright License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      copyright license to reproduce, prepare Derivative Works of,
+      publicly display, publicly perform, sublicense, and distribute the
+      Work and such Derivative Works in Source or Object form.
+
+   3. Grant of Patent License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      (except as stated in this section) patent license to make, have made,
+      use, offer to sell, sell, import, and otherwise transfer the Work,
+      where such license applies only to those patent claims licensable
+      by such Contributor that are necessarily infringed by their
+      Contribution(s) alone or by combination of their Contribution(s)
+      with the Work to which such Contribution(s) was submitted. If You
+      institute patent litigation against any entity (including a
+      cross-claim or counterclaim in a lawsuit) alleging that the Work
+      or a Contribution incorporated within the Work constitutes direct
+      or contributory patent infringement, then any patent licenses
+      granted to You under this License for that Work shall terminate
+      as of the date such litigation is filed.
+
+   4. Redistribution. You may reproduce and distribute copies of the
+      Work or Derivative Works thereof in any medium, with or without
+      modifications, and in Source or Object form, provided that You
+      meet the following conditions:
+
+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and
+
+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and
+
+      (c) You must retain, in the Source form of any Derivative Works
+          that You distribute, all copyright, patent, trademark, and
+          attribution notices from the Source form of the Work,
+          excluding those notices that do not pertain to any part of
+          the Derivative Works; and
+
+      (d) If the Work includes a "NOTICE" text file as part of its
+          distribution, then any Derivative Works that You distribute must
+          include a readable copy of the attribution notices contained
+          within such NOTICE file, excluding those notices that do not
+          pertain to any part of the Derivative Works, in at least one
+          of the following places: within a NOTICE text file distributed
+          as part of the Derivative Works; within the Source form or
+          documentation, if provided along with the Derivative Works; or,
+          within a display generated by the Derivative Works, if and
+          wherever such third-party notices normally appear. The contents
+          of the NOTICE file are for informational purposes only and
+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
+          or as an addendum to the NOTICE text from the Work, provided
+          that such additional attribution notices cannot be construed
+          as modifying the License.
+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
+      for use, reproduction, or distribution of Your modifications, or
+      for any such Derivative Works as a whole, provided Your use,
+      reproduction, and distribution of the Work otherwise complies with
+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+      implied, including, without limitation, any warranties or conditions
+      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
+      replaced with your own identifying information. (Don't include
+      the brackets!)  The text should be enclosed in the appropriate
+      comment syntax for the file format. We also recommend that a
+      file or class name and description of purpose be included on the
+      same "printed page" as the copyright notice for easier
+      identification within third-party archives.
+
+   Copyright [yyyy] [name of copyright owner]
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Fri May 10 17:06:14 2013 -0400
@@ -0,0 +1,25 @@
+This repository contains tool wrappers for the Tabb lab tools
+idqonvert, myrimatch, and tagrecon. There is also an IDPicker3 tool
+wrapper, but it does not work due to bugs in IDPicker3's file merging
+functionality.# 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.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README_GALAXYP.md	Fri May 10 17:06:14 2013 -0400
@@ -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.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README_REPO.md	Fri May 10 17:06:14 2013 -0400
@@ -0,0 +1,4 @@
+This repository contains tool wrappers for the Tabb lab tools
+idqonvert, myrimatch, and tagrecon. There is also an IDPicker3 tool
+wrapper, but it does not work due to bugs in IDPicker3's file merging
+functionality.
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/idpicker.xml	Fri May 10 17:06:14 2013 -0400
@@ -0,0 +1,56 @@
+<tool id="idpicker" name="IDPicker 3" version="0.1.0">
+  <description>
+    Assemble parsimonious protien identifications.
+  </description>
+  <configfiles>
+    <configfile name="group_config"># Simple format group:group_name followed by pairs of name:name and path:path lines
+#for $group in $groups:
+group:$group.group_name
+#for $idpdb_input in $group.idpdb_inputs:
+name:${idpdb_input.display_name}
+path:${idpdb_input}
+#end for
+#end for
+    </configfile>
+  </configfiles>
+  <command interpreter="python">
+    idpicker_wrapper.py --input $group_config --output $output
+  </command>
+  <inputs>
+    <param format="idpdb" name="outside_inputs" type="data" multiple="true" label="idpDB Inputs" help="Run results through idpQonvert tool to produce idpDB files for IDPicker." />
+    <repeat name="groups" title="Experimental Group">
+      <param name="group_name" type="text" label="Group Name" help="Name for the group (use only letters and numbers)." />
+      <param format="idpdb" name="idpdb_inputs" type="data" multiple="true" label="idpDB Inputs" help="Run results through idpQonvert tool to produce idpDB files for IDPicker." />
+    </repeat>
+  </inputs>
+  <outputs>
+    <data format="idpdb" name="output" />
+  </outputs>
+  <requirements>
+    <requirement type="package">idpicker</requirement>
+  </requirements>
+  <help>
+**WARNING**
+
+This tool does not current work.
