changeset 0:ab59b1826345 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
author galaxyp
date Thu, 22 Oct 2015 14:00:58 -0400
parents
children 2a6628075d1f
files COPYING README.md msconvert.xml msconvert_macros.xml msconvert_raw.xml msconvert_raw_wrapper.py msconvert_subset.xml msconvert_wrapper.py test-data/D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML test-data/D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5 test-data/Rpal_01-mzRefinement.mzML test-data/Rpal_01.mz5 test-data/Rpal_01.pepXML.gz test-data/Rpal_01.pepXML.mzRefinement.tsv test-data/small-activation.mzML test-data/small-analyzer-filter.mzML test-data/small-chargeStatePredictor.mzML test-data/small-deisotope-poisson.mzML test-data/small-deisotope.mzML test-data/small-denoise.mzML test-data/small-index-filter.mzML test-data/small-ms-level-filter.mzML test-data/small-mzWindow.mzML test-data/small-numpressL.mzML test-data/small-numpressLP.mzML test-data/small-numpressLS.mzML test-data/small-numpressP.mzML test-data/small-numpressS.mzML test-data/small-off-32.mzML.gz test-data/small-peakpicking-cwt-allMS.mzML test-data/small-polarity-filter.mzML test-data/small-strip-it.mzML test-data/small-threshold.mzML test-data/small-turbocharger.mzML test-data/small-zlib-32.mzXML test-data/small-zlib-64.mz5 test-data/small.RAW test-data/small.mzML
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/COPYING	Thu Oct 22 14:00:58 2015 -0400
@@ -0,0 +1,121 @@
+Creative Commons Legal Code
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Thu Oct 22 14:00:58 2015 -0400
@@ -0,0 +1,67 @@
+GalaxyP - ProteoWizard msconvert
+================================
+
+* Home: <https://github.com/galaxyproteomics/tools-galaxyp/>
+* Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/msconvert>
+* Tool ID: `msconvert`
+
+
+Description
+-----------
+
+msconvert from ProteoWizard.
+
+Note: This requires manual installation of ProteoWizard, and may require a Windows environment.
+
+See:
+
+* <http://proteowizard.sourceforge.net/>
+* <http://proteowizard.sourceforge.net/tools/msconvert.html>
+
+
+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](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>
+
+
+GalaxyP Community
+-----------------
+
+Current governing community policies for [GalaxyP](https://github.com/galaxyproteomics/) and other information can be found at:
+
+<https://github.com/galaxyproteomics>
+
+
+License
+-------
+
+Copyright (c) 2014 Regents of the University of Minnesota and Authors listed below.
+
+To the extent possible under law, the author(s) have dedicated all copyright and related and neighboring rights to this software to the public domain worldwide. This software is distributed without any warranty.
+
+You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see <https://creativecommons.org/publicdomain/zero/1.0/>.
+
+You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission.
+
+
+Contributing
+------------
+
+Contributions to this repository are reviewed through pull requests. If you would like your work acknowledged, please also add yourself to the Authors section. If your pull request is accepted, you will also be acknowledged in <https://github.com/galaxyproteomics/tools-galaxyp/>
+
+
+Authors
+-------
+
+Authors and contributors:
+
+* Björn Grüning
+* Cody Wang
+* Fred Sadler
+* John Chilton <jmchilton@gmail.com>
+* Minnesota Supercomputing Institute, Univeristy of Minnesota
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/msconvert.xml	Thu Oct 22 14:00:58 2015 -0400
@@ -0,0 +1,281 @@
+<tool id="msconvert" name="msconvert" version="0.3.0">
+  <description>Convert and/or filter mass spectrometry files</description>
+
+  <requirements>
+    <requirement type="package" version="3_0_9016">proteowizard</requirement>
+  </requirements>
+
+  <macros>
+    <import>msconvert_macros.xml</import>
+  </macros>
+
+  <expand macro="msconvertCommand" />
+
+  <inputs> 
+    <param format="mzml,mzxml,mz5,mgf,ms2" name="input" type="data" label="Input unrefined MS data" />
+
+    <expand macro="msconvertInputParameters" />
+  </inputs>
+
+  <expand macro="msconvertOutput" />
+
+  <tests>
+    <test>
+      <param name="input" value="small.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="pick_peaks" value="true" />
+      <param name="pick_peaks_algorithm" value="cwt" />
+      <param name="pick_peaks_ms_levels" value="1-" />
+      <output name="output" file="small-peakpicking-cwt-allMS.mzML" />
+    </test>
+
+    <!-- this data file only has profile MS1, so the result is the same -->
+    <test>
+      <param name="input" value="small.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="pick_peaks" value="true" />
+      <param name="pick_peaks_algorithm" value="cwt" />
+      <param name="pick_peaks_ms_levels" value="1" />
+      <output name="output" file="small-peakpicking-cwt-allMS.mzML" /> 
+    </test>
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mz5" />
+      <param name="mz_encoding" value="64" />
+      <param name="intensity_encoding" value="64" />
+      <output name="output" file="small-zlib-64.mz5" compare="sim_size" delta="100" />
+    </test>
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzXML" />
+      <param name="mz_encoding" value="32" />
+      <param name="intensity_encoding" value="32" />
+      <output name="output" file="small-zlib-32.mzXML" />
+    </test>
+    <!-- TODO: how to test gzipped output?
