--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/COPYING	Fri Sep 26 14:44:54 2014 -0400
@@ -0,0 +1,121 @@
+Creative Commons Legal Code
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--- a/LICENSE	Mon Feb 17 17:00:29 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,202 +0,0 @@
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--- a/README.md	Mon Feb 17 17:00:29 2014 -0500
+++ b/README.md	Fri Sep 26 14:44:54 2014 -0400
@@ -1,47 +1,67 @@
-# msconvert
+GalaxyP - ProteoWizard msconvert
+================================
+
+* Home: <https://bitbucket.org/galaxyp/msconvert>
+* Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/msconvert>
+* Tool ID: `msconvert`
+
 
-This repository contains Galaxy tool wrappers for msconvert, part of
-the ProteoWizard (http://proteowizard.sourceforge.net/) package.
+Description
+-----------
 
-# Installing
+msconvert from ProteoWizard.
+
+Note: This requires manual installation of ProteoWizard, and may require a Windows environment.
+
+See:
 
-Due to potential difficulties installing ProteoWizard with vendor
-library support, tools for interacting with vendor types are seperated
-out into their own wrappers. Galaxy is generally deployed under Linux,
-but vendor support in ProteoWizard requires .NET 4.0. There are at
-least two ways to get this to work:
+* <http://proteowizard.sourceforge.net/>
+* <http://proteowizard.sourceforge.net/tools/msconvert.html>
+
+
+Installing
+----------
 
-  * Galaxy jobs may be configured to submit to a Windows host with
-    ProteoWizard installed using the
-    LWR. http://wiki.g2.bx.psu.edu/Admin/Config/LWR
+Due to potential difficulties installing ProteoWizard with vendor library support, tools for interacting with vendor types are seperated out into their own wrappers. Galaxy is generally deployed under Linux, but vendor support in ProteoWizard requires .NET 4.0. There are at least two ways to get this to work:
+
+* Galaxy jobs may be configured to submit to a Windows host with ProteoWizard installed using the [LWR](https://wiki.g2.bx.psu.edu/Admin/Config/LWR).
 
-  * ProteoWizard can be installed under Wine. Guidance on how to set
-    this up and package such environments for cloud deployments can be
-    found here: https://github.com/jmchilton/proteomics-wine-env
+* ProteoWizard can be installed under Wine. Guidance on how to set this up and package such environments for cloud deployments can be found here: <https://github.com/jmchilton/proteomics-wine-env>
+
+
+GalaxyP Community
+-----------------
 
-Wrappers for both msconvert version 2 and version 3+ are provided
-because version 3+ of msconvert with vendor library support requires
-.NET 4.0 and this may difficult or impossible under Wine in Linux with
-all but the most recent versions of Wine (1.4+).
-# Obtaining Tools
+Current governing community policies for [GalaxyP](https://bitbucket.org/galaxyp/) and other information can be found at:
+
+<https://bitbucket.org/galaxyp/galaxyp>
+
+
+License
+-------
 
-Repositories for all Galaxy-P tools can be found at
-https:/bitbucket.org/galaxyp/.
+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.
 
-# Contact
+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.
+
 
-Please send suggestions for improvements and bug reports to
-jmchilton@gmail.com.
+Contributing
+------------
 
-# License
+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.
 
-All Galaxy-P tools are licensed under the Apache License Version 2.0
-unless otherwise documented.
 
-# Tool Versioning
+Authors
+-------
+
+Authors and contributors:
 
-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.
+* Björn Grüning
+* Cody Wang
+* Fred Sadler
+* John Chilton <jmchilton@gmail.com>
+* Minnesota Supercomputing Institute, Univeristy of Minnesota

--- a/README_GALAXYP.md	Mon Feb 17 17:00:29 2014 -0500
+++ /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	Mon Feb 17 17:00:29 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,25 +0,0 @@
-# msconvert
-
-This repository contains Galaxy tool wrappers for msconvert, part of
-the ProteoWizard (http://proteowizard.sourceforge.net/) package.
-
-# Installing
-
-Due to potential difficulties installing ProteoWizard with vendor
-library support, tools for interacting with vendor types are seperated
-out into their own wrappers. Galaxy is generally deployed under Linux,
-but vendor support in ProteoWizard requires .NET 4.0. There are at
-least two ways to get this to work:
-
-  * Galaxy jobs may be configured to submit to a Windows host with
-    ProteoWizard installed using the
-    LWR. http://wiki.g2.bx.psu.edu/Admin/Config/LWR
-
-  * ProteoWizard can be installed under Wine. Guidance on how to set
-    this up and package such environments for cloud deployments can be
-    found here: https://github.com/jmchilton/proteomics-wine-env
-
-Wrappers for both msconvert version 2 and version 3+ are provided
-because version 3+ of msconvert with vendor library support requires
-.NET 4.0 and this may difficult or impossible under Wine in Linux with
-all but the most recent versions of Wine (1.4+).

--- a/TODO	Mon Feb 17 17:00:29 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-Add precursorRefine option.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/msconvert.xml	Fri Sep 26 14:44:54 2014 -0400
@@ -0,0 +1,377 @@
+<tool id="msconvert" name="msconvert" version="0.3.0">
+  <!-- BEGIN_VERSION_DEFAULT -->
+  <description>Convert and filter a mass spec peak list</description>
+  <!-- END_VERSION_DEFAULT -->
+  <!--
+  <requirements>
+    <requirement type="package" version="3_0_4388">proteowizard</requirement>
+  </requirements>
+-->
+  <command interpreter="python">
+    #set $ext = $input.ext
+    msconvert_wrapper.py
+    --input=${input}
+    #if hasattr($input, 'display_name')
+    --input_name='${input.display_name}'
+    #end if
+    --output=${output}
+    ## BEGIN_VERSION_DEFAULT
+    --fromextension=$ext
+    ## END_VERSION_DEFAULT
+
+
+    --toextension=${output_type}
+
+    #if $settings.settingsType == "full"
+    --binaryencoding=${settings.binary_encoding}
+    --mzencoding=${settings.mz_encoding}
+    --intensityencoding=${settings.intensity_encoding}
+    --zlib=${settings.zlib}
+    #end if
+
+    #if $filtering.filtering_use
+
+    #if $filtering.precursor_recalculation.value
+    --filter "precursorRecalculation"
+    #end if
+
+    #if $filtering.peak_picking.pick_peaks
+    --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels"
+    #end if
+
+    #if str($filtering.activation) != "false"
+    --filter "activation $filtering.activation"
+    #end if
+
+    #if len($filtering.indices) > 0
+    --filter "index
+    #for $index in $filtering.indices
+    [${index.from},${index.to}]
+    #end for
+    "
+    #end if
+
+    #if len($filtering.scan_numbers) > 0
+    --filter "scanNumber
+    #for $scan_number in $filtering.scan_numbers
+    [${scan_number.from},${scan_number.to}]
+    #end for
+    "
+    #end if
+
+    #for threshold_entry in $filtering.threshold_repeat
+    --filter "threshold $threshold_entry.threshold.threshold_type $threshold_entry.threshold.value $threshold_entry.orientation"
+    #end for
+
+
+    #if $filtering.strip_it.value
+    --filter "stripIT"
+    #end if
+
+    #if $filtering.filter_mz_windows.do_filter
+    --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]"
+    #end if
+
+
+    #if $filtering.filter_ms_levels.do_filter
+    --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]"
+    #end if
+
+    #if str($filtering.etd_filtering.do_etd_filtering) == "default"
+    --filter "ETDFilter"
+    #end if
+
+    #if str($filtering.etd_filtering.do_etd_filtering) == "advanced"
+    --filter "ETDFilter removePrecursor:$filtering.etd_filtering.remove_precursor removeChargeReduced:$filtering.etd_filtering.remove_charge_reduced  removeNeutralLoss:$filtering.etd_filtering.remove_neutral_loss  blanketRemoval:$filtering.etd_filtering.blanket_removal  MatchingTolerance:$filtering.etd_filtering.matching_tolerance $filtering.etd_filtering.matching_tolerance_units"
+    #end if
+
+    ## BEGIN_VERSION_3
+
+    #if $filtering.precursor_refine.value
+    --filter "precursorRefine"
+    #end if
+
+    #if $filtering.ms2denoise.denoise
+    --filter "MS2Denoise $filtering.ms2denoise.num_peaks $filtering.ms2denoise.window_width $filtering.ms2denoise.relax"
+    #end if
+
+    #if str($filtering.ms2deisotope) == "true"
+    --filter "MS2Deisotope"
+    #end if
+
+    #if str($filtering.polarity) != "false"
+    --filter "polarity $filtering.polarity"
+    #end if
+
+    #if str($filtering.analyzer) != "false"
+    --filter "analyzer $filtering.analyzer"
+    #end if
+
+    ## END_VERSION_3
+
+    #end if
+
+  </command>
+
+  <inputs>
+
+    <!-- BEGIN_VERSION_DEFAULT -->
+    <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>
+    <!-- END_VERSION_DEFAULT -->
+    <param name="output_type" type="select" label="Output Type">
+      <option value="mzML">mzML (indexed)</option>
+      <option value="unindexed_mzML">mzML (unindexed)</option>
+      <option value="mzXML">mzXML (indexed)</option>
+      <option value="unindexed_mzXML">mzXML (unindexed)</option>
+      <option value="mgf">mgf</option>
+      <option value="ms2">ms2</option>
+    </param>
+    <conditional name="filtering">
+      <param name="filtering_use" type="boolean" label="Use Filtering?" truevalue="true" falsevalue="false" />
+      <when value="false" />
+      <when value="true">
+        <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" />
+        <!-- BEGIN_VERSION_3 -->
+        <param type="boolean" name="precursor_refine" label="Refine Precursor?" />
+        <!-- END_VERSION_3 -->
+
+
+        <conditional name="peak_picking">
+          <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" />
+          <when value="false" />
+          <when value="true">
+            <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
+              <option value="1">MS1 Only (1)</option>
+              <option value="2">MS2 Only (2)</option>
+              <option value="2-">MS2 and on (2-)</option>
+              <option value="1-">All Levels (1-)</option>
+            </param>
+            <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/>
+          </when>
+        </conditional>
+
+        <repeat name="threshold_repeat" title="Filter by Threshold">
+          <conditional name="threshold">
+            <param type="select" label="Specify threshold on" name="threshold_type" help="">
+              <option value="count">Peak count</option>
+              <option value="count-after-ties">Peak count (after ties)</option>
+              <option value="absolute">Peak absolute intensity</option><!-- TODO: absolute what? m/z -->
+              <option value="bpi-relative">Percent of base peak intensity</option>
+              <option value="tic-relative">Percent of total ion current</option>
+              <option value="tic-fraction">Aggregate percent of total ion current</option>
+            </param>
+            <when value="count">
+              <param type="integer" name="value" label="Number of peaks to keep" value="100" />
+            </when>
+            <when value="count-after-ties">
+              <param type="integer" name="value" label="Number of peaks to keep (after ties)" value="100" />
+            </when>
+            <when value="absolute">
+              <param type="float" name="value" label="Absolute intensity cut-off" value="100.0" />
+            </when>
+            <when value="bpi-relative">
+              <param type="float" name="value" label="Keep peaks above (or below) this fraction of base peak intensity" value="0.2"
+              />
+            </when>
+            <when value="tic-relative">
+              <param type="float" name="value" label="Keep peaks above (or below) this fraction of total ion current" value="0.2"
+              />
+            </when>
+            <when value="tic-fraction">
+              <param type="float" name="value" label="Keep peaks until this fraction of total ion current is accounted for" value="0.8" />
+            </when>
+          </conditional>
+          <param type="select" label="Keep" name="orientation">
+            <option value="most-intense">Most intense peaks</option>
+            <option value="least-intense">Least intense peaks</option>
+          </param>
+        </repeat>
+
+
+        <param name="activation" type="select" label="Filter by Activation">
+          <option value="false" selected="true">no</option>
+          <option value="ETD">ETD</option>
+          <option value="CID">CID</option>
+          <option value="SA">SA</option>
+          <option value="HCD">HCD</option>
+          <!-- BEGIN_VERSION_3 -->
+          <option>BIRD</option>
+          <option>ECD</option>
+          <option>IRMPD</option>
+          <option>PD</option>
+          <option>PSD</option>
+          <option>PQD</option>
+          <option>SID</option>
+          <option>SORI</option>
+          <!-- END_VERSION_3 -->
+        </param>
+
+        <repeat name="indices" title="Filter Scan Indices">
+          <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
+          <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
+        </repeat>
+
+        <repeat name="scan_numbers" title="Filter Scan Numbers">
+          <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" />
+          <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" />
+        </repeat>
+
+        <conditional name="filter_mz_windows">
+          <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
+          <when value="false" />
+          <when value="true">
+            <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" />
+            <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" />
+          </when>
+        </conditional>
+
+        <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
+
+        <conditional name="filter_ms_levels">
+          <param name="do_filter" type="boolean" label="Filter MS Levels" />
+          <when value="false" />
+          <when value="true">
+            <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" />
+            <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" />
+          </when>
+        </conditional>
+
+        <conditional name="etd_filtering">
+          <param name="do_etd_filtering" type="select" label="ETD Filtering">
+            <option value="none" selected="true">none</option>
+            <option value="default">yes (with default options)</option>
+            <option value="advanced">yes (show advanced options) </option>
+          </param>
+          <when value="none" />
+          <when value="default" />
+          <when value="advanced">
+            <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1">
+            </param>
+            <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">
+              <option value="MZ" selected="true">mz</option>
+              <option value="PPM">ppm</option>
+            </param>
+            <param name="remove_precursor" type="select" label="ETD Remove Precursor">
+              <option value="true" selected="true">yes</option>
+              <option value="false">no</option>
+            </param>
+            <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced">
+              <option value="true" selected="true">yes</option>
+              <option value="false">no</option>
+            </param>
+            <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss">
+              <option value="true" selected="true">yes</option>
+              <option value="false">no</option>
+            </param>
+            <param name="blanket_removal" type="select" label="ETD Blanket Removal">
+              <option value="true" selected="true">yes</option>
+              <option value="false">no</option>
+            </param>
+          </when>
+        </conditional>
+
+
+        <!-- BEGIN_VERSION_3 -->
+        <conditional name="ms2denoise">
+          <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter"  />
+          <when value="true">
+            <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />
+            <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />
+            <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" />
+          </when>
+          <when value="false" />
+        </conditional>
+        <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />
+
+        <param name="polarity" type="select" label="Filter by Polarity">
+          <option value="false" selected="true">no</option>
+          <option value="positive">positive</option>
+          <option value="negative">negative</option>
+        </param>
+
+        <param name="analyzer" type="select" label="Filter by Analyzer">
+          <option value="false" selected="true">no</option>
+          <option value="quad">quad</option>
+          <option value="orbi">orbi</option>
+          <option value="FT">FT</option>
+          <option value="IT">IT</option>
+          <option value="TOF">TOF</option>
+        </param>
+        <!-- END_VERSION_3 -->
+      </when>
+    </conditional>
+
+    <conditional name="settings">
+      <param name="settingsType" type="select" label="Advanced Settings" help="">
+        <option value="default">Use Defaults</option>
+        <option value="full">Full Parameter List</option>
+      </param>
+      <when value="default" />
+      <when value="full">
+        <param type="select" name="binary_encoding" label="Binary Encoding Precision">
+          <option value="64" selected="true">64</option>
+          <option value="32">32</option>
+        </param>
+        <param type="select" name="mz_encoding" label="m/z Encoding Precision">
+          <option value="64" selected="true">64</option>
+          <option value="32">32</option>
+        </param>
+        <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32">
+          <option value="64">64</option>
+          <option value="32" selected="true">32</option>
+        </param>
+        <param type="boolean" name="zlib" label="Use zlib">
+        </param>
+      </when>
+    </conditional>
+
+
+  </inputs>
+  <outputs>
+    <data format="mzml" name="output">
+      <change_format>
+        <when input="output_type" value="mzXML" format="mzxml" />
+        <when input="output_type" value="unindexed_mzXML" format="mzxml" />
+        <when input="output_type" value="ms2" format="ms2" />
+        <when input="output_type" value="mgf" format="mgf" />
+      </change_format>
+    </data>
+  </outputs>
+  <help>
+**What it does**
+
+Allows interconversion within various mass spectrometry peak list formats. Additional options such as filtering and/or precursor recalculation are available.
+
+You can view the original documentation here_.
+
+.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
+
+------
+
+**Citation**
+
+For the underlying tool, please cite `ProteoWizard: Open Source Software for Rapid Proteomics Tools Development. Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick. Bioinformatics 2008; doi: 10.1093/bioinformatics/btn323.`
+
+If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/msconvert
+
+  </help>
+</tool>