+
+**What it does**
+
+
+
+** Building Groups **
+
+Build arbitrary hierarchy by nesting groups with colon (e.g. control:666Gx6).
+
+http://fenchurch.mc.vanderbilt.edu/bumbershoot/idpicker/index_files/image003.gif
+
+------
+
+
+**Citation**
+
+For the underlying tool, please cite `TODO`
+
+If you use this tool in Galaxy, please cite TODO
+  </help>
+</tool>
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/idpicker_wrapper.py	Fri May 10 17:06:14 2013 -0400
@@ -0,0 +1,26 @@
+#!/usr/bin/env python
+import optparse
+import sys
+import os
+
+
+def stop_err(msg):
+    sys.stderr.write("%s\n" % msg)
+    sys.exit(-1)
+
+
+def build_groups(input):
+    os.makedir("input_directory")
+
+
+def main():
+    parser = optparse.OptionParser()
+    parser.add_option('--input')
+    parser.add_option('--output')
+    (options, args) = parser.parse_args()
+    if not len(options.input):
+        stop_err("No input file found")
+    build_groups(options.input)
+
+if __name__ == '__main__':
+    main()

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/idpqonvert.xml	Fri May 10 17:06:14 2013 -0400
@@ -0,0 +1,217 @@
+<tool id="idpQonvert" name="idpQonvert" version="0.1.0">
+  <!-- TODO: Set defaults for weights correctly -->
+  <description>
+    Prepare identification results for IDPicker.
+  </description>
+  <command>
+  #set $db_name = $input_database.display_name.replace(".fasta", "") + ".fasta"
+  #set $input_name = $input.display_name
+  #set $output_name = $input_name.split(".")[0] + ".idpDB"
+  ln -s '$input' '${input_name}';
+  ln -s '$input_database' '${db_name}';
+  idpQonvert -DecoyPrefix '${decoy_prefix}' \
+  -WriteQonversionDetails true \
+  -ProteinDatabase '${db_name}' \
+  -MaxFDR $max_fdr \
+  -EmbedSpectrumScanTimes false \
+  -EmbedSpectrumSources false \
+  #if $scoring.override_scoring
+  #set $score_info = []
+  #for $engine in ["myrimatch:mvh", "xcorr", "sequest:xcorr", "sequest:deltacn", "mascot:score", "x!tandem:expect", "x!tandem:hyperscore", "ms-gf:spacevalue"]
+  #set $weight = $getVar("scoring." + $engine.replace(":", "_").replace("!","") + "_weight.value")
+  #set $type = $getVar("scoring." + $engine.replace(":", "_").replace("!","") + "_type.value")
+  #set $score_info = $score_info + [str($weight) + " " + $type + " " + $engine]
+  #continue
+  #end for
+  #set $score_str = "; ".join($score_info)
+  -ScoreInfo '$score_str' \
+  #end if  
+  #if $advanced_options.use_advanced_options
+  -MaxImportFDR $advanced_options.max_import_fdr \
+  -MaxResultRank $advanced_options.max_result_rank \ 
+  -RerankMatches $advanced_options.rerank_matches \
+  -Gamma $advanced_options.gamma \
+  -Nu $advanced_options.nu \
+  -PolynomialDegree $advanced_options.polynomial_degree \
+  -TruePositiveThreshold $advanced_options.true_positive_threshold \
+  -MaxTrainingRank $advanced_options.max_training_rank \
+  -SVMType $advanced_options.svm_type \ 
+  -Kernel $advanced_options.kernel \ 
+  -ChargeStateHandling $advanced_options.charge_state_handling \ 
+  -QonverterMethod $advanced_options.qonverter_method \
+  -MinPartitionSize $advanced_options.min_partition_size \
+  #end if
+  '${input_name}';
+  mv '$output_name' output
+  </command>
+<!-- idpQonvert needs spectrum available EmbedSpectrumScanTimes or EmbedSpectrumSources is set.