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzXML" />
+      <param name="mz_encoding" value="32" />
+      <param name="intensity_encoding" value="32" />
+      <param name="binary_compression" value="false" />
+      <param name="gzip_compression" value="true" />
+      <output name="output" file="small-off-32.mzXML.gz" compare="sim_size" delta="100" />
+    </test>
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="mz_encoding" value="32" />
+      <param name="intensity_encoding" value="32" />
+      <param name="binary_compression" value="false" />
+      <param name="gzip_compression" value="true" />
+      <output name="output" file="small-off-32.mzML.gz" compare="sim_size" delta="100" />
+    </test>-->
+
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="binary_compression" value="numpressLinearPic" />
+      <output name="output" file="small-numpressLP.mzML" />
+    </test>
+
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="binary_compression" value="numpressLinearSlof" />
+      <output name="output" file="small-numpressLS.mzML" />
+    </test>
+
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="binary_compression" value="numpressLinear" />
+      <output name="output" file="small-numpressL.mzML" />
+    </test>
+
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="binary_compression" value="numpressPic" />
+      <output name="output" file="small-numpressP.mzML" />
+    </test>
+
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="binary_compression" value="numpressSlof" />
+      <output name="output" file="small-numpressS.mzML" />
+    </test>
+
+    <test>
+      <param name="input" value="Rpal_01.mz5" />
+      <param name="output_type" value="mzML" />
+      <param name="binary_compression" value="numpressLinearPic" />
+      <param name="use_mzrefinement" value="true" />
+      <param name="input_ident" value="Rpal_01.pepXML.gz" />
+      <param name="thresholdScore" value="mvh" />
+      <param name="thresholdValue" value="40-" />
+      <output name="output" file="Rpal_01-mzRefinement.mzML" compare="sim_size" delta="0" />
+      <output name="output.refinement" file="Rpal_01.pepXML.mzRefinement.tsv" />
+    </test>
+    
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="binary_compression" value="numpressLinearPic" />
+      <param name="charge_state_calculation_method" value="predictor" />
+      <param name="predictor_overrideExistingCharge" value="true" />
+      <param name="minMultipleCharge" value="2" />
+      <param name="maxMultipleCharge" value="5" />
+      <param name="singleChargeFractionTIC" value="0.95" />
+      <param name="maxKnownCharge" value="8" />
+      <output name="output" file="small-chargeStatePredictor.mzML" />
+    </test>
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="binary_compression" value="numpressLinearPic" />
+      <param name="charge_state_calculation_method" value="turbocharger" />
+      <param name="minCharge" value="1" />
+      <param name="maxCharge" value="5" />
+      <param name="precursorsBefore" value="1" />
+      <param name="precursorsAfter" value="1" />
+      <param name="halfIsoWidth" value="1.5" />
+      <param name="defaultMinCharge" value="1" />
+      <param name="defaultMaxCharge" value="5" />
+      <output name="output" file="small-turbocharger.mzML" />
+    </test>
+    <test>
+      <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" />
+      <param name="output_type" value="mzML" />
+      <param name="do_etd_filtering" value="true" />
+      <param name="remove_precursor" value="true" />
+      <param name="remove_charge_reduced" value="true" />
+      <param name="remove_neutral_loss" value="false" />
+      <param name="blanket_removal" value="false" />
+      <param name="matching_tolerance" value="50" />
+      <param name="matching_tolerance_units" value="ppm" />
+      <param name="binary_compression" value="numpressLinearPic" />
+      <output name="output" file="D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML" />
+    </test>
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="thresholds_0|threshold_type" value="count" />
+      <param name="thresholds_0|value" value="100" />
+      <param name="thresholds_0|orientation" value="most-intense" />
+      <param name="thresholds_1|threshold_type" value="absolute" />
+      <param name="thresholds_1|value" value="1" />
+      <param name="thresholds_1|orientation" value="most-intense" />
+      <param name="binary_compression" value="numpressLinearPic" />
+      <output name="output" file="small-threshold.mzML" />
+    </test>
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="do_mzwindow_filter" value="true" />
+      <param name="mz_window_from" value="420" />
+      <param name="mz_window_to" value="840" />
+      <param name="binary_compression" value="numpressLinearPic" />
+      <output name="output" file="small-mzWindow.mzML" />
+    </test>
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="denoise" value="true" />
+      <param name="num_peaks" value="10" />
+      <param name="window_width" value="40" />
+      <param name="relax" value="false" />
+      <param name="binary_compression" value="numpressLinearPic" />
+      <output name="output" file="small-denoise.mzML" />
+    </test>
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="ms2deisotope" value="true" />
+      <param name="binary_compression" value="numpressLinearPic" />
+      <output name="output" file="small-deisotope.mzML" />
+    </test>
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="activation" value="CID" />
+      <param name="binary_compression" value="numpressLinearPic" />
+      <output name="output" file="small-activation.mzML" />
+    </test>
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="indices_0|from" value="2" />
+      <param name="indices_0|to" value="4" />
+      <param name="indices_1|from" value="10" />
+      <param name="indices_1|to" value="10" />
+      <param name="indices_2|from" value="13" />
+      <param name="indices_2|to" value="15" />
+      <param name="binary_compression" value="numpressLinearPic" />
+      <output name="output" file="small-index-filter.mzML" />
+    </test>
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="strip_it" value="true" />
+      <param name="binary_compression" value="numpressLinearPic" />
+      <output name="output" file="small-strip-it.mzML" />
+    </test>
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="do_ms_level_filter" value="true" />
+      <param name="ms_level_from" value="2" />
+      <param name="ms_level_to" value="2" />
+      <param name="binary_compression" value="numpressLinearPic" />
+      <output name="output" file="small-ms-level-filter.mzML" />
+    </test>
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="polarity" value="positive" />
+      <param name="binary_compression" value="numpressLinearPic" />
+      <output name="output" file="small-polarity-filter.mzML" />
+    </test>
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="analyzer" value="IT" />
+      <param name="binary_compression" value="numpressLinearPic" />
+      <output name="output" file="small-analyzer-filter.mzML" />
+    </test>
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="scan_numbers_0|from" value="3" />
+      <param name="scan_numbers_0|to" value="5" />
+      <param name="scan_numbers_1|from" value="11" />
+      <param name="scan_numbers_1|to" value="11" />
+      <param name="scan_numbers_2|from" value="14" />
+      <param name="scan_numbers_2|to" value="16" />
+      <param name="binary_compression" value="numpressLinearPic" />
+      <output name="output" file="small-index-filter.mzML" /> <!-- the scan numbers here produce the same output as the index test above -->
+    </test>
+    <!--<test>
+      <param name="input" value="small.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="binary_compression" value="numpressLinearPic" />
+      <output name="output" file="small-deisotope-poisson.mzML" />
+    </test>-->
+  </tests>
+  <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
+  </help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btn323</citation>
+        <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
+                                      year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->
+    </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/msconvert_macros.xml	Thu Oct 22 14:00:58 2015 -0400
@@ -0,0 +1,390 @@
+<macros>
+  <xml name="msconvertCommand">
+    <command>
+<![CDATA[
+    #import re
+    #set $output_type_str = str($output_type)
+    #set $input_name = $input.display_name
+    #set $output_name = $input_name.split(".")[0] + "." + $output_type_str
+    ln -s '$input' '${input_name}' &&
+
+    #if $data_processing.precursor_refinement.use_mzrefinement
+      #set $input_ident_name = $data_processing.precursor_refinement.input_ident.display_name
+      ln -s '${data_processing.precursor_refinement.input_ident}' '${input_ident_name}' &&
+    #end if
+
+    mkdir outdir &&
+    msconvert ${input_name} --$output_type_str -o outdir --outfile '$output_name'
+
+    ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!)