--- a/msconvert.xml.template	Mon Feb 17 17:00:29 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,393 +0,0 @@
-<tool id="msconvert$VERSION$DESCRIPTION" name="msconvert$VERSION$DESCRIPTION" version="0.1.0">
-  <!-- BEGIN_VERSION_RAW -->
-  <description>Convert and filter a Thermo Finnigan RAW file</description>
-  <!-- END_VERSION_RAW -->
-  <!-- BEGIN_VERSION_DEFAULT -->
-  <description>Convert and filter a mass spec peak list</description>
-  <!-- END_VERSION_DEFAULT -->
-
-  <command interpreter="python">
-    #set $ext = $input.ext
-    #if $ext.startswith("m:")
-    #set $ext = $ext[len("m:"):]
-    #end if
-    msconvert_wrapper.py 
-    --input=${input}
-    #if hasattr($input, 'display_name')
-    --input_name='${input.display_name}'
-    #end if
-    --output=${output} 
-    ## BEGIN_VERSION_DEFAULT    
-    --fromextension=$ext
-    ## END_VERSION_DEFAULT
-
-    ## BEGIN_VERSION_RAW
-    --fromextension=RAW
-    ## END_VERSION_RAW
-
-    --toextension=${output_type} 
-
-    #if $settings.settingsType == "full"
-    --binaryencoding=${settings.binary_encoding} 
-    --mzencoding=${settings.mz_encoding} 
-    --intensityencoding=${settings.intensity_encoding}
-    --zlib=${settings.zlib}
-    #end if
-
-    #if $filtering.filtering_use
-
-    #if $filtering.precursor_recalculation.value
-    --filter "precursorRecalculation"
-    #end if
-
-    #if $filtering.peak_picking.pick_peaks
-    --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels"
-    #end if
-
-    #if str($filtering.activation) != "false"
-    --filter "activation $filtering.activation"
-    #end if
-
-    #if len($filtering.indices) > 0
-    --filter "index
-    #for $index in $filtering.indices
-    [${index.from},${index.to}]
-    #end for
-    "
-    #end if
-
-    #if len($filtering.scan_numbers) > 0
-    --filter "scanNumber
-    #for $scan_number in $filtering.scan_numbers
-    [${scan_number.from},${scan_number.to}]
-    #end for
-    "
-    #end if
-
-    #for threshold_entry in $filtering.threshold_repeat
-    --filter "threshold $threshold_entry.threshold.threshold_type $threshold_entry.threshold.value $threshold_entry.orientation"
-    #end for
-
-
-    #if $filtering.strip_it.value
-    --filter "stripIT"
-    #end if
-
-    #if $filtering.filter_mz_windows.do_filter
-    --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]"
-    #end if
-
-    
-    #if $filtering.filter_ms_levels.do_filter
-    --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]"
-    #end if
-
-    #if str($filtering.etd_filtering.do_etd_filtering) == "default"
-    --filter "ETDFilter"
-    #end if
-
-    #if str($filtering.etd_filtering.do_etd_filtering) == "advanced"
-    --filter "ETDFilter removePrecursor:$filtering.etd_filtering.remove_precursor removeChargeReduced:$filtering.etd_filtering.remove_charge_reduced  removeNeutralLoss:$filtering.etd_filtering.remove_neutral_loss  blanketRemoval:$filtering.etd_filtering.blanket_removal  MatchingTolerance:$filtering.etd_filtering.matching_tolerance $filtering.etd_filtering.matching_tolerance_units"
-    #end if
-
-    ## BEGIN_VERSION_3
-
-    #if $filtering.precursor_refine.value
-    --filter "precursorRefine"
-    #end if
-
-    #if $filtering.ms2denoise.denoise
-    --filter "MS2Denoise $filtering.ms2denoise.num_peaks $filtering.ms2denoise.window_width $filtering.ms2denoise.relax"
-    #end if 
-
-    #if str($filtering.ms2deisotope) == "true"
-    --filter "MS2Deisotope"
-    #end if
-
-    #if str($filtering.polarity) != "false"
-    --filter "polarity $filtering.polarity"
-    #end if
-
-    #if str($filtering.analyzer) != "false"
-    --filter "analyzer $filtering.analyzer"
-    #end if
-
-    ## END_VERSION_3
-
-    #end if
-
-  </command>
-
-  <inputs>
-    <!-- BEGIN_VERSION_RAW -->
-    <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input"/>
-    <!-- END_VERSION_RAW -->
-
-    <!-- BEGIN_VERSION_DEFAULT -->
-    <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>
-    <!-- END_VERSION_DEFAULT -->    
-    <param name="output_type" type="select" label="Output Type">
-      <option value="mzML">mzML (indexed)</option>
-      <option value="unindexed_mzML">mzML (unindexed)</option>
-      <option value="mzXML">mzXML (indexed)</option>      
-      <option value="unindexed_mzXML">mzXML (unindexed)</option>
-      <option value="mgf">mgf</option>
-      <option value="ms2">ms2</option>  
-    </param>    
-    <conditional name="filtering">
-      <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" />
-      <when value="false" />
-      <when value="true">
-        <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" />
-        <!-- BEGIN_VERSION_3 -->
-        <param type="boolean" name="precursor_refine" label="Refine Precursor?" />
-        <!-- END_VERSION_3 -->
-
-
-        <conditional name="peak_picking">
-          <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" />
-          <when value="false" />
-          <when value="true">
-            <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
-              <option value="1">MS1 Only (1)</option>
-              <option value="2">MS2 Only (2)</option>
-              <option value="2-">MS2 and on (2-)</option>
-              <option value="1-">All Levels (1-)</option>
-            </param>
-            <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/>
-          </when>
-        </conditional>
-
-        <repeat name="threshold_repeat" title="Filter by Threshold">
-          <conditional name="threshold">
-            <param type="select" label="Specify threshold on" name="threshold_type" help="">
-              <option value="count">Peak count</option>
-              <option value="count-after-ties">Peak count (after ties)</option>
-              <option value="absolute">Peak absolute intensity</option><!-- TODO: absolute what? m/z -->
-              <option value="bpi-relative">Percent of base peak intensity</option>
-              <option value="tic-relative">Percent of total ion current</option>
-              <option value="tic-fraction">Aggregate percent of total ion current</option>
-            </param>
-            <when value="count">
-              <param type="integer" name="value" label="Number of peaks to keep" value="100" />
-            </when>
-            <when value="count-after-ties">
-              <param type="integer" name="value" label="Number of peaks to keep (after ties)" value="100" />
-            </when>
-            <when value="absolute">
-              <param type="float" name="value" label="Absolute intensity cut-off" value="100.0" />
-            </when>
-            <when value="bpi-relative">
-              <param type="float" name="value" label="Keep peaks above (or below) this fraction of base peak intensity" value="0.2"
-              />
-            </when>
-            <when value="tic-relative">
-              <param type="float" name="value" label="Keep peaks above (or below) this fraction of total ion current" value="0.2"
-              />
-            </when>
-            <when value="tic-fraction">
-              <param type="float" name="value" label="Keep peaks until this fraction of total ion current is accounted for" value="0.8" />
-            </when>
-          </conditional>
-          <param type="select" label="Keep" name="orientation">
-            <option value="most-intense">Most intense peaks</option>
-            <option value="least-intense">Least intense peaks</option>
-          </param>
-        </repeat>
-
-
-        <param name="activation" type="select" label="Filter by Activation">
-          <option value="false" selected="true">no</option>
-          <option value="ETD">ETD</option>
-          <option value="CID">CID</option>
-          <option value="SA">SA</option>
-          <option value="HCD">HCD</option>
-          <!-- BEGIN_VERSION_3 -->
-          <option>BIRD</option>
-          <option>ECD</option>
-          <option>IRMPD</option>
-          <option>PD</option>
-          <option>PSD</option>
-          <option>PQD</option>
-          <option>SID</option>
-          <option>SORI</option>
-          <!-- END_VERSION_3 -->
-        </param>
-
-        <repeat name="indices" title="Filter Scan Indices">
-          <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
-          <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
-        </repeat>
-
-        <repeat name="scan_numbers" title="Filter Scan Numbers">
-          <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" />
-          <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" />
-        </repeat>
-
-        <conditional name="filter_mz_windows">
-          <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
-          <when value="false" />          
-          <when value="true">
-            <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" />
-            <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" />
-          </when>
-        </conditional>
-
-        <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
-
-        <conditional name="filter_ms_levels">
-          <param name="do_filter" type="boolean" label="Filter MS Levels" />
-          <when value="false" />
-          <when value="true">
-            <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" />
-            <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" />
-          </when>
-        </conditional>
-
-        <conditional name="etd_filtering">
-          <param name="do_etd_filtering" type="select" label="ETD Filtering">
-            <option value="none" selected="true">none</option>
-            <option value="default">yes (with default options)</option>
-            <option value="advanced">yes (show advanced options) </option>
-          </param>
-          <when value="none" />
-          <when value="default" />
-          <when value="advanced">
-            <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1">
-            </param>
-            <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">
-              <option value="MZ" selected="true">mz</option>              
-              <option value="PPM">ppm</option>
-            </param>
-            <param name="remove_precursor" type="select" label="ETD Remove Precursor">
-              <option value="true" selected="true">yes</option>              
-              <option value="false">no</option>
-            </param>
-            <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced">
-              <option value="true" selected="true">yes</option>              
-              <option value="false">no</option>
-            </param>            
-            <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss">
-              <option value="true" selected="true">yes</option>              
-              <option value="false">no</option>
-            </param>
-            <param name="blanket_removal" type="select" label="ETD Blanket Removal">
-              <option value="true" selected="true">yes</option>              
-              <option value="false">no</option>
-            </param>
-          </when>
-        </conditional>
-
-
-        <!-- BEGIN_VERSION_3 -->
-        <conditional name="ms2denoise">
-          <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter"  />
-          <when value="true">
-            <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />
-            <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />
-            <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" />
-          </when>
-          <when value="false" />
-        </conditional>
-        <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />
-
-        <param name="polarity" type="select" label="Filter by Polarity">
-          <option value="false" selected="true">no</option>
-          <option value="positive">positive</option>
-          <option value="negative">negative</option>
-        </param>
-
-        <param name="analyzer" type="select" label="Filter by Analyzer">
-          <option value="false" selected="true">no</option>
-          <option value="quad">quad</option>
-          <option value="orbi">orbi</option>
-          <option value="FT">FT</option>
-          <option value="IT">IT</option>
-          <option value="TOF">TOF</option>
-        </param>
-        <!-- END_VERSION_3 -->
-      </when>
-    </conditional>
-
-    <conditional name="settings">
-      <param name="settingsType" type="select" label="Advanced Settings" help="">
-        <option value="default">Use Defaults</option>
-        <option value="full">Full Parameter List</option>
-      </param>
-      <when value="default" />
-      <when value="full">
-        <param type="select" name="binary_encoding" label="Binary Encoding Precision">
-          <option value="64" selected="true">64</option>
-          <option value="32">32</option>
-        </param>
-        <param type="select" name="mz_encoding" label="m/z Encoding Precision">
-          <option value="64" selected="true">64</option>
-          <option value="32">32</option>
-        </param>
-        <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32">
-          <option value="64">64</option>
-          <option value="32" selected="true">32</option>
-        </param>
-        <param type="boolean" name="zlib" label="Use zlib">      
-        </param>
-      </when>
-    </conditional>
-
-
-  </inputs>
-  <outputs>
-    <data format="mzml" name="output">
-      <change_format>
-        <when input="output_type" value="mzXML" format="mzxml" />
-        <when input="output_type" value="unindexed_mzXML" format="mzxml" />
-        <when input="output_type" value="ms2" format="ms2" />
-        <when input="output_type" value="mgf" format="mgf" />
-      </change_format>
-    </data>
-  </outputs>
-
-  <requirements>
-    <requirement type="package">proteowizard</requirement>    
-    <!-- BEGIN_VERSION_RAW -->
-    <requirement type="platform">windows</requirement>
-    <!-- END_VERSION_RAW -->    
-  </requirements>
-
-  <help>
-**What it does**
-
-Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available.
-
-You can view the original documentation here_.
-    
-.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
-
-------
-
-**Citation**
-
-For the underlying tool, please cite `ProteoWizard: Open Source Software for Rapid Proteomics Tools Development. Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick. Bioinformatics 2008; doi: 10.1093/bioinformatics/btn323.`
-
-If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert
-
-  </help>
-</tool>