+-->
+  <stdio>
+    <exit_code range="1:" level="fatal" description="Job Failed" />
+    <regex match="^Could not find the default configuration file.*$"
+      source="both"
+      level="warning" />
+  </stdio>
+  <inputs>
+    <conditional name="type">
+      <param name="input_type" type="select" label="Input Type">
+        <option value="mzid">mzIdentML</option>
+        <option value="pepXML">pepXML</option>
+      </param>
+      <when value="mzid">
+        <param format="mzid" name="input" type="data" label="Input mzIdentML"/>
+      </when>
+      <when value="pepXML">
+        <param format="pepXML" name="input" type="data" label="Input pepXML"/>
+      </when>
+    </conditional>
+    <param format="fasta" name="input_database" type="data" label="Protein Database"/>
+    <param name="decoy_prefix" type="text" label="Decoy Prefix"/>
+    <param name="max_fdr" type="float" label="Max FDR" value="0.05" />
+	<conditional name="advanced_options">
+      <param name="use_advanced_options" type="boolean" truevalue="true" falsevalue="false" label="Set Advanced Options" help="" />
+      <when value="false" />          
+      <when value="true">
+        <param name="max_import_fdr" type="float" label="Max Import FDR" value="0.25" />
+        <param name="max_result_rank" type="integer" label="Max Result Rank" value="3" />
+        <param name="max_training_rank" type="integer" label="Max Training Rank" value="1" />
+        <param name="rerank_matches" type="boolean" label="Rerank Matches" checked="false" truevalue="true" falsevalue="false" />
+	    <param name="gamma" type="float" label="Gamma" value="5" />
+        <param name="nu" type="float" label="Nu" value="-0.5" />
+		<param name="true_positive_threshold" type="float" label="True Positive Threshold" value="0.01" />
+        <param name="polynomial_degree" type="integer" label="Polynomial Degree" value="3" />
+        <param name="min_partition_size" type="integer" label="Minimum Partition Size" value="10" />
+		<param name="svm_type" label="SVM Type" type="select">
+		  <option value="CSVC" selected="true">CSVC</option>
+		  <option value="NuSVC">Nu SCV</option>
+		  <option value="OneClass">One Class</option>
+		  <option value="NuSVR">Nu SVR</option>
+		  <option value="EpsilonSVR">Epsilon SVR</option>
+	    </param>	    
+		<param name="kernel" label="Kernel" type="select">
+		  <option value="Linear" selected="true">Linear</option>
+		  <option value="Polynomial">Polynomial</option>
+		  <option value="RBR">Radial Basis Function</option>
+		  <option value="Sigmoid">Sigmoid</option>
+	    </param>
+	    <param name="charge_state_handling" label="Charge State Handling" type="select">
+		  <option value="Partition" selected="true">Partition</option>
+		  <option value="Ignore">Ignore</option>
+		  <option value="Feature">Feature</option>
+	    </param>
+	    <param name="terminal_specificity_handling" label="Terminal Specificity Handling" type="select">
+		  <option value="Partition" selected="true">Partition</option>
+		  <option value="Ignore">Ignore</option>
+		  <option value="Feature">Feature</option>
+	    </param>
+	    <param name="missed_cleavages_handling" label="Missed Cleavages Handling" type="select">
+		  <option value="Ignore" selected="true">Ignore</option>
+		  <option value="Feature">Feature</option>
+	    </param>
+	    <param name="missed_cleavages_handling" label="Missed Cleavages Handling" type="select">
+		  <option value="Ignore" selected="true">Ignore</option>
+		  <option value="Feature">Feature</option>
+	    </param>
+	    <param name="mass_error_handling" label="Mass Error Handling" type="select">
+		  <option value="Ignore" selected="true">Ignore</option>
+		  <option value="Feature">Feature</option>
+	    </param>
+	    <param name="qonverter_method" label="Qonverter Method" type="select">
+		  <option value="MonteCarlo" selected="true">Monte Carlo</option>
+		  <option value="SingleSVM">SVM (single)</option>
+		  <option value="PartitionSVM">SVM (parition)</option>
+		  <option value="StaticWeighted">Static Weighted</option>
+	    </param>
+      </when>
+    </conditional>
+    <conditional name="scoring">
+      <param name="override_scoring" type="boolean" truevalue="true" falsevalue="false" label="Modify Search Application Weights" />
+      <when value="false" />
+      <when value="true">
+      	<param name="myrimatch_mvh_weight" label="Myrimatch (mvh) Weight" type="float" value="1" />
+		<param name="myrimatch_mvh_type" label="Myrimatch (mvh) Normalization" type="select">