+      #if $data_processing.peak_picking.pick_peaks
+      --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels"
+      #end if
+
+      #if $data_processing.precursor_refinement.use_mzrefinement
+      --filter "mzRefiner $input_ident_name
+        msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels
+        thresholdScore=$data_processing.precursor_refinement.thresholdScore
+        thresholdValue=$data_processing.precursor_refinement.thresholdValue
+        thresholdStep=$data_processing.precursor_refinement.thresholdStep
+        maxSteps=$data_processing.precursor_refinement.thresholdMaxSteps"
+      #end if
+
+      #if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "predictor"
+      --filter "chargeStatePredictor
+        overrideExistingCharge=$data_processing.charge_state_calculation.predictor_overrideExistingCharge
+        minMultipleCharge=$data_processing.charge_state_calculation.minMultipleCharge
+        maxMultipleCharge=$data_processing.charge_state_calculation.maxMultipleCharge
+        singleChargeFractionTIC=$data_processing.charge_state_calculation.singleChargeFractionTIC
+        maxKnownCharge=$data_processing.charge_state_calculation.maxKnownCharge"
+      #else if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "turbocharger"
+      --filter "turbocharger
+        minCharge=$data_processing.charge_state_calculation.minCharge
+        maxCharge=$data_processing.charge_state_calculation.maxCharge
+        precursorsBefore=$data_processing.charge_state_calculation.precursorsBefore
+        precursorsAfter=$data_processing.charge_state_calculation.precursorsAfter
+        halfIsoWidth=$data_processing.charge_state_calculation.halfIsoWidth
+        defaultMinCharge=$data_processing.charge_state_calculation.defaultMinCharge
+        defaultMaxCharge=$data_processing.charge_state_calculation.defaultMaxCharge"
+      #end if
+
+      #for threshold_entry in $data_processing.thresholds
+      --filter "threshold $threshold_entry.threshold_type $threshold_entry.value $threshold_entry.orientation"
+      #end for
+
+      #if $data_processing.filter_mz_windows.do_mzwindow_filter
+      --filter "mzWindow [$data_processing.filter_mz_windows.mz_window_from,$data_processing.filter_mz_windows.mz_window_to]"
+      #end if
+
+      #if $data_processing.etd_filtering.do_etd_filtering
+      --filter "ETDFilter $data_processing.etd_filtering.remove_precursor
+        $data_processing.etd_filtering.remove_charge_reduced
+        $data_processing.etd_filtering.remove_neutral_loss
+        $data_processing.etd_filtering.blanket_removal
+        $data_processing.etd_filtering.matching_tolerance $data_processing.etd_filtering.matching_tolerance_units"
+      #end if
+
+      #if $data_processing.ms2denoise.denoise
+      --filter "MS2Denoise $data_processing.ms2denoise.num_peaks $data_processing.ms2denoise.window_width $data_processing.ms2denoise.relax"
+      #end if
+
+      #if str($data_processing.ms2deisotope) == "true"
+      --filter "MS2Deisotope"
+      #end if
+
+
+    ## SCAN INCLUSION/EXCLUSION FILTERS
+      #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
+
+      #if $filtering.strip_it.value
+      --filter "stripIT"
+      #end if
+
+      #if $filtering.filter_ms_levels.do_ms_level_filter
+      --filter "msLevel [$filtering.filter_ms_levels.ms_level_from, $filtering.filter_ms_levels.ms_level_to]"
+      #end if
+
+      #if str($filtering.polarity) != "false"
+      --filter "polarity $filtering.polarity"
+      #end if
+
+      #if str($filtering.analyzer) != "false"
+      --filter "analyzer $filtering.analyzer"
+      #end if
+      
+    ## OUTPUT ENCODING
+      #set $mz_encoding = str($settings.mz_encoding)
+      #set $intensity_encoding = str($settings.intensity_encoding)
+      #if $mz_encoding == $intensity_encoding
+        #if $mz_encoding == "64"
+          --64
+        #else
+          --32
+        #end if
+      #else
+        --mz${mz_encoding}
+        --inten${intensity_encoding}
+      #end if
+
+      #set binary_compression = str($settings.binary_compression)
+      #if $binary_compression == "zlib"
+      --zlib
+      #else if $binary_compression == "numpressLinearPic"
+      --numpressLinear --numpressPic
+      #else if $binary_compression == "numpressLinearSlof"
+      --numpressLinear --numpressSlof
+      #else if $binary_compression == "numpressLinear"
+      --numpressLinear
+      #else if $binary_compression == "numpressPic"
+      --numpressPic
+      #else if $binary_compression == "numpressSlof"
+      --numpressSlof
+      #end if
+
+      #if $settings.gzip_compression
+      --gzip
+      #end if
+
+      &&
+
+    #if $data_processing.precursor_refinement.use_mzrefinement
+      mv '${input.name.rsplit('.',1)[0]}.mzRefinement.tsv' output.refinement &&
+    #end if
+
+    mv 'outdir/$output_name' output &&
+    rmdir outdir
+]]>
+    </command>
+  </xml>
+
+  <xml name="msconvertInputParameters">
+    <param name="output_type" type="select" label="Output Type">
+      <option value="mz5" selected="true">mz5</option>
+      <option value="mzML">mzML</option>
+      <option value="mzXML">mzXML</option>
+      <option value="mgf">mgf</option>
+      <option value="ms2">ms2</option>
+    </param>
+
+    <section name="data_processing" title="Data Processing Filters">
+      
+      <conditional name="peak_picking">
+        <param type="boolean" name="pick_peaks" label="Apply peak picking?" truevalue="true" falsevalue="false" />
+        <when value="false" />
+        <when value="true">
+          <param name="pick_peaks_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-" selected="true">All Levels (1-)</option>
+          </param>
+          <param type="select" name="pick_peaks_algorithm" label="Peak Picking - Algorithm" help="The vendor method only works on Agilent, Bruker, Sciex, Thermo data, and only on Windows (although some vendors work on Wine)">
+            <option value="vendor" selected="true">Prefer vendor algorithm, fallback to local-maximum</option>
+            <option value="cwt">CantWaiT - continuous wavelet transform</option>
+          </param>
+        </when>
+      </conditional>
+
+      <conditional name="precursor_refinement" title="MZRefinery Precursor Refinement" expanded="true">
+        <param type="boolean" name="use_mzrefinement" label="Apply m/z refinement with identification data?" truevalue="true" falsevalue="false" checked="False" />
+        <when value="false"></when>
+        <when value="true">
+          <param name="input_ident" type="data" format="pepxml,mzid" label="MZRefinery - Input identification data" />
