--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/COPYING	Fri Sep 26 18:45:34 2014 -0400
@@ -0,0 +1,121 @@
+Creative Commons Legal Code
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--- a/LICENSE	Fri May 10 10:40:10 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,202 +0,0 @@
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--- a/README.md	Fri May 10 10:40:10 2013 -0400
+++ b/README.md	Fri Sep 26 18:45:34 2014 -0400
@@ -1,25 +1,47 @@
-The repository contains the tool wrapper for the TINT MGF
-formatter. This produces specially formatted MGF files for picky
-applications such as ProteinPilot and ms2preproc.
-# Obtaining Tools
+GalaxyP - MGF Formatter
+=======================
+
+* Home: <https://bitbucket.org/galaxyp/mgf_formatter>
+* Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/mgf_formatter>
+* Tool ID: `mgf_formatter`
+
+
+Description
+-----------
 
-Repositories for all Galaxy-P tools can be found at
-https:/bitbucket.org/galaxyp/.
+This produces specially formatted MGF files for picky applications such as `ProteinPilot` and `ms2preproc`.
+
 
-# Contact
+GalaxyP Community
+-----------------
 
-Please send suggestions for improvements and bug reports to
-jmchilton@gmail.com.
+Current governing community policies for [GalaxyP](https://bitbucket.org/galaxyp/) and other information can be found at:
+
+<https://bitbucket.org/galaxyp/galaxyp>
+
 
-# License
+License
+-------
+
+Copyright (c) 2014 Regents of the University of Minnesota and Authors listed below.
 
-All Galaxy-P tools are licensed under the Apache License Version 2.0
-unless otherwise documented.
+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.
+
 
-# Tool Versioning
+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.
+
 
-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.
+Authors
+-------
+
+Authors and contributors:
+
+* John Chilton <jmchilton@gmail.com>
+* Minnesota Supercomputing Institute, Univeristy of Minnesota

--- a/README_GALAXYP.md	Fri May 10 10:40:10 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +0,0 @@
-# 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.

--- a/README_REPO.md	Fri May 10 10:40:10 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-The repository contains the tool wrapper for the TINT MGF
-formatter. This produces specially formatted MGF files for picky
-applications such as ProteinPilot and ms2preproc.

--- a/mgf_formatter.xml	Fri May 10 10:40:10 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,45 +0,0 @@
-<tool id="mgf_formatter" name="MGF Formatter" version="0.1.0">
-  <description>convert peak lists into MGF files formatted for particular downstream applications.</description>
-
-  <command>
-  MgfFormatter --mgf_format $mgf_format --output '$output' $itraq_filter 
-  #if $type.input_type == "mgf"
-  $type.split_multiple_charge_states
-  #end if
-  $type.inputs
-  </command>
-  <inputs>
-    <conditional name="type">
-      <param name="input_type" type="select" label="Input Type">
-        <option value="mzml">mzML</option>
-        <option value="mzxml">mzXML</option>
-        <option value="mgf">MGF</option>
-      </param>
-      <when value="mzml">
-        <param format="mzml" name="inputs" type="data" label="Input mzML" />
-      </when>
-      <when value="mzxml">
-        <param format="mzxml" name="inputs" type="data" label="Input mzXML" />
-      </when>
-      <when value="mgf">
-        <param format="mgf" name="inputs" type="data" label="Input MGF" />
-        <param type="boolean" name="split_multiple_charge_states" label="Split up scans with multiple charge states specified in MGF." truevalue="" falsevalue="--no_split_multiple_charge_states" checked="true" />
-      </when>
-    </conditional>
-    <param name="mgf_format" type="select" label="MGF Format">
-      <option value="DEFAULT">Mascot (default, probably should use msconvert instead)</option>
-      <option value="PROTEIN_PILOT">ProteinPilot</option>
-      <option value="MS2PREPROC">ms2preproc</option>
-      <option value="MSM">MSM</option>
-    </param>
-    <param name="itraq_filter" type="boolean" label="Preselect iTRAQ reporter ions" help="Recent versions of ProteinPilot fail to find the correct report ions, this tool filters out extra peaks in that region to circumvent this bug if this is checked. This is an advanced option and should only be checked if you are certain you want it." truevalue="--itraq_filter" falsevalue="" />
-  </inputs>
-  <outputs>
-    <data format="mgf" name="output" label="${mgf_format.value_label.split()[0]} formatted MGF of ${on_string}" />
-  </outputs>
-  <requirements>
-    <requirement type="package">tint_proteomics_scripts</requirement>    
-  </requirements>
-  <help>
-  </help>
-</tool>