+		  <option value="off" selected="true">None</option>
+		  <option value="quantile">Quantile</option>
+		  <option value="linear">Linear</option>
+	    </param>
+	    <param name="xcorr_weight" label="XCorr Weight" type="float" value="1" />
+		<param name="xcorr_type" label="XCorr Normalization" type="select">
+		  <option value="off" selected="true">None</option>
+		  <option value="quantile">Quantile</option>
+		  <option value="linear">Linear</option>
+	    </param>
+      	<param name="sequest_xcorr_weight" label="Sequest (xcorr) Weight" type="float" value="1" />
+		<param name="sequest_xcorr_type" label="Sequest (xcorr) Normalization" type="select">
+		  <option value="off" selected="true">None</option>
+		  <option value="quantile">Quantile</option>
+		  <option value="linear">Linear</option>
+	    </param>	    
+	    <param name="sequest_deltacn_weight" label="Sequest (deltacn) Weight" type="float" value="1" />
+		<param name="sequest_deltacn_type" label="Sequest (deltacn) Normalization" type="select">
+		  <option value="off" selected="true">None</option>
+		  <option value="quantile">Quantile</option>
+		  <option value="linear">Linear</option>
+	    </param>
+        <param name="mascot_score_weight" label="Mascot Score Weight" type="float" value="1" />
+		<param name="mascot_score_type" label="Mascot Score Normalization" type="select">
+		  <option value="off" selected="true">None</option>
+		  <option value="quantile">Quantile</option>
+		  <option value="linear">Linear</option>
+	    </param>	    
+        <param name="xtandem_expect_weight" label="X! Tandem (Expectation) Weight" type="float" value="-1" />
+		<param name="xtandem_expect_type" label="X! Tandem (Expectation) Normalization" type="select">
+		  <option value="off" selected="true">None</option>
+		  <option value="quantile">Quantile</option>
+		  <option value="linear">Linear</option>
+	    </param>	    
+        <param name="xtandem_hyperscore_weight" label="X! Tandem (hyperscore) Weight" type="float" value="1" />
+		<param name="xtandem_hyperscore_type" label="X! Tandem (hyperscore)Normalization" type="select">
+		  <option value="off" selected="true">None</option>
+		  <option value="quantile">Quantile</option>
+		  <option value="linear">Linear</option>
+	    </param>	    
+        <param name="ms-gf_spacevalue_weight" label="MS-GF (spacevalue) Weight" type="float" value="-1" />
+		<param name="ms-gf_spacevalue_type" label="MS-GF (spacevalue) Normalization" type="select">
+		  <option value="off" selected="true">None</option>
+		  <option value="quantile">Quantile</option>
+		  <option value="linear">Linear</option>
+	    </param>	    
+      </when>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data format="idpdb" name="output" from_work_dir="output" />
+  </outputs>
+  <requirements>
+    <requirement type="package">idpqonvert</requirement>
+  </requirements>
+  <help>
+**What it does**
+
+------
+
+**Citation**
+
+For the underlying tool, please cite `TODO`
+
+If you use this tool in Galaxy, please cite TODO
+  </help>
+</tool>
+<!-- idpQonvert needs spectrum available EmbedSpectrumScanTimes or EmbedSpectrumSources is set.
+
+idpQonvert -OverwriteExistingFiles true -MaxFDR 0.05 -MaxImportFDR 0.25  -MaxResultRank 3 -RerankMatches false -TruePositiveThreshold 0.01 -MaxTrainingRank 1 -Gamma 5 -Nu -0.5 -PolynomialDegree 3 -ScoreInfo "1 off myrimatch:mvh; 1 off xcorr; 1 off sequest:xcorr; 1 off sequest:deltacn; 1 off mascot:score; -1 off xexpect; 1 off x\!tandem:hyperscore; -1 off ms-gf:specevalue" -SVMType CSVC -Kernel Linear -ChargeStateHandling Partition -QonverterMethod MonteCarlo -MinPartitionSize 10 -DecoyPrefix RRRRRR -ProteinDatabase test2.fasta input.pepXML
+
+
+ScoreInfo: 1 off myrimatch:mvh; 1 off xcorr; 1 off sequest:xcorr; 1 off sequest:deltacn; 1 off mascot:score; -1 off x!tandem:expect; 1 off x!tandem:hyperscore; -1 off ms-gf:specevalue
+
+off is normalization: quantile, linear, or off
+
+SVMType: CSVC, NuSVC, OneClass, EpsilonSVR, NuSVR
+Kernel: Linear, Polynomial, RBF (radial basis function), Sigmoid
+ChargeStateHandling: Parition, Ignore, Feature
+TerminalSpecificityHandling: Partition, Ignore, Feature
+MissedCleavagesHandling: Ignore, Feature
+MassErrorHandling: Ignore, Feature
+QonverterMethod: MonteCarlo, SingleSVM, PartitionedSVM, StaticWeighted
+
+-->

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/myrimatch.xml	Fri May 10 17:06:14 2013 -0400
@@ -0,0 +1,192 @@
+<tool id="myrimatch" name="myrimatch" version="0.1.0">
+  <description></description>
+  <command>
+  #set $mod_rep_chars = "*$^@.%!"