--- a/msconvert2.xml	Mon Feb 17 17:00:29 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,315 +0,0 @@
-<tool id="msconvert2" name="msconvert2" version="0.2.1">
-  <!-- BEGIN_VERSION_DEFAULT -->
-  <description>Convert and filter a mass spec peak list</description>
-  <!-- END_VERSION_DEFAULT -->
-  <requirements>
-    <requirement type="package">proteowizard</requirement>
-  </requirements>
-  <command interpreter="python">
-    #set $ext = $input.ext
-    #if $ext.startswith("m:")
-    #set $ext = $ext[len("m:"):]
-    #end if
-    msconvert_wrapper.py 
-    --input=${input}
-    #if hasattr($input, 'display_name')
-    --input_name='${input.display_name}'
-    #end if
-    --output=${output} 
-    ## BEGIN_VERSION_DEFAULT    
-    --fromextension=$ext
-    ## END_VERSION_DEFAULT
-
-
-    --toextension=${output_type} 
-
-    #if $settings.settingsType == "full"
-    --binaryencoding=${settings.binary_encoding} 
-    --mzencoding=${settings.mz_encoding} 
-    --intensityencoding=${settings.intensity_encoding}
-    --zlib=${settings.zlib}
-    #end if
-
-    #if $filtering.filtering_use
-
-    #if $filtering.precursor_recalculation.value
-    --filter "precursorRecalculation"
-    #end if
-
-    #if $filtering.peak_picking.pick_peaks
-    --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels"
-    #end if
-
-    #if str($filtering.activation) != "false"
-    --filter "activation $filtering.activation"
-    #end if
-
-    #if len($filtering.indices) > 0
-    --filter "index
-    #for $index in $filtering.indices
-    [${index.from},${index.to}]
-    #end for
-    "
-    #end if
-
-    #if len($filtering.scan_numbers) > 0
-    --filter "scanNumber
-    #for $scan_number in $filtering.scan_numbers
-    [${scan_number.from},${scan_number.to}]
-    #end for
-    "
-    #end if
-
-    #for threshold_entry in $filtering.threshold_repeat
-    --filter "threshold $threshold_entry.threshold.threshold_type $threshold_entry.threshold.value $threshold_entry.orientation"
-    #end for
-
-
-    #if $filtering.strip_it.value
-    --filter "stripIT"
-    #end if
-
-    #if $filtering.filter_mz_windows.do_filter
-    --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]"
-    #end if
-
-    
-    #if $filtering.filter_ms_levels.do_filter
-    --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]"
-    #end if
-
-    #if str($filtering.etd_filtering.do_etd_filtering) == "default"
-    --filter "ETDFilter"
-    #end if
-
-    #if str($filtering.etd_filtering.do_etd_filtering) == "advanced"
-    --filter "ETDFilter removePrecursor:$filtering.etd_filtering.remove_precursor removeChargeReduced:$filtering.etd_filtering.remove_charge_reduced  removeNeutralLoss:$filtering.etd_filtering.remove_neutral_loss  blanketRemoval:$filtering.etd_filtering.blanket_removal  MatchingTolerance:$filtering.etd_filtering.matching_tolerance $filtering.etd_filtering.matching_tolerance_units"
-    #end if
-
-
-    #end if
-
-  </command>
-
-  <inputs>
-
-    <!-- BEGIN_VERSION_DEFAULT -->
-    <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>
-    <!-- END_VERSION_DEFAULT -->    
-    <param name="output_type" type="select" label="Output Type">
-      <option value="mzML">mzML (indexed)</option>
-      <option value="unindexed_mzML">mzML (unindexed)</option>
-      <option value="mzXML">mzXML (indexed)</option>      
-      <option value="unindexed_mzXML">mzXML (unindexed)</option>
-      <option value="mgf">mgf</option>
-      <option value="ms2">ms2</option>  
-    </param>    
-    <conditional name="filtering">
-      <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" />
-      <when value="false" />
-      <when value="true">
-        <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" />
-
-
-        <conditional name="peak_picking">
-          <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" />
-          <when value="false" />
-          <when value="true">
-            <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
-              <option value="1">MS1 Only (1)</option>
-              <option value="2">MS2 Only (2)</option>
-              <option value="2-">MS2 and on (2-)</option>
-              <option value="1-">All Levels (1-)</option>
-            </param>
-            <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/>
-          </when>
-        </conditional>
-
-        <repeat name="threshold_repeat" title="Filter by Threshold">
-          <conditional name="threshold">
-            <param type="select" label="Specify threshold on" name="threshold_type" help="">
-              <option value="count">Peak count</option>
-              <option value="count-after-ties">Peak count (after ties)</option>
-              <option value="absolute">Peak absolute intensity</option><!-- TODO: absolute what? m/z -->
-              <option value="bpi-relative">Percent of base peak intensity</option>
-              <option value="tic-relative">Percent of total ion current</option>
-              <option value="tic-fraction">Aggregate percent of total ion current</option>
-            </param>
-            <when value="count">
-              <param type="integer" name="value" label="Number of peaks to keep" value="100" />
-            </when>
-            <when value="count-after-ties">
-              <param type="integer" name="value" label="Number of peaks to keep (after ties)" value="100" />
-            </when>
-            <when value="absolute">
-              <param type="float" name="value" label="Absolute intensity cut-off" value="100.0" />
-            </when>
-            <when value="bpi-relative">
-              <param type="float" name="value" label="Keep peaks above (or below) this fraction of base peak intensity" value="0.2"
-              />
-            </when>
-            <when value="tic-relative">
-              <param type="float" name="value" label="Keep peaks above (or below) this fraction of total ion current" value="0.2"
-              />
-            </when>
-            <when value="tic-fraction">
-              <param type="float" name="value" label="Keep peaks until this fraction of total ion current is accounted for" value="0.8" />
-            </when>
-          </conditional>
-          <param type="select" label="Keep" name="orientation">
-            <option value="most-intense">Most intense peaks</option>
-            <option value="least-intense">Least intense peaks</option>
-          </param>
-        </repeat>
-
-
-        <param name="activation" type="select" label="Filter by Activation">
-          <option value="false" selected="true">no</option>
-          <option value="ETD">ETD</option>
-          <option value="CID">CID</option>
-          <option value="SA">SA</option>
-          <option value="HCD">HCD</option>
-        </param>
-
-        <repeat name="indices" title="Filter Scan Indices">
-          <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
-          <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
-        </repeat>
-
-        <repeat name="scan_numbers" title="Filter Scan Numbers">
-          <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" />
-          <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" />
-        </repeat>
-
-        <conditional name="filter_mz_windows">
-          <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
-          <when value="false" />          
-          <when value="true">
-            <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" />
-            <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" />
-          </when>
-        </conditional>
-
-        <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
-
-        <conditional name="filter_ms_levels">
-          <param name="do_filter" type="boolean" label="Filter MS Levels" />
-          <when value="false" />
-          <when value="true">
-            <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" />
-            <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" />
-          </when>
-        </conditional>
-
-        <conditional name="etd_filtering">
-          <param name="do_etd_filtering" type="select" label="ETD Filtering">
-            <option value="none" selected="true">none</option>
-            <option value="default">yes (with default options)</option>
-            <option value="advanced">yes (show advanced options) </option>
-          </param>
-          <when value="none" />
-          <when value="default" />
-          <when value="advanced">
-            <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1">
-            </param>
-            <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">
-              <option value="MZ" selected="true">mz</option>              
-              <option value="PPM">ppm</option>
-            </param>
-            <param name="remove_precursor" type="select" label="ETD Remove Precursor">
-              <option value="true" selected="true">yes</option>              
-              <option value="false">no</option>
-            </param>
-            <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced">
-              <option value="true" selected="true">yes</option>              
-              <option value="false">no</option>
-            </param>            
-            <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss">
-              <option value="true" selected="true">yes</option>              
-              <option value="false">no</option>
-            </param>
-            <param name="blanket_removal" type="select" label="ETD Blanket Removal">
-              <option value="true" selected="true">yes</option>              
-              <option value="false">no</option>
-            </param>
-          </when>
-        </conditional>
-
-
-      </when>
-    </conditional>
-
-    <conditional name="settings">
-      <param name="settingsType" type="select" label="Advanced Settings" help="">
-        <option value="default">Use Defaults</option>
-        <option value="full">Full Parameter List</option>
-      </param>
-      <when value="default" />
-      <when value="full">
-        <param type="select" name="binary_encoding" label="Binary Encoding Precision">
-          <option value="64" selected="true">64</option>
-          <option value="32">32</option>
-        </param>
-        <param type="select" name="mz_encoding" label="m/z Encoding Precision">
-          <option value="64" selected="true">64</option>
-          <option value="32">32</option>
-        </param>
-        <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32">
-          <option value="64">64</option>
-          <option value="32" selected="true">32</option>
-        </param>
-        <param type="boolean" name="zlib" label="Use zlib">      
-        </param>
-      </when>
-    </conditional>
-
-
-  </inputs>
-  <outputs>
-    <data format="mzml" name="output">
-      <change_format>
-        <when input="output_type" value="mzXML" format="mzxml" />
-        <when input="output_type" value="unindexed_mzXML" format="mzxml" />
-        <when input="output_type" value="ms2" format="ms2" />
-        <when input="output_type" value="mgf" format="mgf" />
-      </change_format>
-    </data>
-  </outputs>
-  <help>
-**What it does**
-
-Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available.
-
-You can view the original documentation here_.
-    
-.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
-
-------
-
-**Citation**
-
-For the underlying tool, please cite `ProteoWizard: Open Source Software for Rapid Proteomics Tools Development. Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick. Bioinformatics 2008; doi: 10.1093/bioinformatics/btn323.`
-
-If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert
-
-  </help>
-</tool>