+          <param name="thresholdScore" type="text" value="mvh" label="MZRefinery - Threshold Score Name" help="E.g. 'mvh' for MyriMatch, 'xcorr' for Sequest, 'specevalue' for MS-GF+" />
+          <param name="thresholdValue" type="text" value="50-" label="MZRefinery - Threshold Score Value" help="MZRefinery uses peptide-spectrum-matches with scores from this range to build its model. '100-' means score equal to or greater than 100. '-1e-10' means less than or equal to 1e-10." />
+          <param name="thresholdStep" type="float" value="0" label="MZRefinery - Threshold Score Step" help="If there are not enough quality hits at the given score threshold value, the threshold can be increased by this step (until maxSteps is reached)." />
+          <param name="thresholdMaxSteps" type="integer" value="0" label="MZRefinery - At most, how many steps to widen the threshold?" />
+          <param name="precursor_refinement_ms_levels" type="select" label="MZRefinery - 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-" selected="true">All Levels (1-)</option>
+          </param>
+        </when>
+      </conditional>
+
+      <conditional name="charge_state_calculation">
+        <param name="charge_state_calculation_method" type="select" label="(Re-)calculate charge states?">
+          <option value="false">no</option>
+          <option value="predictor">Based on how much intensity is above vs. below the precursor m/z in the MS/MS scan</option>
+          <option value="turbocharger">Based on isotopic distribution of the precursor in nearby survey scans</option>
+        </param>
+        <when value="false" />
+        <when value="predictor">
+          <param name="predictor_overrideExistingCharge" type="boolean" label="Always override existing charge?" value="false" />
+          <param name="minMultipleCharge" type="integer" label="Minimum multiple charge state" value="2" />
+          <param name="maxMultipleCharge" type="integer" label="Maximum multiple charge state" value="3" />
+          <param name="singleChargeFractionTIC" type="float" label="Fraction of intensity below the precursor to be considered singly charged" max="1" min="0" value="0.9" />
+          <param name="maxKnownCharge" type="integer" label="Maximum charge allowed for &quot;known&quot; charges" help="This is applied even when not overriding existing charges (i.e. it overrides only obviously bogus charge states)" value="0" />
+        </when>
+        <when value="turbocharger">
+          <param name="minCharge" type="integer" label="Minimum possible charge state" value="1" min="1" help="Charge states lower than this will not be considered." />
+          <param name="maxCharge" type="integer" label="Maximum possible charge state" value="8" min="2" help="Charge states greater than this will not be considered." />
+          <param name="precursorsBefore" type="integer" label="Number of preceding survey scans to check for precursor isotopes" value="2" min="1" />
+          <param name="precursorsAfter" type="integer" label="Number of succeeding survey scans to check for precursor isotopes" value="0" min="0" />
+          <param name="halfIsoWidth" type="float" label="Half-width of isolation window" min="0.0001" value="1.25" />
+          <param name="defaultMinCharge" type="integer" label="Minimum possible charge state to apply if no isotope is found" value="0" />
+          <param name="defaultMaxCharge" type="integer" label="Maximum possible charge state to apply if no isotope is found" value="0" />
+        </when>
+      </conditional>
+
+      <repeat name="thresholds" title="Filter by 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>
+          <option value="bpi-relative">Fraction of base peak intensity</option>
+          <option value="tic-relative">Fraction of total ion current</option>
+          <option value="tic-fraction">Aggregate fraction of total ion current</option>
+        </param>
+        <param type="float" name="value" label="Threshold" value="1" help="For count methods, this is the number of peaks to keep. For the absolute method, this is the raw intensity above/below which peak will be accepted. For the &quot;Aggregated fraction&quot; method, peaks are accepted until this fraction of the TIC is accounted for." />
+        <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>
+
+      <conditional name="filter_mz_windows">
+        <param name="do_mzwindow_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
+        <when value="false" />
+        <when value="true">
+          <param name="mz_window_from" type="float" label="Filter m/z From" value="0.0" optional="false" />
+          <param name="mz_window_to" type="float" label="Filter m/z To" value="0.0" optional="true" />
+        </when>
+      </conditional>
+
+      <conditional name="etd_filtering">
+        <param type="boolean" name="do_etd_filtering" label="Filter out ETD precursor peaks?" truevalue="true" falsevalue="false" />
+        <when value="false" />
+        <when value="true">
+          <param name="remove_precursor" type="select" label="ETD Remove Unreacted 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 Precursors">
+            <option value="true" selected="true">yes</option>
+            <option value="false">no</option>
+          </param>
+          <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Losses" help="Remove neutral loss species from nominal and charge reduced precursors">
+            <option value="true" selected="true">yes</option>
+            <option value="false">no</option>
+          </param>
+          <param name="blanket_removal" type="select" label="ETD Blanket Removal of Neutral Losses" help="Remove neutral losses in a charge-scaled 60 Da swath (rather than only around known loss species)">
+            <option value="true" selected="true">yes</option>
+            <option value="false">no</option>
+          </param>
+          <param name="matching_tolerance" type="float" label="ETD Matching Tolerance" value="3.1" />
+          <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>
+        </when>
+      </conditional>
+
+      <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" />
+
+    </section>
+
+
+    <section name="filtering" title="Scan Inclusion/Exclusion Filters">
+      
+      <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>
+        <option>BIRD</option>
+        <option>ECD</option>
+        <option>IRMPD</option>
+        <option>PD</option>
+        <option>PSD</option>
+        <option>PQD</option>
+        <option>SID</option>
+        <option>SORI</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>
+