+  #set $db_name = $input_database.display_name.replace(".fasta", "") + ".fasta"
+  #if $output_type.value == "mzid"
+  #set $output_ext="mzid"
+  #set $output_format="mzIdentML"
+  #else 
+  #set $output_ext="pepXML"
+  #set $output_format="pepXML"
+  #end if
+  #set $input_name = $input.display_name
+  #set $output_name = $input_name.split(".")[0] + "." + $output_ext
+  #set $static_mods_str = ""
+  #for $static_mod in $static_mods
+  #set $static_mods_str = $static_mods_str + "" + str($static_mod.aa) + " " + str($static_mod.mass)
+  #end for
+  #set $dynamic_mods_str = ""
+  #set $dynamic_mod_index = 0
+  #for $dynamic_mod in $dynamic_mods
+  #set $dynamic_mods_str = $dynamic_mods_str + "" + str($dynamic_mod.motif) + " " + $mod_rep_chars[$dynamic_mod_index] + " " + str($dynamic_mod.mass)
+  #set $dynamic_mod_index = $dynamic_mod_index + 1
+  #end for
+  ln -s '$input' '${input_name}';
+  ln -s '$input_database' '${db_name}';
+  myrimatch -DecoyPrefix '${decoy_prefix}' \
+  -ProteinDatabase '${db_name}' \
+  -OutputFormat '${$output_format}' \
+  '${input_name}' \
+  -StaticMods '${static_mods_str}' \
+  -DynamicMods '${dynamic_mods_str}' \
+  -CleavageRules '${protease}' \
+  #set $percursor_type = $percursor_tolerance.percursor_type
+  -PrecursorMzToleranceRule '${percursor_type}' \
+  #if $percursor_type == "auto" or $percursor_type == "mono"
+  -MonoPrecursorMzTolerance '${percursor_tolerance.mono_precursor_mz_tolerance}${percursor_tolerance.mono_precursor_mz_tolerance_units}' \
+  #end if
+  #if $percursor_type == "auto" or $percursor_type == "avg"
+  -AvgPrecursorMzTolerance '${percursor_tolerance.avg_precursor_mz_tolerance}${percursor_tolerance.avg_precursor_mz_tolerance_units}' \
+  #end if
+  -FragmentMzTolerance '${fragment_mz_tolerance}${fragment_mz_tolerance_units}' \
+  #if $advanced.use_advanced
+  -UseSmartPlusThreeModel $advanced.use_smart_plus_three_model \
+  -MinPeptideLength $advanced.min_peptide_length \
+  -MaxPeptideLength $advanced.max_peptide_length \
+  #if $advanced.max_peak_count
+  -MaxPeakCount $advanced.max_peak_count \
+  #end if
+  #if $advanced.fragmentation_rule.override
+  -FragmentationAutoRule false -FragmentationRule 'manual:${advanced.fragmentation_rule.fragmentation_rule}' \
+  #end if
+  #end if
+  ;
+  mv '$output_name' output
+  </command>
+  <stdio>
+    <exit_code range="1:" level="fatal" description="Job Failed" />
+    <regex match="^Could not find the default configuration file.*$"
+      source="both"
+      level="warning" />
+  </stdio>
+  <inputs>
+    <conditional name="type">
+      <param name="input_type" type="select" label="Input Type">
+        <option value="mzml">mzML</option>
+        <option value="mzxml">mzXML</option>
+        <option value="mgf">mgf</option>
+        <option value="ms2">ms2</option>
+      </param>
+      <when value="mzml">
+        <param format="mzml" name="input" type="data" label="Input mzML"/>
+      </when>
+      <when value="mzxml">
+        <param format="mzxml" name="input" type="data" label="Input mzXML"/>
+      </when>
+      <when value="mgf">
+        <param format="mgf" name="input" type="data" label="Input mgf"/>
+      </when>
+      <when value="ms2">
+        <param format="ms2" name="input" type="data" label="Input ms2"/>
+      </when>
+    </conditional>
+    <param name="output_type" type="select" label="Output Type">
+      <option value="raw_pepxml">pepXML</option>
+      <option value="mzid">mzIdentML</option>
+    </param> 
+    <param format="fasta" name="input_database" type="data" label="Protein Database"/>
+    <param name="decoy_prefix" type="text" label="Decoy Prefix"/>
+    <param name="protease" type="select" label="Protease"> 
+      <options from_file="proteases.loc">
+        <column name="name" index="0" />
+        <column name="value" index="1" />
+      </options>
+    </param>    
+    <repeat name="static_mods" title="Static Modifications">
+      <param name="aa" type="text" label="Amino Acid" />
+      <param name="mass" type="float" label="Mass" value="0" />
+    </repeat>
+    <repeat name="dynamic_mods" title="Dynamic Modifications" max="7">
+      <param name="motif" type="text" label="Amino Acid Motif" />
+      <param name="mass" type="float" label="Mass" value="0" />
+    </repeat>
+    <conditional name="percursor_tolerance">
+      <param name="percursor_type" type="select" label="Percursor Mass Type" help="For data from Thermo instruments, using the 'auto' setting on a will automatically choose monoisotopic or average mass values, for other instruments monoisotopic or average should be chosen.">
+        <option value="auto">Auto</option>
+        <option value="avg">Average</option>