--- a/msconvert2_raw.xml	Mon Feb 17 17:00:29 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,299 +0,0 @@
-<tool id="msconvert2_raw" name="msconvert2_raw" version="0.2.1">
-  <!-- BEGIN_VERSION_RAW -->
-  <description>Convert and filter a Thermo Finnigan RAW file</description>
-  <!-- END_VERSION_RAW -->
-  <requirements>
-    <requirement type="package">proteowizard</requirement>
-    <!-- BEGIN_VERSION_RAW -->
-    <requirement type="platform">windows</requirement>
-    <!-- END_VERSION_RAW -->
-  </requirements>
-  <command interpreter="python">
-    #set $ext = $input.ext
-    #if $ext.startswith("m:")
-    #set $ext = $ext[len("m:"):]
-    #end if
-    msconvert_wrapper.py 
-    --input=${input}
-    #if hasattr($input, 'display_name')
-    --input_name='${input.display_name}'
-    #end if
-    --output=${output} 
-
-    ## BEGIN_VERSION_RAW
-    --fromextension=RAW
-    ## END_VERSION_RAW
-
-    --toextension=${output_type} 
-
-    #if $settings.settingsType == "full"
-    --binaryencoding=${settings.binary_encoding} 
-    --mzencoding=${settings.mz_encoding} 
-    --intensityencoding=${settings.intensity_encoding}
-    --zlib=${settings.zlib}
-    #end if
-
-    #if $filtering.filtering_use
-
-    #if $filtering.precursor_recalculation.value
-    --filter "precursorRecalculation"
-    #end if
-
-    #if $filtering.peak_picking.pick_peaks
-    --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels"
-    #end if
-
-    #if str($filtering.activation) != "false"
-    --filter "activation $filtering.activation"
-    #end if
-
-    #if len($filtering.indices) > 0
-    --filter "index
-    #for $index in $filtering.indices
-    [${index.from},${index.to}]
-    #end for
-    "
-    #end if
-
-    #if len($filtering.scan_numbers) > 0
-    --filter "scanNumber
-    #for $scan_number in $filtering.scan_numbers
-    [${scan_number.from},${scan_number.to}]
-    #end for
-    "
-    #end if
-
-    #for threshold_entry in $filtering.threshold_repeat
-    --filter "threshold $threshold_entry.threshold.threshold_type $threshold_entry.threshold.value $threshold_entry.orientation"
-    #end for
-
-
-    #if $filtering.strip_it.value
-    --filter "stripIT"
-    #end if
-
-    #if $filtering.filter_mz_windows.do_filter
-    --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]"
-    #end if
-
-    
-    #if $filtering.filter_ms_levels.do_filter
-    --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]"
-    #end if
-
-    #if str($filtering.etd_filtering.do_etd_filtering) == "default"
-    --filter "ETDFilter"
-    #end if
-
-    #if str($filtering.etd_filtering.do_etd_filtering) == "advanced"
-    --filter "ETDFilter removePrecursor:$filtering.etd_filtering.remove_precursor removeChargeReduced:$filtering.etd_filtering.remove_charge_reduced  removeNeutralLoss:$filtering.etd_filtering.remove_neutral_loss  blanketRemoval:$filtering.etd_filtering.blanket_removal  MatchingTolerance:$filtering.etd_filtering.matching_tolerance $filtering.etd_filtering.matching_tolerance_units"
-    #end if
-
-
-    #end if
-
-  </command>
-
-  <inputs>
-    <!-- BEGIN_VERSION_RAW -->
-    <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input"/>
-    <!-- END_VERSION_RAW -->
-
-    <param name="output_type" type="select" label="Output Type">
-      <option value="mzML">mzML (indexed)</option>
-      <option value="unindexed_mzML">mzML (unindexed)</option>
-      <option value="mzXML">mzXML (indexed)</option>      
-      <option value="unindexed_mzXML">mzXML (unindexed)</option>
-      <option value="mgf">mgf</option>
-      <option value="ms2">ms2</option>  
-    </param>    
-    <conditional name="filtering">
-      <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" />
-      <when value="false" />
-      <when value="true">
-        <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" />
-
-
-        <conditional name="peak_picking">
-          <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" />
-          <when value="false" />
-          <when value="true">
-            <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
-              <option value="1">MS1 Only (1)</option>
-              <option value="2">MS2 Only (2)</option>
-              <option value="2-">MS2 and on (2-)</option>
-              <option value="1-">All Levels (1-)</option>
-            </param>
-            <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/>
-          </when>
-        </conditional>
-
-        <repeat name="threshold_repeat" title="Filter by Threshold">
-          <conditional name="threshold">
-            <param type="select" label="Specify threshold on" name="threshold_type" help="">
-              <option value="count">Peak count</option>
-              <option value="count-after-ties">Peak count (after ties)</option>
-              <option value="absolute">Peak absolute intensity</option><!-- TODO: absolute what? m/z -->
-              <option value="bpi-relative">Percent of base peak intensity</option>
-              <option value="tic-relative">Percent of total ion current</option>
-              <option value="tic-fraction">Aggregate percent of total ion current</option>
-            </param>
-            <when value="count">
-              <param type="integer" name="value" label="Number of peaks to keep" value="100" />
-            </when>
-            <when value="count-after-ties">
-              <param type="integer" name="value" label="Number of peaks to keep (after ties)" value="100" />
-            </when>
-            <when value="absolute">
-              <param type="float" name="value" label="Absolute intensity cut-off" value="100.0" />
-            </when>
-            <when value="bpi-relative">
-              <param type="float" name="value" label="Keep peaks above (or below) this fraction of base peak intensity" value="0.2"
-              />
-            </when>
-            <when value="tic-relative">
-              <param type="float" name="value" label="Keep peaks above (or below) this fraction of total ion current" value="0.2"
-              />
-            </when>
-            <when value="tic-fraction">
-              <param type="float" name="value" label="Keep peaks until this fraction of total ion current is accounted for" value="0.8" />
-            </when>
-          </conditional>
-          <param type="select" label="Keep" name="orientation">
-            <option value="most-intense">Most intense peaks</option>
-            <option value="least-intense">Least intense peaks</option>
-          </param>
-        </repeat>
-
-
-        <param name="activation" type="select" label="Filter by Activation">
-          <option value="false" selected="true">no</option>
-          <option value="ETD">ETD</option>
-          <option value="CID">CID</option>
-          <option value="SA">SA</option>
-          <option value="HCD">HCD</option>
-        </param>
-
-        <repeat name="indices" title="Filter Scan Indices">
-          <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
-          <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
-        </repeat>
-
-        <repeat name="scan_numbers" title="Filter Scan Numbers">
-          <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" />
-          <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" />
-        </repeat>
-
-        <conditional name="filter_mz_windows">
-          <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
-          <when value="false" />          
-          <when value="true">
-            <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" />
-            <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" />
-          </when>
-        </conditional>
-
-        <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
-
-        <conditional name="filter_ms_levels">
-          <param name="do_filter" type="boolean" label="Filter MS Levels" />
-          <when value="false" />
-          <when value="true">
-            <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" />
-            <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" />
-          </when>
-        </conditional>
-
-        <conditional name="etd_filtering">
-          <param name="do_etd_filtering" type="select" label="ETD Filtering">
-            <option value="none" selected="true">none</option>
-            <option value="default">yes (with default options)</option>
-            <option value="advanced">yes (show advanced options) </option>
-          </param>
-          <when value="none" />
-          <when value="default" />
-          <when value="advanced">
-            <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1">
-            </param>
-            <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">
-              <option value="MZ" selected="true">mz</option>              
-              <option value="PPM">ppm</option>
-            </param>
-            <param name="remove_precursor" type="select" label="ETD Remove Precursor">
-              <option value="true" selected="true">yes</option>              
-              <option value="false">no</option>
-            </param>
-            <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced">
-              <option value="true" selected="true">yes</option>              
-              <option value="false">no</option>
-            </param>            
-            <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss">
-              <option value="true" selected="true">yes</option>              
-              <option value="false">no</option>
-            </param>
-            <param name="blanket_removal" type="select" label="ETD Blanket Removal">
-              <option value="true" selected="true">yes</option>              
-              <option value="false">no</option>
-            </param>
-          </when>
-        </conditional>
-
-
-      </when>
-    </conditional>
-
-    <conditional name="settings">
-      <param name="settingsType" type="select" label="Advanced Settings" help="">
-        <option value="default">Use Defaults</option>
-        <option value="full">Full Parameter List</option>
-      </param>
-      <when value="default" />
-      <when value="full">
-        <param type="select" name="binary_encoding" label="Binary Encoding Precision">
-          <option value="64" selected="true">64</option>
-          <option value="32">32</option>
-        </param>
-        <param type="select" name="mz_encoding" label="m/z Encoding Precision">
-          <option value="64" selected="true">64</option>
-          <option value="32">32</option>
-        </param>
-        <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32">
-          <option value="64">64</option>
-          <option value="32" selected="true">32</option>
-        </param>
-        <param type="boolean" name="zlib" label="Use zlib">      
-        </param>
-      </when>
-    </conditional>
-
-
-  </inputs>
-  <outputs>
-    <data format="mzml" name="output">
-      <change_format>
-        <when input="output_type" value="mzXML" format="mzxml" />
-        <when input="output_type" value="unindexed_mzXML" format="mzxml" />
-        <when input="output_type" value="ms2" format="ms2" />
-        <when input="output_type" value="mgf" format="mgf" />
-      </change_format>
-    </data>
-  </outputs>
-  <help>
-**What it does**
-
-Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available.
-
-You can view the original documentation here_.
-    
-.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
-
-------
-
-**Citation**
-
-For the underlying tool, please cite `ProteoWizard: Open Source Software for Rapid Proteomics Tools Development. Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick. Bioinformatics 2008; doi: 10.1093/bioinformatics/btn323.`
-
-If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert
-
-  </help>
-</tool>