+      <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
+
+      <conditional name="filter_ms_levels">
+        <param name="do_ms_level_filter" type="boolean" label="Filter MS Levels" />
+        <when value="false" />
+        <when value="true">
+          <param name="ms_level_from" type="integer" label="Filter MS Level From" value="0" optional="false" />
+          <param name="ms_level_to" type="integer" label="Filter MS Level To" value="0" optional="true" />
+        </when>
+      </conditional>
+
+      <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">Quadrupole</option>
+        <option value="orbi">Orbitrap</option>
+        <option value="FT">Fourier-transform</option>
+        <option value="IT">Ion trap</option>
+        <option value="TOF">Time of flight</option>
+      </param>
+    </section>
+
+
+    <section name="settings" title="Output Encoding Settings">
+      <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">
+        <option value="64">64</option>
+        <option value="32" selected="true">32</option>
+      </param>
+      <param type="select" name="binary_compression" label="Binary data compression">
+        <option value="false">None</option>
+        <option value="zlib" selected="true">zlib</option>
+        <option value="numpressLinearPic">numpressLinear/numpressPic</option>
+        <option value="numpressLinearSlof">numpressLinear/numpressSlof</option>
+        <option value="numpressLinear">numpressLinear only</option>
+        <option value="numpressPic">numpressPic only</option>
+        <option value="numpressSlof">numpressSlof only</option>
+      </param>
+      <param type="boolean" name="gzip_compression" label="Compress output file with gzip" truevalue="true" falsevalue="false" />
+    </section>
+  </xml>
+  
+  <xml name="msconvertOutput">
+    <outputs>
+      <data format="mzml" name="output" from_work_dir="output" label="${input.name.rsplit('.',1)[0]}.${output_type}" >
+        <change_format>
+          <when input="output_type" value="mz5" format="mz5" />
+          <when input="output_type" value="mzXML" format="mzxml" />
+          <when input="output_type" value="ms2" format="ms2" />
+          <when input="output_type" value="mgf" format="mgf" />
+        </change_format>
+      </data>
+      <data format="csv" name="output.refinement" from_work_dir="output.refinement" label="${input.name.rsplit('.',1)[0]}.mzRefinement.tsv">
+  
+      </data>
+    </outputs>
+  </xml>
+</macros>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/msconvert_raw.xml	Thu Oct 22 14:00:58 2015 -0400
@@ -0,0 +1,282 @@
+<tool id="msconvert_raw" name="msconvert" version="0.3.0">
+  <description>Convert and/or filter mass spectrometry files (with vendor support on Windows)</description>
+
+  <requirements>
+    <requirement type="package" version="3_0_9016">proteowizard</requirement>
+  </requirements>
+
+  <macros>
+    <import>msconvert_macros.xml</import>
+  </macros>
+
+  <expand macro="msconvertCommand" />
+
+  <inputs>
+    <!-- TODO: add Bruker, Waters, Agilent types -->
+    <param format="mzml,mzxml,mz5,mgf,wiff,raw" name="input" type="data" label="Input unrefined MS data" />
+
+    <expand macro="msconvertInputParameters" />
+  </inputs>
+
+  <expand macro="msconvertOutput" />
+
+  <tests>
+    <test>
+      <param name="input" value="small.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="pick_peaks" value="true" />
+      <param name="pick_peaks_algorithm" value="cwt" />
+      <param name="pick_peaks_ms_levels" value="1-" />
+      <output name="output" file="small-peakpicking-cwt-allMS.mzML" />
+    </test>
+
+    <!-- this data file only has profile MS1, so the result is the same -->
+    <test>
+      <param name="input" value="small.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="pick_peaks" value="true" />
+      <param name="pick_peaks_algorithm" value="cwt" />
+      <param name="pick_peaks_ms_levels" value="1" />
+      <output name="output" file="small-peakpicking-cwt-allMS.mzML" /> 
+    </test>
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mz5" />
+      <param name="mz_encoding" value="64" />
+      <param name="intensity_encoding" value="64" />
+      <output name="output" file="small-zlib-64.mz5" compare="sim_size" delta="100" />
+    </test>
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzXML" />
+      <param name="mz_encoding" value="32" />
+      <param name="intensity_encoding" value="32" />
+      <output name="output" file="small-zlib-32.mzXML" />
+    </test>
+    <!-- TODO: how to test gzipped output?
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzXML" />
+      <param name="mz_encoding" value="32" />
+      <param name="intensity_encoding" value="32" />
+      <param name="binary_compression" value="false" />
+      <param name="gzip_compression" value="true" />
+      <output name="output" file="small-off-32.mzXML.gz" compare="sim_size" delta="100" />
+    </test>
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="mz_encoding" value="32" />
+      <param name="intensity_encoding" value="32" />
+      <param name="binary_compression" value="false" />
+      <param name="gzip_compression" value="true" />
+      <output name="output" file="small-off-32.mzML.gz" compare="sim_size" delta="100" />
+    </test>-->
+
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="binary_compression" value="numpressLinearPic" />
+      <output name="output" file="small-numpressLP.mzML" />
+    </test>
+
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="binary_compression" value="numpressLinearSlof" />
+      <output name="output" file="small-numpressLS.mzML" />
+    </test>
+
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="binary_compression" value="numpressLinear" />
+      <output name="output" file="small-numpressL.mzML" />
+    </test>
+
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="binary_compression" value="numpressPic" />
+      <output name="output" file="small-numpressP.mzML" />
+    </test>
+
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="binary_compression" value="numpressSlof" />
+      <output name="output" file="small-numpressS.mzML" />
+    </test>
+
+    <test>
+      <param name="input" value="Rpal_01.mz5" />
+      <param name="output_type" value="mzML" />
+      <param name="binary_compression" value="numpressLinearPic" />
+      <param name="use_mzrefinement" value="true" />
+      <param name="input_ident" value="Rpal_01.pepXML.gz" />
+      <param name="thresholdScore" value="mvh" />
+      <param name="thresholdValue" value="40-" />
+      <output name="output" file="Rpal_01-mzRefinement.mzML" compare="sim_size" delta="0" />