+        <option value="mono">Monoisotopic</option>
+      </param>
+      <when value="auto">
+        <param name="mono_precursor_mz_tolerance" type="float" value="10" label="Monoisotopic Percursor m/z Tolerance" />
+        <param name="mono_precursor_mz_tolerance_units" type="select" label="Monoisotopic Percursor m/z Tolerance Units">
+          <option value="ppm">Parts per million</option>
+          <option value="daltons">Daltons</option>
+        </param>
+        <param name="avg_precursor_mz_tolerance" type="float" value="1.5" label="Average Percursor m/z Tolerance" />
+        <param name="avg_precursor_mz_tolerance_units" type="select" label="Average Percursor m/z Tolerance Units">
+          <option value="ppm">Parts per million</option>
+          <option value="daltons" selected="true">Daltons</option>          
+        </param>
+      </when>
+      <when value="avg">
+        <param name="avg_precursor_mz_tolerance" type="float" value="1.5" label="Average Percursor m/z Tolerance" />
+        <param name="avg_precursor_mz_tolerance_units" type="select" label="Average Percursor m/z Tolerance Units">
+          <option value="ppm">Parts per million</option>
+          <option value="daltons" selected="true">Daltons</option>          
+        </param>
+      </when>
+      <when value="mono">
+        <param name="mono_precursor_mz_tolerance" type="float" value="10" label="Monoisotopic Percursor m/z Tolerance" />
+        <param name="mono_precursor_mz_tolerance_units" type="select" label="Monoisotopic Percursor m/z Tolerance Units">
+          <option value="ppm">Parts per million</option>
+          <option value="daltons">Daltons</option>
+        </param>        
+      </when>
+    </conditional>
+    <param name="fragment_mz_tolerance" type="float" value="1.5" label="Fragement m/z Tolerance" />
+    <param name="fragment_mz_tolerance_units" type="select" label="Fragment m/z Tolerance Units">
+      <option value="ppm">Parts per million</option>
+      <option value="daltons" selected="true">Daltons</option>
+    </param>
+    <conditional name="advanced">
+      <param name="use_advanced" type="boolean" label="Set Advanced Options" />
+      <when value="false">
+      </when>
+      <when value="true">
+        <param name="max_peak_count" type="integer" value="" optional="true" label="Use Max Peaks" help="Filter out all but the specified number of peaks, keep empty to use all peaks." />
+        <conditional name="fragmentation_rule">
+          <param name="override" type="boolean" label="Override Fragmentation Rule (Ion Series)" />
+          <when value="false" />
+          <when value="true">
+            <param type="text" name="fragmentation_rule" label="Fragmentation Rule" help="specify as a comma-separated list of a, b, c, x, y, z, or z* (z+1), e.g. b,y,z" />
+          </when>
+        </conditional>
+        <param name="min_peptide_length" type="integer" value="5" label="Minimum Peptide Length" />
+        <param name="max_peptide_length" type="integer" value="75" label="Maximum Peptide Length" />
+        <param name="use_smart_plus_three_model" type="boolean" truevalue="true" falsevalue="false" label="Use Smart Plus 3 Model"  help="For +3 and higher precursors, the fragment ions predicted depend on the way this parameter is set. When this parameter is true, then for each peptide bond, an internal calculation is done to estimate the basicity of the b and y fragment sequence. When this parameter is false, however, ALL possible charge distributions for the fragment ions are generated for every peptide bond." checked="true" />
+
+      </when>
+    </conditional>
+    <!--
+    <param name="max_peptide_length" value="75"
+
+    <param name="use_smart_plus_three_model" type="boolean" truevalue="true" falsevalue="false" label="Use Smart Plus 3 Model"  help="For +3 and higher precursors, the fragment ions predicted depend on the way this parameter is set. When this parameter is true, then for each peptide bond, an internal calculation is done to estimate the basicity of the b and y fragment sequence. When this parameter is false, however, ALL possible charge distributions for the fragment ions are generated for every peptide bond." checked="true" />
+  -->
+  </inputs>
+  <outputs>
+    <data format="raw_pepxml" name="output" from_work_dir="output">
+      <change_format>
+        <when input="output_type" value="mzid" format="mzid" />
+      </change_format>
+    </data>
+  </outputs>
+
+  <requirements>
+    <requirement type="package">myrimatch</requirement>
+  </requirements>
+
+  <help>
+**What it does**
+
+Performs protein identification via database search using MyriMatch.