--- a/msconvert3.xml	Mon Feb 17 17:00:29 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,378 +0,0 @@
-<tool id="msconvert3" name="msconvert3" version="0.2.1">
-  <!-- BEGIN_VERSION_DEFAULT -->
-  <description>Convert and filter a mass spec peak list</description>
-  <!-- END_VERSION_DEFAULT -->
-  <requirements>
-    <requirement type="package">proteowizard</requirement>
-  </requirements>
-  <command interpreter="python">
-    #set $ext = $input.ext
-    #if $ext.startswith("m:")
-    #set $ext = $ext[len("m:"):]
-    #end if
-    msconvert_wrapper.py 
-    --input=${input}
-    #if hasattr($input, 'display_name')
-    --input_name='${input.display_name}'
-    #end if
-    --output=${output} 
-    ## BEGIN_VERSION_DEFAULT
-    --fromextension=$ext
-    ## END_VERSION_DEFAULT
-
-
-    --toextension=${output_type} 
-
-    #if $settings.settingsType == "full"
-    --binaryencoding=${settings.binary_encoding} 
-    --mzencoding=${settings.mz_encoding} 
-    --intensityencoding=${settings.intensity_encoding}
-    --zlib=${settings.zlib}
-    #end if
-
-    #if $filtering.filtering_use
-
-    #if $filtering.precursor_recalculation.value
-    --filter "precursorRecalculation"
-    #end if
-
-    #if $filtering.peak_picking.pick_peaks
-    --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels"
-    #end if
-
-    #if str($filtering.activation) != "false"
-    --filter "activation $filtering.activation"
-    #end if
-
-    #if len($filtering.indices) > 0
-    --filter "index
-    #for $index in $filtering.indices
-    [${index.from},${index.to}]
-    #end for
-    "
-    #end if
-
-    #if len($filtering.scan_numbers) > 0
-    --filter "scanNumber
-    #for $scan_number in $filtering.scan_numbers
-    [${scan_number.from},${scan_number.to}]
-    #end for
-    "
-    #end if
-
-    #for threshold_entry in $filtering.threshold_repeat
-    --filter "threshold $threshold_entry.threshold.threshold_type $threshold_entry.threshold.value $threshold_entry.orientation"
-    #end for
-
-
-    #if $filtering.strip_it.value
-    --filter "stripIT"
-    #end if
-
-    #if $filtering.filter_mz_windows.do_filter
-    --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]"
-    #end if
-
-    
-    #if $filtering.filter_ms_levels.do_filter
-    --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]"
-    #end if
-
-    #if str($filtering.etd_filtering.do_etd_filtering) == "default"
-    --filter "ETDFilter"
-    #end if
-
-    #if str($filtering.etd_filtering.do_etd_filtering) == "advanced"
-    --filter "ETDFilter removePrecursor:$filtering.etd_filtering.remove_precursor removeChargeReduced:$filtering.etd_filtering.remove_charge_reduced  removeNeutralLoss:$filtering.etd_filtering.remove_neutral_loss  blanketRemoval:$filtering.etd_filtering.blanket_removal  MatchingTolerance:$filtering.etd_filtering.matching_tolerance $filtering.etd_filtering.matching_tolerance_units"
-    #end if
-
-    ## BEGIN_VERSION_3
-
-    #if $filtering.precursor_refine.value
-    --filter "precursorRefine"
-    #end if
-
-    #if $filtering.ms2denoise.denoise
-    --filter "MS2Denoise $filtering.ms2denoise.num_peaks $filtering.ms2denoise.window_width $filtering.ms2denoise.relax"
-    #end if 
-
-    #if str($filtering.ms2deisotope) == "true"
-    --filter "MS2Deisotope"
-    #end if
-
-    #if str($filtering.polarity) != "false"
-    --filter "polarity $filtering.polarity"
-    #end if
-
-    #if str($filtering.analyzer) != "false"
-    --filter "analyzer $filtering.analyzer"
-    #end if
-
-    ## END_VERSION_3
-
-    #end if
-
-  </command>
-
-  <inputs>
-
-    <!-- BEGIN_VERSION_DEFAULT -->
-    <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>
-    <!-- END_VERSION_DEFAULT -->    
-    <param name="output_type" type="select" label="Output Type">
-      <option value="mzML">mzML (indexed)</option>
-      <option value="unindexed_mzML">mzML (unindexed)</option>
-      <option value="mzXML">mzXML (indexed)</option>      
-      <option value="unindexed_mzXML">mzXML (unindexed)</option>
-      <option value="mgf">mgf</option>
-      <option value="ms2">ms2</option>  
-    </param>    
-    <conditional name="filtering">
-      <param name="filtering_use" type="boolean" label="Use Filtering?" truevalue="true" falsevalue="false" />
-      <when value="false" />
-      <when value="true">
-        <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" />
-        <!-- BEGIN_VERSION_3 -->
-        <param type="boolean" name="precursor_refine" label="Refine Precursor?" />
-        <!-- END_VERSION_3 -->
-
-
-        <conditional name="peak_picking">
-          <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" />
-          <when value="false" />
-          <when value="true">
-            <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
-              <option value="1">MS1 Only (1)</option>
-              <option value="2">MS2 Only (2)</option>
-              <option value="2-">MS2 and on (2-)</option>
-              <option value="1-">All Levels (1-)</option>
-            </param>
-            <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/>
-          </when>
-        </conditional>
-
-        <repeat name="threshold_repeat" title="Filter by Threshold">
-          <conditional name="threshold">
-            <param type="select" label="Specify threshold on" name="threshold_type" help="">
-              <option value="count">Peak count</option>
-              <option value="count-after-ties">Peak count (after ties)</option>
-              <option value="absolute">Peak absolute intensity</option><!-- TODO: absolute what? m/z -->
-              <option value="bpi-relative">Percent of base peak intensity</option>
-              <option value="tic-relative">Percent of total ion current</option>
-              <option value="tic-fraction">Aggregate percent of total ion current</option>
-            </param>
-            <when value="count">
-              <param type="integer" name="value" label="Number of peaks to keep" value="100" />
-            </when>
-            <when value="count-after-ties">
-              <param type="integer" name="value" label="Number of peaks to keep (after ties)" value="100" />
-            </when>
-            <when value="absolute">
-              <param type="float" name="value" label="Absolute intensity cut-off" value="100.0" />
-            </when>
-            <when value="bpi-relative">
-              <param type="float" name="value" label="Keep peaks above (or below) this fraction of base peak intensity" value="0.2"
-              />
-            </when>
-            <when value="tic-relative">
-              <param type="float" name="value" label="Keep peaks above (or below) this fraction of total ion current" value="0.2"
-              />
-            </when>
-            <when value="tic-fraction">
-              <param type="float" name="value" label="Keep peaks until this fraction of total ion current is accounted for" value="0.8" />
-            </when>
-          </conditional>
-          <param type="select" label="Keep" name="orientation">
-            <option value="most-intense">Most intense peaks</option>
-            <option value="least-intense">Least intense peaks</option>
-          </param>
-        </repeat>
-
-
-        <param name="activation" type="select" label="Filter by Activation">
-          <option value="false" selected="true">no</option>
-          <option value="ETD">ETD</option>
-          <option value="CID">CID</option>
-          <option value="SA">SA</option>
-          <option value="HCD">HCD</option>
-          <!-- BEGIN_VERSION_3 -->
-          <option>BIRD</option>
-          <option>ECD</option>
-          <option>IRMPD</option>
-          <option>PD</option>
-          <option>PSD</option>
-          <option>PQD</option>
-          <option>SID</option>
-          <option>SORI</option>
-          <!-- END_VERSION_3 -->
-        </param>
-
-        <repeat name="indices" title="Filter Scan Indices">
-          <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
-          <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
-        </repeat>
-
-        <repeat name="scan_numbers" title="Filter Scan Numbers">
-          <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" />
-          <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" />
-        </repeat>
-
-        <conditional name="filter_mz_windows">
-          <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
-          <when value="false" />          
-          <when value="true">
-            <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" />
-            <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" />
-          </when>
-        </conditional>
-
-        <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
-
-        <conditional name="filter_ms_levels">
-          <param name="do_filter" type="boolean" label="Filter MS Levels" />
-          <when value="false" />
-          <when value="true">
-            <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" />
-            <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" />
-          </when>
-        </conditional>
-
-        <conditional name="etd_filtering">
-          <param name="do_etd_filtering" type="select" label="ETD Filtering">
-            <option value="none" selected="true">none</option>
-            <option value="default">yes (with default options)</option>
-            <option value="advanced">yes (show advanced options) </option>
-          </param>
-          <when value="none" />
-          <when value="default" />
-          <when value="advanced">
-            <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1">
-            </param>
-            <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">
-              <option value="MZ" selected="true">mz</option>              
-              <option value="PPM">ppm</option>
-            </param>
-            <param name="remove_precursor" type="select" label="ETD Remove Precursor">
-              <option value="true" selected="true">yes</option>              
-              <option value="false">no</option>
-            </param>
-            <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced">
-              <option value="true" selected="true">yes</option>              
-              <option value="false">no</option>
-            </param>            
-            <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss">
-              <option value="true" selected="true">yes</option>              
-              <option value="false">no</option>
-            </param>
-            <param name="blanket_removal" type="select" label="ETD Blanket Removal">
-              <option value="true" selected="true">yes</option>              
-              <option value="false">no</option>
-            </param>
-          </when>
-        </conditional>
-
-
-        <!-- BEGIN_VERSION_3 -->
-        <conditional name="ms2denoise">
-          <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter"  />
-          <when value="true">
-            <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />
-            <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />
-            <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" />
-          </when>
-          <when value="false" />
-        </conditional>
-        <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />
-
-        <param name="polarity" type="select" label="Filter by Polarity">
-          <option value="false" selected="true">no</option>
-          <option value="positive">positive</option>
-          <option value="negative">negative</option>
-        </param>
-
-        <param name="analyzer" type="select" label="Filter by Analyzer">
-          <option value="false" selected="true">no</option>
-          <option value="quad">quad</option>
-          <option value="orbi">orbi</option>
-          <option value="FT">FT</option>
-          <option value="IT">IT</option>
-          <option value="TOF">TOF</option>
-        </param>
-        <!-- END_VERSION_3 -->
-      </when>
-    </conditional>
-
-    <conditional name="settings">
-      <param name="settingsType" type="select" label="Advanced Settings" help="">
-        <option value="default">Use Defaults</option>
-        <option value="full">Full Parameter List</option>
-      </param>
-      <when value="default" />
-      <when value="full">
-        <param type="select" name="binary_encoding" label="Binary Encoding Precision">
-          <option value="64" selected="true">64</option>
-          <option value="32">32</option>
-        </param>
-        <param type="select" name="mz_encoding" label="m/z Encoding Precision">
-          <option value="64" selected="true">64</option>
-          <option value="32">32</option>
-        </param>
-        <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32">
-          <option value="64">64</option>
-          <option value="32" selected="true">32</option>
-        </param>
-        <param type="boolean" name="zlib" label="Use zlib">      
-        </param>
-      </when>
-    </conditional>
-
-
-  </inputs>
-  <outputs>
-    <data format="mzml" name="output">
-      <change_format>
-        <when input="output_type" value="mzXML" format="mzxml" />
-        <when input="output_type" value="unindexed_mzXML" format="mzxml" />
-        <when input="output_type" value="ms2" format="ms2" />
-        <when input="output_type" value="mgf" format="mgf" />
-      </change_format>
-    </data>
-  </outputs>
-  <help>
-**What it does**
-
-Allows interconversion within various mass spectrometry peak list formats. Additional options such as filtering and/or precursor recalculation are available.
-
-You can view the original documentation here_.
-    
-.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
-
-------
-
-**Citation**
-
-For the underlying tool, please cite `ProteoWizard: Open Source Software for Rapid Proteomics Tools Development. Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick. Bioinformatics 2008; doi: 10.1093/bioinformatics/btn323.`
-
-If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert
-
-  </help>
-</tool>