--- a/repository_dependencies.xml	Fri May 10 10:40:10 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-<?xml version="1.0"?>
-<repositories description="Required proteomics dependencies.">
-  <repository toolshed="http://toolshed.g2.bx.psu.edu" name="tint" owner="galaxyp" changeset_revision="ab43b5ba7a4e"/>
-  <repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="f74290b136fc" />
-</repositories>

--- a/tool_dependencies.xml	Fri May 10 10:40:10 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="tint_proteomics_scripts" version="1.19.19">
-    <repository toolshed="http://toolshed.g2.bx.psu.edu" name="tint" owner="galaxyp" changeset_revision="ab43b5ba7a4e"/>
-  </package>
-</tool_dependency>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mgf_formatter/mgf_formatter.xml	Fri Sep 26 18:45:34 2014 -0400
@@ -0,0 +1,49 @@
+<tool id="mgf_formatter" name="MGF Formatter" version="0.1.0">
+  <requirements>
+    <requirement type="package" version="22">binaries_for_package_mgf_formatter</requirement>
+  </requirements>
+
+  <description>convert peak lists into MGF files formatted for particular downstream applications.</description>
+
+  <command>
+    MgfFormatter --mgf_format $mgf_format --output '$output' $itraq_filter
+    #if $type.input_type == "mgf"
+    $type.split_multiple_charge_states
+    #end if
+    $type.inputs
+  </command>
+  <inputs>
+    <conditional name="type">
+      <param name="input_type" type="select" label="Input Type">
+        <option value="mzml">mzML</option>
+        <option value="mzxml">mzXML</option>
+        <option value="mgf">MGF</option>
+      </param>
+      <when value="mzml">
+        <param format="mzml" name="inputs" type="data" label="Input mzML" />
+      </when>
+      <when value="mzxml">
+        <param format="mzxml" name="inputs" type="data" label="Input mzXML" />
+      </when>
+      <when value="mgf">
+        <param format="mgf" name="inputs" type="data" label="Input MGF" />
+        <param type="boolean" name="split_multiple_charge_states" label="Split up scans with multiple charge states specified in MGF." truevalue="" falsevalue="--no_split_multiple_charge_states" checked="true" />
+      </when>
+    </conditional>
+    <param name="mgf_format" type="select" label="MGF Format">
+      <option value="DEFAULT">Mascot (default, probably should use msconvert instead)</option>
+      <option value="PROTEIN_PILOT">ProteinPilot</option>
+      <option value="MS2PREPROC">ms2preproc</option>
+      <option value="MSM">MSM</option>
+    </param>
+    <param name="itraq_filter" type="boolean" label="Preselect iTRAQ reporter ions" help="Recent versions of ProteinPilot fail to find the correct report ions, this tool filters out extra peaks in that region to circumvent this bug if this is checked. This is an advanced option and should only be checked if you are certain you want it." truevalue="--itraq_filter" falsevalue="" />
+  </inputs>
+  <outputs>
+    <data format="mgf" name="output" label="${mgf_format.value_label.split()[0]} formatted MGF of ${on_string}" />
+  </outputs>
+  <stdio>
+    <exit_code range="1:" level="fatal" description="Unknown error, exit code non-zero" />
+  </stdio>
+  <help>
+  </help>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mgf_formatter/repository_dependencies.xml	Fri Sep 26 18:45:34 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/mgf_formatter/tool_dependencies.xml	Fri Sep 26 18:45:34 2014 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="binaries_for_package_mgf_formatter" version="22">
+        <repository changeset_revision="36f70ca62ec1" name="package_mgf_formatter" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>

--- a/update.sh	Fri May 10 10:40:10 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,35 +0,0 @@
-#!/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