+
+------
+
+**Citation**
+
+For the underlying tool, please cite `MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. Tabb DL, Fernando CG, Chambers MC. J Proteome Res. 6(2) 654-61. 2007 Feb. PMCID PMC2525619`
+
+If you use this tool in Galaxy, please cite TODO
+  </help>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tagrecon.xml	Fri May 10 17:06:14 2013 -0400
@@ -0,0 +1,210 @@
+<tool id="tagrecon" name="TagRecon" version="0.1.0">
+  <description></description>
+  <command>    
+  #set $db_name = $input_database.display_name.replace(".fasta", "") + ".fasta"
+  #if $output_type.value == "mzid"
+  #set $output_ext="mzid"
+  #set $output_format="mzIdentML"
+  #else 
+  #set $output_ext="pepXML"
+  #set $output_format="pepXML"
+  #end if
+  #set $input_name = $input.display_name
+  #set $tags_name = $input_name.split(".")[0] + ".tags"
+  #set $output_name = $input_name.split(".")[0] + "." + $output_ext
+  #set $static_mods_str = ""
+  #for $static_mod in $static_mods
+  #set $static_mods_str = $static_mods_str + "" + str($static_mod.aa) + " " + str($static_mod.mass)
+  #end for
+  #set $dynamic_mods_str = ""
+  #set $dynamic_mod_index = 0
+  #for $dynamic_mod in $dynamic_mods
+  #set $dynamic_mods_str = $dynamic_mods_str + "" + str($dynamic_mod.motif) + " " + $mod_rep_chars[$dynamic_mod_index] + " " + str($dynamic_mod.mass)
+  #set $dynamic_mod_index = $dynamic_mod_index + 1
+  #end for
+  ln -s '$input' '${input_name}';
+  ln -s '$input_database' '${db_name}';
+  cp \${TAGRECON_UNIMOD_PATH:-${GALAXY_DATA_INDEX_DIR}/unimod.xml} .;
+  cp \${TAGRECON_BLOSUM_PATH:-${GALAXY_DATA_INDEX_DIR}/blosum62.fas} .;
+  directag '${input_name}' \
+  -StaticMods '${static_mods_str}' \
+  -DynamicMods '${dynamic_mods_str}' \
+  -MaxDynamicMods '$max_dynamic_mods' \
+  -MaxResults ${max_tags} \
+  -FragmentMzTolerance ${tag_mz_tolerance} \
+  #if $advanced_charge_options.specify
+  -UseChargeStateFromMS $advanced_charge_options.use_ms_charge_state \
+  #end if
+  #if $tag_weights.specify
+  -IntensityScoreWeight $tag_weights.intensity \
+  -MzFidelityScoreWeight $tag_weights.mz \
+  -ComplementScoreWeight $tag_weights.complement \
+  #end if
+  ;
+  tagrecon -DecoyPrefix '${decoy_prefix}' \
+  -ProteinDatabase '${db_name}' \
+  -OutputFormat '${$output_format}' \
+  -StaticMods '${static_mods_str}' \
+  -DynamicMods '${dynamic_mods_str}' \
+  -MaxDynamicMods '$max_dynamic_mods' \
+  -CleavageRules '${protease}' \
+  -MaxMissedCleavages ${max_missed_cleavages} \
+  #if $advanced_cleavage_options.specify
+  -MinTerminiCleavages $advanced_cleavage_options.min_termini_cleavages \
+  -UseNETAdjustment $advanced_cleavage_options.use_net_adjustment \
+  #end if
+  #if $advanced_charge_options.specify
+  -UseChargeStateFromMS $advanced_charge_options.use_ms_charge_state \
+  #end if
+  #if $search_untagged.search
+  -SearchUntaggedSpectra true \
+  -UntaggedSpectraPrecMZTol $search_untagged.precursor_mz_tolerance
+  #end if
+  '${tags_name}';
+  mv '$output_name' output
+  </command>
+  <stdio>
+    <exit_code range="1:" level="fatal" description="Job Failed" />
+    <regex match="^Could not find the default configuration file.*$"
+      source="both"
+      level="warning" />
+  </stdio>
+  <inputs>
+    <conditional name="type">
+      <param name="input_type" type="select" label="Input Type">
+        <option value="mzml">mzML</option>
+        <option value="mzxml">mzXML</option>
+        <option value="mgf">mgf</option>
+        <option value="ms2">ms2</option>
+      </param>
+      <when value="mzml">
+        <param format="mzml" name="input" type="data" label="Input mzML"/>
+      </when>
+      <when value="mzxml">
+        <param format="mzxml" name="input" type="data" label="Input mzXML"/>
+      </when>
+      <when value="mgf">
+        <param format="mgf" name="input" type="data" label="Input mgf"/>
+      </when>
+      <when value="ms2">
+        <param format="ms2" name="input" type="data" label="Input ms2"/>
+      </when>
+    </conditional>
+    <param name="output_type" type="select" label="Output Type">
+      <option value="raw_pepxml">pepXML</option>
+      <option value="mzid">mzIdentML</option>
+    </param> 
+    <param format="fasta" name="input_database" type="data" label="Protein Database"/>
+    <param name="decoy_prefix" type="text" label="Decoy Prefix"/>
+    <repeat name="static_mods" title="Static Modifications (used by both directag and tagrecon) ">
+      <param name="aa" type="text" label="Amino Acid" />
+      <param name="mass" type="float" label="Mass" value="0" />
+    </repeat>
+    <repeat name="dynamic_mods" title="Dynamic Modifications  (used by both directag and tagrecon)" max="7">
+      <param name="motif" type="text" label="Amino Acid Motif" />
+      <param name="mass" type="float" label="Mass" value="0" />
+    </repeat>
+    <param name="max_dynamic_mods" type="integer" label="Maximum Dynamic Mods per Sequence" value="2" />
+    <param name="tag_length" type="integer" label="Tag Length" value="3" help="A sequence tag is generated from the gaps between a number of peaks equal to this parameter plus one. Longer tag lengths are more specific, but harder to find because many consecutive ion fragments are rare." />