--- a/msconvert3_raw.xml	Mon Feb 17 17:00:29 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,362 +0,0 @@
-<tool id="msconvert3_raw" name="msconvert3_raw" version="0.2.1">
-  <!-- BEGIN_VERSION_RAW -->
-  <description>Convert and filter a Thermo Finnigan RAW file</description>
-  <!-- END_VERSION_RAW -->
-  <requirements>
-    <requirement type="package">proteowizard</requirement>
-    <!-- BEGIN_VERSION_RAW -->
-    <requirement type="platform">windows</requirement>
-    <!-- END_VERSION_RAW -->
-  </requirements>
-  <command interpreter="python">
-    #set $ext = $input.ext
-    #if $ext.startswith("m:")
-    #set $ext = $ext[len("m:"):]
-    #end if
-    msconvert_wrapper.py 
-    --input=${input}
-    #if hasattr($input, 'display_name')
-    --input_name='${input.display_name}'
-    #end if
-    --output=${output} 
-
-    ## BEGIN_VERSION_RAW
-    --fromextension=RAW
-    ## END_VERSION_RAW
-
-    --toextension=${output_type} 
-
-    #if $settings.settingsType == "full"
-    --binaryencoding=${settings.binary_encoding} 
-    --mzencoding=${settings.mz_encoding} 
-    --intensityencoding=${settings.intensity_encoding}
-    --zlib=${settings.zlib}
-    #end if
-
-    #if $filtering.filtering_use
-
-    #if $filtering.precursor_recalculation.value
-    --filter "precursorRecalculation"
-    #end if
-
-    #if $filtering.peak_picking.pick_peaks
-    --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels"
-    #end if
-
-    #if str($filtering.activation) != "false"
-    --filter "activation $filtering.activation"
-    #end if
-
-    #if len($filtering.indices) > 0
-    --filter "index
-    #for $index in $filtering.indices
-    [${index.from},${index.to}]
-    #end for
-    "
-    #end if
-
-    #if len($filtering.scan_numbers) > 0
-    --filter "scanNumber
-    #for $scan_number in $filtering.scan_numbers
-    [${scan_number.from},${scan_number.to}]
-    #end for
-    "
-    #end if
-
-    #for threshold_entry in $filtering.threshold_repeat
-    --filter "threshold $threshold_entry.threshold.threshold_type $threshold_entry.threshold.value $threshold_entry.orientation"
-    #end for
-
-
-    #if $filtering.strip_it.value
-    --filter "stripIT"
-    #end if
-
-    #if $filtering.filter_mz_windows.do_filter
-    --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]"
-    #end if
-
-    
-    #if $filtering.filter_ms_levels.do_filter
-    --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]"
-    #end if
-
-    #if str($filtering.etd_filtering.do_etd_filtering) == "default"
-    --filter "ETDFilter"
-    #end if
-
-    #if str($filtering.etd_filtering.do_etd_filtering) == "advanced"
-    --filter "ETDFilter removePrecursor:$filtering.etd_filtering.remove_precursor removeChargeReduced:$filtering.etd_filtering.remove_charge_reduced  removeNeutralLoss:$filtering.etd_filtering.remove_neutral_loss  blanketRemoval:$filtering.etd_filtering.blanket_removal  MatchingTolerance:$filtering.etd_filtering.matching_tolerance $filtering.etd_filtering.matching_tolerance_units"
-    #end if
-
-    ## BEGIN_VERSION_3
-
-    #if $filtering.precursor_refine.value
-    --filter "precursorRefine"
-    #end if
-
-    #if $filtering.ms2denoise.denoise
-    --filter "MS2Denoise $filtering.ms2denoise.num_peaks $filtering.ms2denoise.window_width $filtering.ms2denoise.relax"
-    #end if 
-
-    #if str($filtering.ms2deisotope) == "true"
-    --filter "MS2Deisotope"
-    #end if
-
-    #if str($filtering.polarity) != "false"
-    --filter "polarity $filtering.polarity"
-    #end if
-
-    #if str($filtering.analyzer) != "false"
-    --filter "analyzer $filtering.analyzer"
-    #end if
-
-    ## END_VERSION_3
-
-    #end if
-
-  </command>
-
-  <inputs>
-    <!-- BEGIN_VERSION_RAW -->
-    <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input" help="select input file in RAW format"/>
-    <!-- END_VERSION_RAW -->
-
-    <param name="output_type" type="select" label="Output Type">
-      <option value="mzML">mzML (indexed)</option>
-      <option value="unindexed_mzML">mzML (unindexed)</option>
-      <option value="mzXML">mzXML (indexed)</option>      
-      <option value="unindexed_mzXML">mzXML (unindexed)</option>
-      <option value="mgf">mgf</option>
-      <option value="ms2">ms2</option>  
-    </param>    
-    <conditional name="filtering">
-      <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" />
-      <when value="false" />
-      <when value="true">
-        <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" />
-        <!-- BEGIN_VERSION_3 -->
-        <param type="boolean" name="precursor_refine" label="Refine Precursor?" />
-        <!-- END_VERSION_3 -->
-
-
-        <conditional name="peak_picking">
-          <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" />
-          <when value="false" />
-          <when value="true">
-            <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
-              <option value="1">MS1 Only (1)</option>
-              <option value="2">MS2 Only (2)</option>
-              <option value="2-">MS2 and on (2-)</option>
-              <option value="1-">All Levels (1-)</option>
-            </param>
-            <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/>
-          </when>
-        </conditional>
-
-        <repeat name="threshold_repeat" title="Filter by Threshold">
-          <conditional name="threshold">
-            <param type="select" label="Specify threshold on" name="threshold_type" help="">
-              <option value="count">Peak count</option>
-              <option value="count-after-ties">Peak count (after ties)</option>
-              <option value="absolute">Peak absolute intensity</option><!-- TODO: absolute what? m/z -->
-              <option value="bpi-relative">Percent of base peak intensity</option>
-              <option value="tic-relative">Percent of total ion current</option>
-              <option value="tic-fraction">Aggregate percent of total ion current</option>
-            </param>
-            <when value="count">
-              <param type="integer" name="value" label="Number of peaks to keep" value="100" />
-            </when>
-            <when value="count-after-ties">
-              <param type="integer" name="value" label="Number of peaks to keep (after ties)" value="100" />
-            </when>
-            <when value="absolute">
-              <param type="float" name="value" label="Absolute intensity cut-off" value="100.0" />
-            </when>
-            <when value="bpi-relative">
-              <param type="float" name="value" label="Keep peaks above (or below) this fraction of base peak intensity" value="0.2"
-              />
-            </when>
-            <when value="tic-relative">
-              <param type="float" name="value" label="Keep peaks above (or below) this fraction of total ion current" value="0.2"
-              />
-            </when>
-            <when value="tic-fraction">
-              <param type="float" name="value" label="Keep peaks until this fraction of total ion current is accounted for" value="0.8" />
-            </when>
-          </conditional>
-          <param type="select" label="Keep" name="orientation">
-            <option value="most-intense">Most intense peaks</option>
-            <option value="least-intense">Least intense peaks</option>
-          </param>
-        </repeat>
-
-
-        <param name="activation" type="select" label="Filter by Activation">
-          <option value="false" selected="true">no</option>
-          <option value="ETD">ETD</option>
-          <option value="CID">CID</option>
-          <option value="SA">SA</option>
-          <option value="HCD">HCD</option>
-          <!-- BEGIN_VERSION_3 -->
-          <option>BIRD</option>
-          <option>ECD</option>
-          <option>IRMPD</option>
-          <option>PD</option>
-          <option>PSD</option>
-          <option>PQD</option>
-          <option>SID</option>
-          <option>SORI</option>
-          <!-- END_VERSION_3 -->
-        </param>
-
-        <repeat name="indices" title="Filter Scan Indices">
-          <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
-          <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
-        </repeat>
-
-        <repeat name="scan_numbers" title="Filter Scan Numbers">
-          <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" />
-          <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" />
-        </repeat>
-
-        <conditional name="filter_mz_windows">
-          <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
-          <when value="false" />          
-          <when value="true">
-            <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" />
-            <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" />
-          </when>
-        </conditional>
-
-        <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
-
-        <conditional name="filter_ms_levels">
-          <param name="do_filter" type="boolean" label="Filter MS Levels" />
-          <when value="false" />
-          <when value="true">
-            <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" />
-            <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" />
-          </when>
-        </conditional>
-
-        <conditional name="etd_filtering">
-          <param name="do_etd_filtering" type="select" label="ETD Filtering">
-            <option value="none" selected="true">none</option>
-            <option value="default">yes (with default options)</option>
-            <option value="advanced">yes (show advanced options) </option>
-          </param>
-          <when value="none" />
-          <when value="default" />
-          <when value="advanced">
-            <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1">
-            </param>
-            <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">
-              <option value="MZ" selected="true">mz</option>              
-              <option value="PPM">ppm</option>
-            </param>
-            <param name="remove_precursor" type="select" label="ETD Remove Precursor">
-              <option value="true" selected="true">yes</option>              
-              <option value="false">no</option>
-            </param>
-            <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced">
-              <option value="true" selected="true">yes</option>              
-              <option value="false">no</option>
-            </param>            
-            <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss">
-              <option value="true" selected="true">yes</option>              
-              <option value="false">no</option>
-            </param>
-            <param name="blanket_removal" type="select" label="ETD Blanket Removal">
-              <option value="true" selected="true">yes</option>              
-              <option value="false">no</option>
-            </param>
-          </when>
-        </conditional>
-
-
-        <!-- BEGIN_VERSION_3 -->
-        <conditional name="ms2denoise">
-          <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter"  />
-          <when value="true">
-            <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />
-            <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />
-            <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" />
-          </when>
-          <when value="false" />
-        </conditional>
-        <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />
-
-        <param name="polarity" type="select" label="Filter by Polarity">
-          <option value="false" selected="true">no</option>
-          <option value="positive">positive</option>
-          <option value="negative">negative</option>
-        </param>
-
-        <param name="analyzer" type="select" label="Filter by Analyzer">
-          <option value="false" selected="true">no</option>
-          <option value="quad">quad</option>
-          <option value="orbi">orbi</option>
-          <option value="FT">FT</option>
-          <option value="IT">IT</option>
-          <option value="TOF">TOF</option>
-        </param>
-        <!-- END_VERSION_3 -->
-      </when>
-    </conditional>
-
-    <conditional name="settings">
-      <param name="settingsType" type="select" label="Advanced Settings" help="">
-        <option value="default">Use Defaults</option>
-        <option value="full">Full Parameter List</option>
-      </param>
-      <when value="default" />
-      <when value="full">
-        <param type="select" name="binary_encoding" label="Binary Encoding Precision">
-          <option value="64" selected="true">64</option>
-          <option value="32">32</option>
-        </param>
-        <param type="select" name="mz_encoding" label="m/z Encoding Precision">
-          <option value="64" selected="true">64</option>
-          <option value="32">32</option>
-        </param>
-        <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32">
-          <option value="64">64</option>
-          <option value="32" selected="true">32</option>
-        </param>
-        <param type="boolean" name="zlib" label="Use zlib">      
-        </param>
-      </when>
-    </conditional>
-
-
-  </inputs>
-  <outputs>
-    <data format="mzml" name="output">
-      <change_format>
-        <when input="output_type" value="mzXML" format="mzxml" />
-        <when input="output_type" value="unindexed_mzXML" format="mzxml" />
-        <when input="output_type" value="ms2" format="ms2" />
-        <when input="output_type" value="mgf" format="mgf" />
-      </change_format>
-    </data>
-  </outputs>
-  <help>
-**What it does**
-
-Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available.
-
-You can view the original documentation here_.
-    
-.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
-
-------
-
-**Citation**
-
-For the underlying tool, please cite `ProteoWizard: Open Source Software for Rapid Proteomics Tools Development. Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick. Bioinformatics 2008; doi: 10.1093/bioinformatics/btn323.`
-
-If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert
-
-  </help>
-</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/msconvert_raw.xml	Fri Sep 26 14:44:54 2014 -0400
@@ -0,0 +1,396 @@
+<tool id="msconvert_raw" name="msconvert RAW" version="0.3.0">
+  <!-- BEGIN_VERSION_RAW -->
+  <description>Convert and filter a Thermo Finnigan RAW file</description>
+  <!-- END_VERSION_RAW -->
+  <requirements>
+<!--
+    <requirement type="package" version="3_0_4388">proteowizard</requirement>
+-->
+    <!-- BEGIN_VERSION_RAW -->
+    <requirement type="platform">windows</requirement>
+    <!-- END_VERSION_RAW -->
+  </requirements>
+  <command interpreter="python">
+    #set $ext = $input.ext
+    msconvert_wrapper.py
+    --input=${input}
+    #if hasattr($input, 'display_name')
+    --input_name='${input.display_name}'
+    #end if
+    --output=${output}
+
+    ## BEGIN_VERSION_RAW
+    --fromextension=RAW
+    ## END_VERSION_RAW
+
+    --toextension=${output_type}
+
+    #if $settings.settingsType == "full"
+    --binaryencoding=${settings.binary_encoding}
+    --mzencoding=${settings.mz_encoding}
+    --intensityencoding=${settings.intensity_encoding}
+    --zlib=${settings.zlib}
+    #end if
+
+    #if $filtering.filtering_use
+
+    #if $filtering.precursor_recalculation.value
+    --filter "precursorRecalculation"
+    #end if
+
+    #if $filtering.peak_picking.pick_peaks
+    --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels"