+      <output name="output.refinement" file="Rpal_01.pepXML.mzRefinement.tsv" />
+    </test>
+    
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="binary_compression" value="numpressLinearPic" />
+      <param name="charge_state_calculation_method" value="predictor" />
+      <param name="predictor_overrideExistingCharge" value="true" />
+      <param name="minMultipleCharge" value="2" />
+      <param name="maxMultipleCharge" value="5" />
+      <param name="singleChargeFractionTIC" value="0.95" />
+      <param name="maxKnownCharge" value="8" />
+      <output name="output" file="small-chargeStatePredictor.mzML" />
+    </test>
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="binary_compression" value="numpressLinearPic" />
+      <param name="charge_state_calculation_method" value="turbocharger" />
+      <param name="minCharge" value="1" />
+      <param name="maxCharge" value="5" />
+      <param name="precursorsBefore" value="1" />
+      <param name="precursorsAfter" value="1" />
+      <param name="halfIsoWidth" value="1.5" />
+      <param name="defaultMinCharge" value="1" />
+      <param name="defaultMaxCharge" value="5" />
+      <output name="output" file="small-turbocharger.mzML" />
+    </test>
+    <test>
+      <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" />
+      <param name="output_type" value="mzML" />
+      <param name="do_etd_filtering" value="true" />
+      <param name="remove_precursor" value="true" />
+      <param name="remove_charge_reduced" value="true" />
+      <param name="remove_neutral_loss" value="false" />
+      <param name="blanket_removal" value="false" />
+      <param name="matching_tolerance" value="50" />
+      <param name="matching_tolerance_units" value="ppm" />
+      <param name="binary_compression" value="numpressLinearPic" />
+      <output name="output" file="D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML" />
+    </test>
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="thresholds_0|threshold_type" value="count" />
+      <param name="thresholds_0|value" value="100" />
+      <param name="thresholds_0|orientation" value="most-intense" />
+      <param name="thresholds_1|threshold_type" value="absolute" />
+      <param name="thresholds_1|value" value="1" />
+      <param name="thresholds_1|orientation" value="most-intense" />
+      <param name="binary_compression" value="numpressLinearPic" />
+      <output name="output" file="small-threshold.mzML" />
+    </test>
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="do_mzwindow_filter" value="true" />
+      <param name="mz_window_from" value="420" />
+      <param name="mz_window_to" value="840" />
+      <param name="binary_compression" value="numpressLinearPic" />
+      <output name="output" file="small-mzWindow.mzML" />
+    </test>
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="denoise" value="true" />
+      <param name="num_peaks" value="10" />
+      <param name="window_width" value="40" />
+      <param name="relax" value="false" />
+      <param name="binary_compression" value="numpressLinearPic" />
+      <output name="output" file="small-denoise.mzML" />
+    </test>
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="ms2deisotope" value="true" />
+      <param name="binary_compression" value="numpressLinearPic" />
+      <output name="output" file="small-deisotope.mzML" />
+    </test>
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="activation" value="CID" />
+      <param name="binary_compression" value="numpressLinearPic" />
+      <output name="output" file="small-activation.mzML" />
+    </test>
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="indices_0|from" value="2" />
+      <param name="indices_0|to" value="4" />
+      <param name="indices_1|from" value="10" />
+      <param name="indices_1|to" value="10" />
+      <param name="indices_2|from" value="13" />
+      <param name="indices_2|to" value="15" />
+      <param name="binary_compression" value="numpressLinearPic" />
+      <output name="output" file="small-index-filter.mzML" />
+    </test>
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="strip_it" value="true" />
+      <param name="binary_compression" value="numpressLinearPic" />
+      <output name="output" file="small-strip-it.mzML" />
+    </test>
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="do_ms_level_filter" value="true" />
+      <param name="ms_level_from" value="2" />
+      <param name="ms_level_to" value="2" />
+      <param name="binary_compression" value="numpressLinearPic" />
+      <output name="output" file="small-ms-level-filter.mzML" />
+    </test>
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="polarity" value="positive" />
+      <param name="binary_compression" value="numpressLinearPic" />
+      <output name="output" file="small-polarity-filter.mzML" />
+    </test>
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="analyzer" value="IT" />
+      <param name="binary_compression" value="numpressLinearPic" />
+      <output name="output" file="small-analyzer-filter.mzML" />
+    </test>
+    <test>
+      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="scan_numbers_0|from" value="3" />
+      <param name="scan_numbers_0|to" value="5" />
+      <param name="scan_numbers_1|from" value="11" />
+      <param name="scan_numbers_1|to" value="11" />
+      <param name="scan_numbers_2|from" value="14" />
+      <param name="scan_numbers_2|to" value="16" />
+      <param name="binary_compression" value="numpressLinearPic" />
+      <output name="output" file="small-index-filter.mzML" /> <!-- the scan numbers here produce the same output as the index test above -->
+    </test>
+    <!--<test>
+      <param name="input" value="small.mzML" />
+      <param name="output_type" value="mzML" />
+      <param name="binary_compression" value="numpressLinearPic" />
+      <output name="output" file="small-deisotope-poisson.mzML" />
+    </test>-->
+  </tests>
+  <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
+  </help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btn323</citation>
+        <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
+                                      year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->
+    </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/msconvert_raw_wrapper.py	Thu Oct 22 14:00:58 2015 -0400
@@ -0,0 +1,124 @@
+#!/usr/bin/env python
+import optparse
+import os
+import sys
+import tempfile
+import shutil
+import subprocess
+import re
+from os.path import basename
+import logging
+
+assert sys.version_info[:2] >= ( 2, 6 )
+
+log = logging.getLogger(__name__)