+    <param name="max_tags" type="integer" label="Maximum Number of Tags per Spectrum" value="20" />
+    <param name="tag_mz_tolerance" type="float" label="Fragment m/z Tolerance during Tag Generation (Da/z)" value=".5" />
+    <param name="protease" type="select" label="Protease"> 
+      <options from_file="proteases.loc">
+        <column name="name" index="0" />
+        <column name="value" index="1" />
+      </options>
+    </param>
+    <param name="max_missed_cleavages" label="Maximum Number of Missed Cleavages" type="integer" value="-1" />
+    <conditional name="advanced_cleavage_options">
+      <param name="specify" type="boolean" label="Specify advanced cleavage options" help="" truevalue="true" falsevalue="false" />
+      <when value="false" />
+      <when value="true">
+        <param name="min_termini_cleavages" type="select" label="Minimum Termini Cleavages" value="2" help="A peptide must start after a cleavage and end before a cleavage. Setting this parameter to 0 or 1 will reduce that requirement, so that neither terminus or only one terminus of the peptide must match one of the cleavage rules specified above.">
+          <option value="2">2</option>
+          <option value="1">1</option>
+          <option value="0">0</option>
+        </param>
+        <param name="use_net_adjustment" type="boolean" label="Use NET Adjustment" help="When enabled, TagRecon adds a probabilistic bonus to peptide scores depending on whether the peptides are fully-enzymatic, semi-enzymatic, or non-enzymatic." truevalue="true" falsevalue="false" />
+      </when>
+    </conditional>
+    <conditional name="advanced_charge_options">
+      <param name="specify" type="boolean" label="Specify Advanced Charge State Handling Options" help="" truevalue="true" falsevalue="false" />
+      <when value="false" />
+      <when value="true">
+        <param name="use_ms_charge_state" type="boolean" label="Use Charge State from MS" truevalue="true" falsevalue="false" help="When enabled, DirecTag and TagRecon will not use their internal algorithm to determine charge state of a spectrum when it is available in the input file." />
+        <!-- TODO: Add DuplicateSpectra, NumChargeStates -->
+      </when>
+    </conditional>
+    <!-- TODO: Advanced Peptide Filtering: Min/Max Peptide Mass/Length -->
+    <conditional name="tag_weights">
+      <param name="specify" type="boolean" label="Override Default Tag Weighting" help="By default equal weights are assigned to intensity, m/z fidelity, and complement scores." truevalue="true" falsevalue="false" />
+      <when value="false" />
+      <when value="true">
+        <param name="intensity" type="float" label="Intensity Score Weight" help="" value="1.0" />
+        <param name="mz" type="float" label="m/z Fidelity Score Weight" help="" value="1.0" />
+        <param name="complement" type="float" label="Complement Score Weight" help="" value="1.0" />
+      </when>
+    </conditional>
+    <conditional name="search_untagged">
+      <param name="search" type="boolean" label="Search Untagged Spectra" help="Search untagged spectra like a database search." truevalue="true" falsevalue="false" />
+      <when value="false" />
+      <when value="true">
+        <param name="precursor_mz_tolerance" type="float" label="Untagged Spectra Precursor m/z Tolerance" value="1.25" />
+      </when>
+    </conditional>
+    <conditional name="unknown_mass_shifts">
+      <param name="how" type="select" label="Explaination for Unknown Mass Shifts">
+        <option value="">None, disable delta mass interpretation by TagRecon</option>
+        <option value="blindptms">Blind PTMs</option>
+        <option value="mutations">Mutations</option>
+        <!-- TODO: Add preferredptms -->
+      </param>
+      <when value="blindptms">
+        <!-- BlindPTMResidues ??? -->
+      </when>
+      <when value="mutations">
+        <!-- BlosumScoreThreshold ??? BlosumThreshold ???-->
+      </when>
+      <when value="" />
+    </conditional>
+  </inputs>
+<!-- 
+  Both:
+  AdjustPrecursorMass (defaults to false)
+
+  TagRecon:
+  Skip for now: ComputeXCorr
+  Skip forever: ProteinSampleSize
+
+  TO ADD:
+
+  Both: Advanced, ClassSizeMultiplier, float 2.0.
+-->
+  <outputs>
+    <data format="raw_pepxml" name="output" from_work_dir="output">
+      <change_format>
+        <when input="output_type" value="mzid" format="mzid" />
+      </change_format>
+    </data>
+  </outputs>
+
+  <requirements>
+    <requirement type="package">directag</requirement>
+    <requirement type="package">tagrecon</requirement>
+  </requirements>
+
+  <help>
+**What it does**
+
+Performs protein identification via Directag and TagRecon.
+
+------
+
+**Citation**
+
+For the underlying tool, please cite `TODO`.
+
+If you use this tool in Galaxy, please cite TODO.
+  </help>
+</tool>
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/update.sh	Fri May 10 17:06:14 2013 -0400
@@ -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