+    #end if
+
+    #if str($filtering.activation) != "false"
+    --filter "activation $filtering.activation"
+    #end if
+
+    #if len($filtering.indices) > 0
+    --filter "index
+    #for $index in $filtering.indices
+    [${index.from},${index.to}]
+    #end for
+    "
+    #end if
+
+    #if len($filtering.scan_numbers) > 0
+    --filter "scanNumber
+    #for $scan_number in $filtering.scan_numbers
+    [${scan_number.from},${scan_number.to}]
+    #end for
+    "
+    #end if
+
+    #for threshold_entry in $filtering.threshold_repeat
+    --filter "threshold $threshold_entry.threshold.threshold_type $threshold_entry.threshold.value $threshold_entry.orientation"
+    #end for
+
+    $filtering.strip_it
+    $filtering.metadataFixer
+    $filtering.sortByScanTime
+
+    #if $filtering.filter_mz_windows.do_filter
+    --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]"
+    #end if
+
+    #if $filtering.filter_chargeStatePredictor.do_filter
+        --filter "chargeStatePredictor $filtering.filter_chargeStatePredictor.overrideExistingCharge $filtering.filter_chargeStatePredictor.maxMultipleCharge $filtering.filter_chargeStatePredictor.minMultipleCharge $filtering.filter_chargeStatePredictor.singleChargeFractionTIC $filtering.filter_chargeStatePredictor.algorithmMakeMS2"
+    #end if
+
+
+    #if $filtering.filter_ms_levels.do_filter
+    --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]"
+    #end if
+
+    #if str($filtering.etd_filtering.do_etd_filtering) == "default"
+    --filter "ETDFilter"
+    #end if
+
+    #if str($filtering.etd_filtering.do_etd_filtering) == "advanced"
+    --filter "ETDFilter removePrecursor:$filtering.etd_filtering.remove_precursor removeChargeReduced:$filtering.etd_filtering.remove_charge_reduced  removeNeutralLoss:$filtering.etd_filtering.remove_neutral_loss  blanketRemoval:$filtering.etd_filtering.blanket_removal  MatchingTolerance:$filtering.etd_filtering.matching_tolerance $filtering.etd_filtering.matching_tolerance_units"
+    #end if
+
+    ## BEGIN_VERSION_3
+
+    #if $filtering.precursor_refine.value
+    --filter "precursorRefine"
+    #end if
+
+    #if $filtering.ms2denoise.denoise
+    --filter "MS2Denoise $filtering.ms2denoise.num_peaks $filtering.ms2denoise.window_width $filtering.ms2denoise.relax"
+    #end if
+
+    #if str($filtering.ms2deisotope) == "true"
+    --filter "MS2Deisotope"
+    #end if
+
+    #if str($filtering.polarity) != "false"
+    --filter "polarity $filtering.polarity"
+    #end if
+
+    #if str($filtering.analyzer) != "false"
+    --filter "analyzer $filtering.analyzer"
+    #end if
+
+    ## END_VERSION_3
+
+    #end if
+
+  </command>
+
+  <inputs>
+    <!-- BEGIN_VERSION_RAW -->
+    <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input" help="select input file in RAW format"/>
+    <!-- END_VERSION_RAW -->
+
+    <param name="output_type" type="select" label="Output Type">
+      <option value="mzML">mzML (indexed)</option>
+      <option value="unindexed_mzML">mzML (unindexed)</option>
+      <option value="mzXML">mzXML (indexed)</option>
+      <option value="unindexed_mzXML">mzXML (unindexed)</option>
+      <option value="mgf">mgf</option>
+      <option value="ms2">ms2</option>
+    </param>
+    <conditional name="filtering">
+      <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" />
+      <when value="false" />
+      <when value="true">
+        <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" />
+        <!-- BEGIN_VERSION_3 -->
+        <param type="boolean" name="precursor_refine" label="Refine Precursor?" />
+        <!-- END_VERSION_3 -->
+
+
+        <conditional name="peak_picking">
+          <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" />
+          <when value="false" />
+          <when value="true">
+            <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
+              <option value="1">MS1 Only (1)</option>
+              <option value="2">MS2 Only (2)</option>
+              <option value="2-">MS2 and on (2-)</option>
+              <option value="1-">All Levels (1-)</option>
+            </param>
+            <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/>
+          </when>
+        </conditional>
+
+        <repeat name="threshold_repeat" title="Filter by Threshold">
+          <conditional name="threshold">
+            <param type="select" label="Specify threshold on" name="threshold_type" help="">
+              <option value="count">Peak count</option>
+              <option value="count-after-ties">Peak count (after ties)</option>
+              <option value="absolute">Peak absolute intensity</option><!-- TODO: absolute what? m/z -->
+              <option value="bpi-relative">Percent of base peak intensity</option>
+              <option value="tic-relative">Percent of total ion current</option>
+              <option value="tic-fraction">Aggregate percent of total ion current</option>
+            </param>
+            <when value="count">
+              <param type="integer" name="value" label="Number of peaks to keep" value="100" />
+            </when>
+            <when value="count-after-ties">
+              <param type="integer" name="value" label="Number of peaks to keep (after ties)" value="100" />
+            </when>
+            <when value="absolute">
+              <param type="float" name="value" label="Absolute intensity cut-off" value="100.0" />
+            </when>
+            <when value="bpi-relative">
+              <param type="float" name="value" label="Keep peaks above (or below) this fraction of base peak intensity" value="0.2"
+              />
+            </when>
+            <when value="tic-relative">
+              <param type="float" name="value" label="Keep peaks above (or below) this fraction of total ion current" value="0.2"
+              />
+            </when>
+            <when value="tic-fraction">
+              <param type="float" name="value" label="Keep peaks until this fraction of total ion current is accounted for" value="0.8" />
+            </when>
+          </conditional>
+          <param type="select" label="Keep" name="orientation">
+            <option value="most-intense">Most intense peaks</option>
+            <option value="least-intense">Least intense peaks</option>
+          </param>
+        </repeat>
+
+        <param name="activation" type="select" label="Filter by Activation">
+          <option value="false" selected="true">no</option>
+          <option value="ETD">ETD</option>
+          <option value="CID">CID</option>
+          <option value="SA">SA</option>
+          <option value="HCD">HCD</option>
+          <!-- BEGIN_VERSION_3 -->
+          <option>BIRD</option>
+          <option>ECD</option>
+          <option>IRMPD</option>
+          <option>PD</option>
+          <option>PSD</option>
+          <option>PQD</option>
+          <option>SID</option>
+          <option>SORI</option>
+          <!-- END_VERSION_3 -->
+        </param>
+
+        <repeat name="indices" title="Filter Scan Indices">
+          <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
+          <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
+        </repeat>
+
+        <repeat name="scan_numbers" title="Filter Scan Numbers">
+          <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" />
+          <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" />
+        </repeat>
+
+        <conditional name="filter_mz_windows">
+          <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
+          <when value="false" />
+          <when value="true">
+            <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" />
+            <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" />
+          </when>
+        </conditional>
+
+        <param name="strip_it" type="boolean"
+            truevalue="--filter 'stripIT'" falsevalue=""
+            label="Strip Ion Trap MS1 Scans" />
+        <param name="metadataFixer" type="boolean" truevalue="--filter 'metadataFixer'" falsevalue=""
+            label="This filter is used to add or replace a spectra's TIC/BPI metadata"
+            help="It is usually used after peakPicking where the change from profile to centroided data may make the TIC and BPI values inconsistent with the revised scan data." />
+        <param name="sortByScanTime" type="boolean"
+            truevalue="--filter 'sortByScanTime'" falsevalue=""
+            label=" This filter reorders spectra, sorting them by ascending scan start time." />
+
+        <conditional name="filter_chargeStatePredictor">
+            <param name="do_filter" type="boolean"
+                label=" Predicts MSn spectrum precursors to be singly or multiply charged depending on the ratio of intensity above and below the precursor m/z"
+                help="or optionally using the 'makeMS2' algorithm" />
+            <when value="false" />
+            <when value="true">
+                <param name="overrideExistingCharge" type="boolean" checked="True" truevalue="true" falsevalue="false"
+                    label="always override existing charge information"/>
+                <param name="minMultipleCharge" type="integer" value="2" optional="true"
+                    label="Minimum of the range of values to add to the spectrum's existing 'MS_possible_charge_state' values."
+                    help="If these are the same values, the spectrum's MS_possible_charge_state values are removed and replaced with this single."/>
+                <param name="maxMultipleCharge" type="integer" value="3" optional="false"
+                    label="Maximum of the range of values to add to the spectrum's existing 'MS_possible_charge_state' values." />
+
+                <param name="singleChargeFractionTIC" type="float" min="0.0" max="1.0" value="0.9"
+                    help="Is a percentage expressed as a value between 0 and 1"
+                    label="This is the value used as the previously mentioned ratio of intensity above and below the precursor m/z." />
+
+                <param name="algorithmMakeMS2" type="boolean" checked="False" truevalue="true" falsevalue="false"
+                    label="Use 'makeMS2' algorithm instead of the one described above"/>
+
+          </when>
+          <when value="false"/>
+        </conditional>
+
+        <conditional name="filter_ms_levels">
+          <param name="do_filter" type="boolean" label="Filter MS Levels" />
+          <when value="false" />
+          <when value="true">
+            <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" />
+            <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" />
+          </when>
+        </conditional>
+
+        <conditional name="etd_filtering">
+          <param name="do_etd_filtering" type="select" label="ETD Filtering">
+            <option value="none" selected="true">none</option>
+            <option value="default">yes (with default options)</option>
+            <option value="advanced">yes (show advanced options) </option>
+          </param>
+          <when value="none" />
+          <when value="default" />
+          <when value="advanced">
+            <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1">
+            </param>
+            <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">
+              <option value="MZ" selected="true">mz</option>
+              <option value="PPM">ppm</option>
+            </param>
+            <param name="remove_precursor" type="select" label="ETD Remove Precursor">
+              <option value="true" selected="true">yes</option>
+              <option value="false">no</option>
+            </param>
+            <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced">
+              <option value="true" selected="true">yes</option>
+              <option value="false">no</option>
+            </param>
+            <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss">
+              <option value="true" selected="true">yes</option>
+              <option value="false">no</option>
+            </param>
+            <param name="blanket_removal" type="select" label="ETD Blanket Removal">
+              <option value="true" selected="true">yes</option>
+              <option value="false">no</option>
+            </param>
+          </when>
+        </conditional>
+
+
+        <!-- BEGIN_VERSION_3 -->
+        <conditional name="ms2denoise">
+          <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter"  />
+          <when value="true">
+            <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />
+            <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />
+            <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" />
+          </when>
+          <when value="false" />
+        </conditional>
+        <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />
+
+        <param name="polarity" type="select" label="Filter by Polarity">
+          <option value="false" selected="true">no</option>
+          <option value="positive">positive</option>
+          <option value="negative">negative</option>
+        </param>
+
+        <param name="analyzer" type="select" label="Filter by Analyzer">
+          <option value="false" selected="true">no</option>
+          <option value="quad">quad</option>
+          <option value="orbi">orbi</option>
+          <option value="FT">FT</option>
+          <option value="IT">IT</option>
+          <option value="TOF">TOF</option>
+        </param>
+        <!-- END_VERSION_3 -->
+      </when>
+    </conditional>
+
+    <conditional name="settings">
+      <param name="settingsType" type="select" label="Advanced Settings" help="">
+        <option value="default">Use Defaults</option>
+        <option value="full">Full Parameter List</option>
+      </param>
+      <when value="default" />
+      <when value="full">
+        <param type="select" name="binary_encoding" label="Binary Encoding Precision">
+          <option value="64" selected="true">64</option>
+          <option value="32">32</option>
+        </param>
+        <param type="select" name="mz_encoding" label="m/z Encoding Precision">
+          <option value="64" selected="true">64</option>
+          <option value="32">32</option>
+        </param>
+        <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32">
+          <option value="64">64</option>
+          <option value="32" selected="true">32</option>
+        </param>
+        <param type="boolean" name="zlib" label="Use zlib">
+        </param>
+      </when>
+    </conditional>
+
+
+  </inputs>
+  <outputs>
+    <data format="mzml" name="output">
+      <change_format>
+        <when input="output_type" value="mzXML" format="mzxml" />
+        <when input="output_type" value="unindexed_mzXML" format="mzxml" />
+        <when input="output_type" value="ms2" format="ms2" />
+        <when input="output_type" value="mgf" format="mgf" />
+      </change_format>
+    </data>
+  </outputs>
+  <help>
+**What it does**
+
+Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available.
+
+You can view the original documentation here_.
+
+.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
+
+------
+
+**Citation**
+
+For the underlying tool, please cite `ProteoWizard: Open Source Software for Rapid Proteomics Tools Development. Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick. Bioinformatics 2008; doi: 10.1093/bioinformatics/btn323.`
+
+If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/msconvert
+
+  </help>
+</tool>