+working_directory = os.getcwd()
+tmp_stderr_name = tempfile.NamedTemporaryFile(dir = working_directory, suffix = '.stderr').name
+tmp_stdout_name = tempfile.NamedTemporaryFile(dir = working_directory, suffix = '.stdout').name
+
+def stop_err( msg ):
+    sys.stderr.write( "%s\n" % msg )
+    sys.exit()
+
+def read_stderr():
+    stderr = ''
+    if(os.path.exists(tmp_stderr_name)):
+        with open(tmp_stderr_name, 'rb') as tmp_stderr:
+            buffsize = 1048576
+            try:
+                while True:
+                    stderr += tmp_stderr.read(buffsize)
+                    if not stderr or len(stderr) % buffsize != 0:
+                        break
+            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()))
+
+def delete_file(path):
+    if os.path.exists(path):
+        try:
+            os.remove(path)
+        except:
+            pass
+
+def delete_directory(directory):
+    if os.path.exists(directory):
+        try:
+            shutil.rmtree(directory)
+        except:
+            pass
+
+def symlink(source, link_name):
+    import platform
+    if platform.system() == 'Windows':
+        import win32file
+        win32file.CreateSymbolicLink(source, link_name, 1)
+    else:
+        os.symlink(source, link_name)
+
+
+def copy_to_working_directory(data_file, relative_path):
+    if os.path.abspath(data_file) != os.path.abspath(relative_path):
+        shutil.copy(data_file, relative_path)
+    return relative_path
+
+def __main__():
+    run_script()
+
+#ENDTEMPLATE
+
+to_extensions = ['mzML', 'mzXML', 'mgf', 'txt', 'ms2', 'cms2']
+
+def str_to_bool(v):
+    """ From http://stackoverflow.com/questions/715417/converting-from-a-string-to-boolean-in-python """
+    return v.lower() in ["yes", "true", "t", "1"]
+
+
+def run_script():
+    parser = optparse.OptionParser()
+    parser.add_option('--input', dest='input')
+    parser.add_option('--output', dest='output')
+    parser.add_option('--fromextension', dest='fromextension')
+    parser.add_option('--toextension', dest='toextension', default='mzML', choices=to_extensions)
+    parser.add_option('--binaryencoding', dest='binaryencoding', choices=['32', '64'])
+    parser.add_option('--mzencoding', dest='mzencoding', choices=['32', '64'])
+    parser.add_option('--intensityencoding', dest='intensityencoding', choices=['32', '64'])
+    parser.add_option('--noindex', dest='noindex')
+    parser.add_option('--zlib', dest='zlib')
+    parser.add_option('--filter', dest='filter', action='append', default=[])
+
+    (options, args) = parser.parse_args()
+
+    filter_commands = ''
+    for filter in options.filter:
+        filter_commands = "%s --filter \"%s\"" % (filter_commands, filter)
+
+    input_file = 'input.%s' % options.fromextension
+    copy_to_working_directory(options.input, input_file)
+    os.mkdir('output')
+    cmd = "msconvert --%s -o output" % (options.toextension)
+    if str_to_bool(options.noindex):
+        cmd = "%s %s" % (cmd, "--noindex")
+    if str_to_bool(options.zlib):
+        cmd = "%s %s" % (cmd, "--zlib")
+    cmd = "%s --%s" % (cmd, options.binaryencoding)
+    cmd = "%s --mz%s" % (cmd, options.mzencoding)
+    cmd = "%s --inten%s" % (cmd, options.intensityencoding)
+    cmd = "%s %s" % (cmd, input_file)
+    cmd = "%s %s" % (cmd, filter_commands)
+    print(cmd)
+    execute(cmd)
+    output_files = os.listdir('output')
+    assert len(output_files) == 1
+    output_file = output_files[0]
+    shutil.copy(os.path.join('output', output_file), options.output)
+
+if __name__ == '__main__': __main__()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/msconvert_subset.xml	Thu Oct 22 14:00:58 2015 -0400
@@ -0,0 +1,105 @@
+<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" version="3_0_4388">proteowizard</requirement>
+  </requirements>
+-->
+  <command interpreter="python">
+    msconvert_wrapper.py
+    --input=${input}
+    --output=${output}
+    --fromextension=${input.ext}
+    --toextension=${output_type}
+    #if $settings.settingsType == "full"
+    --binaryencoding=${settings.binary_encoding}
+    --mzencoding=${settings.mz_encoding}
+    --intensityencoding=${settings.intensity_encoding}
+    --zlib=${settings.zlib}
+    #end if
+    --filter_table="$filter.filterList"
+    #if $filter.filterType == "scan_number"
+    --filter_table_type="number"
+    #else
+    --filter_table_type="index"
+    #end if
+  </command>
+
+  <inputs>
+    <conditional name="type">
+      <param name="input_type" type="select" label="Input Type">
+        <option value="mzml">mzML</option>
+        <option value="mzxml">mzXML</option>
+        <option value="mgf">mgf</option>
+        <option value="ms2">ms2</option>
+      </param>
+      <when value="mzml">
+        <param format="mzml" name="input" type="data" label="Input mzML"/>
+      </when>
+      <when value="mzxml">
+        <param format="mzxml" name="input" type="data" label="Input mzXML"/>
+      </when>
+      <when value="mgf">
+        <param format="mgf" name="input" type="data" label="Input mgf"/>
+      </when>
+      <when value="ms2">
+        <param format="ms2" name="input" type="data" label="Input ms2"/>
+      </when>
+    </conditional>
+    <param name="output_type" type="select" label="Output Type">
+      <option value="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="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>
+      <when value="scan_number">
+        <param format="text" name="filterList" type="data" label="Scan Numbers"/>
+      </when>
+      <when value="scan_index">
+        <param format="text" name="filterList" type="data" label="Scan Indices"/>
+      </when>
+    </conditional>
+    <conditional name="settings">
+      <param name="settingsType" type="select" label="Advanced msconvert 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"  label="${type.input.name.rsplit('.',1)[0]}.${output_type}" >
+      <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>
+  </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/msconvert_wrapper.py	Thu Oct 22 14:00:58 2015 -0400
@@ -0,0 +1,281 @@
+#!/usr/bin/env python
+import optparse
+import os
+import sys
+import tempfile
+import shutil
+import subprocess
+import re
+import logging
+
+assert sys.version_info[:2] >= (2, 6)
+
+log = logging.getLogger(__name__)
+working_directory = os.getcwd()
+tmp_stderr_name = tempfile.NamedTemporaryFile(dir=working_directory, suffix='.stderr').name
+tmp_stdout_name = tempfile.NamedTemporaryFile(dir=working_directory, suffix='.stdout').name
+
+
+def stop_err(msg):
+    sys.stderr.write("%s\n" % msg)
+    sys.exit()
+
+
+def read_stderr():
+    stderr = ''
