--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/COPYING	Fri Sep 26 15:26:14 2014 -0400
@@ -0,0 +1,121 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Fri Sep 26 15:26:14 2014 -0400
@@ -0,0 +1,51 @@
+GalaxyP - MyriMatch
+===================
+
+* Home: <https://bitbucket.org/galaxyp/myrimatch>
+* Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/myrimatch>
+* Tool ID: `myrimatch`
+
+
+Description
+-----------
+
+Bumbershoot MyriMatch.
+
+See:
+
+* <http://fenchurch.mc.vanderbilt.edu/bumbershoot/myrimatch/>
+
+
+GalaxyP Community
+-----------------
+
+Current governing community policies for [GalaxyP](https://bitbucket.org/galaxyp/) and other information can be found at:
+
+<https://bitbucket.org/galaxyp/galaxyp>
+
+
+License
+-------
+
+Copyright (c) 2014 Regents of the University of Minnesota and Authors listed below.
+
+To the extent possible under law, the author(s) have dedicated all copyright and related and neighboring rights to this software to the public domain worldwide. This software is distributed without any warranty.
+
+You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see <https://creativecommons.org/publicdomain/zero/1.0/>.
+
+You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission.
+
+
+Contributing
+------------
+
+Contributions to this repository are reviewed through pull requests. If you would like your work acknowledged, please also add yourself to the Authors section. If your pull request is accepted, you will also be acknowledged in <https://bitbucket.org/galaxyp/galaxyp/CONTRIBUTORS.md> unless you opt-out.
+
+
+Authors
+-------
+
+Authors and contributors:
+
+* John Chilton <jmchilton@gmail.com>
+* Minnesota Supercomputing Institute, Univeristy of Minnesota

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/proteases.loc.sample	Fri Sep 26 15:26:14 2014 -0400
@@ -0,0 +1,22 @@
+Trypsin	Trypsin
+Trypsin/P	Trypsin/P
+2-iodobenzoate	2-iodobenzoate
+Arg-C	Arg-C
+Asp-N	Asp-N
+Asp-N_ambic	Asp-N_ambic
+CNBr	CNBr
+Chymotrypsin	Chymotrypsin
+Formic_acid	Formic_acid
+Lys-C	Lys-C
+Lys-C/P	Lys-C/P
+NoEnzyme	NoEnzyme
+PepsinA	PepsinA
+TrypChymo	TrypChymo
+V8-DE	V8-DE
+V8-E	V8-E
+glutamyl endopeptidase	glutamyl endopeptidase
+leukocyte elastase	leukocyte elastase
+no cleavage	no cleavage
+proline endopeptidase	proline endopeptidase
+unspecific cleavage	unspecific cleavage
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/myrimatch.xml	Fri Sep 26 15:26:14 2014 -0400
@@ -0,0 +1,192 @@
+<tool id="myrimatch" version="0.1.0" name="MyriMatch">
+  <requirements>
+    <requirement type="package" version="333">binaries_for_package_myrimatch</requirement>
+  </requirements>
+
+  <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>
+
+  <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/tools/repository_dependencies.xml	Fri Sep 26 15:26:14 2014 -0400
@@ -0,0 +1,4 @@
+<?xml version="1.0"?>
+<repositories>
+  <repository changeset_revision="f66f8ca7b7b9" name="proteomics_datatypes" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" />
+</repositories>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/tool_dependencies.xml	Fri Sep 26 15:26:14 2014 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="binaries_for_package_myrimatch" version="333">
+    <repository changeset_revision="fd3893bf3008" name="package_myrimatch" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" />
+  </package>
+</tool_dependency>