--- a/msconvert_raw_wrapper.py	Mon Feb 17 17:00:29 2014 -0500
+++ b/msconvert_raw_wrapper.py	Fri Sep 26 14:44:54 2014 -0400
@@ -3,7 +3,7 @@
 import os
 import sys
 import tempfile
-import shutil 
+import shutil
 import subprocess
 import re
 from os.path import basename
@@ -33,14 +33,14 @@
             except OverflowError:
                 pass
     return stderr
-    
+
 def execute(command, stdin=None):
     with open(tmp_stderr_name, 'wb') as tmp_stderr:
         with open(tmp_stdout_name, 'wb') as tmp_stdout:
             proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ)
             returncode = proc.wait()
             if returncode != 0:
-                raise Exception, "Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr())
+                raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr()))
 
 def delete_file(path):
     if os.path.exists(path):
@@ -114,7 +114,7 @@
     cmd = "%s --inten%s" % (cmd, options.intensityencoding)
     cmd = "%s %s" % (cmd, input_file)
     cmd = "%s %s" % (cmd, filter_commands)
-    print cmd
+    print(cmd)
     execute(cmd)
     output_files = os.listdir('output')
     assert len(output_files) == 1

--- a/msconvert_subset.xml	Mon Feb 17 17:00:29 2014 -0500
+++ b/msconvert_subset.xml	Fri Sep 26 14:44:54 2014 -0400
@@ -1,17 +1,19 @@
-<tool id="msconvert_subset" name="Subset Peak List" version="0.2.1">
+<tool id="msconvert_subset" name="msconvert Subset Peak List" version="0.3.0">
   <description>against list of scan numbers or indices.</description>
+  <!--
   <requirements>
-    <requirement type="package">proteowizard</requirement>
+    <requirement type="package" version="3_0_4388">proteowizard</requirement>
   </requirements>
+-->
   <command interpreter="python">
-    msconvert_wrapper.py 
-    --input=${input} 
-    --output=${output} 
-    --fromextension=${input.ext} 
-    --toextension=${output_type} 
+    msconvert_wrapper.py
+    --input=${input}
+    --output=${output}
+    --fromextension=${input.ext}
+    --toextension=${output_type}
     #if $settings.settingsType == "full"
-    --binaryencoding=${settings.binary_encoding} 
-    --mzencoding=${settings.mz_encoding} 
+    --binaryencoding=${settings.binary_encoding}
+    --mzencoding=${settings.mz_encoding}
     --intensityencoding=${settings.intensity_encoding}
     --zlib=${settings.zlib}
     #end if
@@ -47,16 +49,16 @@
     <param name="output_type" type="select" label="Output Type">
       <option value="mzML">mzML (indexed)</option>
       <option value="unindexed_mzML">mzML (unindexed)</option>
-      <option value="mzXML">mzXML (indexed)</option>      
+      <option value="mzXML">mzXML (indexed)</option>
       <option value="unindexed_mzXML">mzXML (unindexed)</option>
       <option value="mgf">mgf</option>
-      <option value="ms2">ms2</option>  
+      <option value="ms2">ms2</option>
     </param>
     <conditional name="filter">
       <param name="filterType" type="select" label="Filter by" help="">
         <option value="scan_number" selected="true">Scan Number</option>
         <option value="scan_index">Scan Index</option>
-      </param>    
+      </param>
       <when value="scan_number">
         <param format="text" name="filterList" type="data" label="Scan Numbers"/>
       </when>
@@ -83,7 +85,7 @@
           <option value="64">64</option>
           <option value="32" selected="true">32</option>
         </param>
-        <param type="boolean" name="zlib" label="Use zlib">      
+        <param type="boolean" name="zlib" label="Use zlib">
         </param>
       </when>
     </conditional>

--- a/msconvert_wrapper.py	Mon Feb 17 17:00:29 2014 -0500
+++ b/msconvert_wrapper.py	Fri Sep 26 14:44:54 2014 -0400
@@ -45,8 +45,8 @@
                 if returncode != 0:
                     raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr()))
     finally:
-        print open(tmp_stderr_name, "r").read()
-        print open(tmp_stdout_name, "r").read()
+        print(( open(tmp_stderr_name, "r").read() ))
+        print(( open(tmp_stdout_name, "r").read() ))
 
 
 def delete_file(path):
@@ -167,7 +167,7 @@
 
     filters_file.close()
     if debug:
-        print open(filters_file_path, "r").read()
+        print(( open(filters_file_path, "r").read() ))
     return filters_file_path
 
 
@@ -195,7 +195,7 @@
     os.mkdir(output_dir)
     cmd = "%s -o %s %s" % (base_cmd, shellquote(output_dir), inputs_as_str)
     if debug:
-        print cmd
+        print(cmd)
     execute(cmd)
     output_files = os.listdir(output_dir)
     assert len(output_files) == 1
@@ -234,12 +234,19 @@
         input_base = None
         if len(options.input_names) > i:
             input_base = options.input_names[i]
+            input_base = input_base.replace("'", "").replace("\"", "")
+            print("1- input_base: %s" % input_base)
         if not input_base:
             input_base = 'input%s' % i
+            print("2- input_base: %s" % input_base)
         if not input_base.lower().endswith(options.fromextension.lower()):
             input_file = '%s.%s' % (input_base, options.fromextension)
+            print("3- input_base: %s" % input_base)
+            print("3- input_file: %s" % input_file)
         else:
             input_file = input_base
+            print("4- input_base: %s" % input_base)
+            print("4- input_file: %s" % input_file)
         input_file = input_file
         copy_to_working_directory(input, input_file)
         input_files.append(input_file)

--- a/repository_dependencies.xml	Mon Feb 17 17:00:29 2014 -0500
+++ b/repository_dependencies.xml	Fri Sep 26 14:44:54 2014 -0400
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories description="Required proteomics dependencies.">
-    <repository changeset_revision="b82d4034e0f8" name="proteomics_datatypes" owner="iracooke" toolshed="http://toolshed.g2.bx.psu.edu" />
+  <repository changeset_revision="f66f8ca7b7b9" name="proteomics_datatypes" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" />
 </repositories>

--- a/tool_dependencies.xml	Mon Feb 17 17:00:29 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="proteowizard" version="3_0_4388">
-        <repository changeset_revision="863462ea0187" name="protk_proteowizard" owner="iracooke" toolshed="http://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>

--- a/update.sh	Mon Feb 17 17:00:29 2014 -0500
+++ /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

--- a/update_repo.sh	Mon Feb 17 17:00:29 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-#!/bin/bash
-
-sed -e '/BEGIN_VERSION_RAW/,/END_VERSION_RAW/d'  -e '/BEGIN_VERSION_3/,/END_VERSION_3/d'  -e 's/\$VERSION/2/g' -e 's/\$DESCRIPTION//g' msconvert.xml.template > msconvert2.xml
-sed -e '/BEGIN_VERSION_DEFAULT/,/END_VERSION_DEFAULT/d' -e '/BEGIN_VERSION_3/,/END_VERSION_3/d'  -e 's/\$VERSION/2/g' -e 's/\$DESCRIPTION/_raw/g' msconvert.xml.template > msconvert2_raw.xml
-
-
-sed -e '/BEGIN_VERSION_RAW/,/END_VERSION_RAW/d' -e 's/\$VERSION/3/g' -e 's/\$DESCRIPTION//g' msconvert.xml.template > msconvert3.xml
-sed -e '/BEGIN_VERSION_DEFAULT/,/END_VERSION_DEFAULT/d' -e 's/\$VERSION/3/g' -e 's/\$DESCRIPTION/_raw/g' msconvert.xml.template > msconvert3_raw.xml
-

--- a/version	Mon Feb 17 17:00:29 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-0.2.1