+    if(os.path.exists(tmp_stderr_name)):
+        with open(tmp_stderr_name, 'rb') as tmp_stderr:
+            buffsize = 1048576
+            try:
+                while True:
+                    stderr += tmp_stderr.read(buffsize)
+                    if not stderr or len(stderr) % buffsize != 0:
+                        break
+            except OverflowError:
+                pass
+    return stderr
+
+
+def execute(command, stdin=None):
+    try:
+        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()))
+    finally:
+        print(( open(tmp_stderr_name, "r").read() ))
+        print(( open(tmp_stdout_name, "r").read() ))
+
+
+def delete_file(path):
+    if os.path.exists(path):
+        try:
+            os.remove(path)
+        except:
+            pass
+
+
+def delete_directory(directory):
+    if os.path.exists(directory):
+        try:
+            shutil.rmtree(directory)
+        except:
+            pass
+
+
+def symlink(source, link_name):
+    import platform
+    if platform.system() == 'Windows':
+        try:
+            import win32file
+            win32file.CreateSymbolicLink(source, link_name, 1)
+        except:
+            shutil.copy(source, link_name)
+    else:
+        os.symlink(source, link_name)
+
+
+def copy_to_working_directory(data_file, relative_path):
+    if os.path.abspath(data_file) != os.path.abspath(relative_path):
+        symlink(data_file, relative_path)
+    return relative_path
+
+
+def __main__():
+    run_script()
+
+#ENDTEMPLATE
+
+to_extensions = ['mzML', 'mzXML', 'unindexed_mzML', 'unindexed_mzXML', 'mgf', 'txt', 'ms2', 'cms2']
+
+
+def str_to_bool(v):
+    """ From http://stackoverflow.com/questions/715417/converting-from-a-string-to-boolean-in-python """
+    return v.lower() in ["yes", "true", "t", "1"]
+
+
+def _add_filter(filters_file, contents):
+    filters_file.write("filter=%s\n" % contents)
+
+
+def _skip_line(options, file_num, line_parts):
+    file_num_column = options.filter_table_file_column
+    if not file_num_column:
+        return False
+    else:
+        target_file_num_val = str(file_num).strip()
+        query_file_num_val = line_parts[int(file_num_column) - 1].strip()
+        #print "target %s, query %s" % (target_file_num_val, query_file_num_val)
+        return target_file_num_val != query_file_num_val
+
+
+def _read_table_numbers(path, options, file_num=None):
+    unique_numbers = set([])
+    column_num = options.filter_table_column
+    input = open(path, "r")
+    first_line = True
+    for line in input:
+        if not line:
+            continue
+        line = line.strip()
+        if line.startswith("#"):
+            first_line = False
+            continue
+        if column_num == None:
+            column = line
+        else:
+            line_parts = line.split("\t")
+            if _skip_line(options, file_num, line_parts):
+                continue
+            column = line_parts[int(column_num) - 1]
+        match = re.match("\d+", column)
+        if match:
+            unique_numbers.add(int(match.group()))
+        first_line = False
+    return unique_numbers
+
+
+def shellquote(s):
+    return '"' + s.replace('"', '\\"') + '"'
+
+
+def _add_filter_line_from_file(filter_file, options, file_num=None):
+    file = options.filter_table
+    if not file:
+        return
+    numbers = _read_table_numbers(file, options, file_num)
+    msconvert_int_set = " ".join([str(number) for number in numbers])
+    filter_type = options.filter_table_type
+    if filter_type == 'number':
+        filter_prefix = 'scanNumber'
+    else:
+        filter_prefix = 'index'
+    _add_filter(filter_file, "%s %s" % (filter_prefix, msconvert_int_set))
+
+
+def _create_filters_file(options, file_num=None, debug=False):
+    suffix = "" if not file_num else str(file_num)
+    filters_file_path = "filters%s" % suffix
+    filters_file = open(filters_file_path, "w")
+    if options.filters_file:
+        filters_file.write(open(options.filters_file, "r").read())
+    for filter in options.filter:
+        _add_filter(filters_file, filter)
+    _add_filter_line_from_file(filters_file, options, file_num=file_num)
+
+    filters_file.close()
+    if debug:
+        print(( open(filters_file_path, "r").read() ))
+    return filters_file_path
+
+
+def _build_base_cmd(options):
+    to_extension = options.toextension
+    if to_extension.startswith("unindexed_"):
+        to_extension = to_extension[len("unindexed_"):]
+        to_params = "--noindex"
+    else:
+        to_params = ""
+    cmd = "msconvert --%s %s" % (to_extension, to_params)
+    if str_to_bool(options.zlib):
+        cmd = "%s %s" % (cmd, "--zlib")
+    if options.binaryencoding:
+        cmd = "%s --%s" % (cmd, options.binaryencoding)
+    if options.mzencoding:
+        cmd = "%s --mz%s" % (cmd, options.mzencoding)
+    if options.intensityencoding:
+        cmd = "%s --inten%s" % (cmd, options.intensityencoding)
+    return cmd
+
+
+def _run(base_cmd, output_dir='output', inputs=[], debug=False):
+    inputs_as_str = " ".join(['%s' % shellquote(input) for input in inputs])
+    os.mkdir(output_dir)
+    cmd = "%s -o %s %s" % (base_cmd, shellquote(output_dir), inputs_as_str)
+    if debug:
+        print(cmd)
+    execute(cmd)
+    output_files = os.listdir(output_dir)
+    assert len(output_files) == 1
+    output_file = output_files[0]
+    return os.path.join(output_dir, output_file)
+
+
+def run_script():
+    parser = optparse.OptionParser()
+    parser.add_option('--input', dest='inputs', action='append', default=[])
+    parser.add_option('--input_name', dest='input_names', action='append', default=[])
+    parser.add_option('--implicit', dest='implicits', action='append', default=[], help='input files that should NOT be on the msconvert command line.')
+    parser.add_option('--output', dest='output')
+    parser.add_option('--fromextension', dest='fromextension')
+    parser.add_option('--toextension', dest='toextension', default='mzML', choices=to_extensions)
+    parser.add_option('--binaryencoding', dest='binaryencoding', choices=['32', '64'])
+    parser.add_option('--mzencoding', dest='mzencoding', choices=['32', '64'])
+    parser.add_option('--intensityencoding', dest='intensityencoding', choices=['32', '64'])
+    parser.add_option('--zlib', dest='zlib', default="false")
+    parser.add_option('--filter', dest='filter', action='append', default=[])
+    parser.add_option('--filters_file', dest='filters_file', default=None)
+    parser.add_option('--filter_table', default=None)
+    parser.add_option('--filter_table_type', default='index', choices=['index', 'number'])
+    parser.add_option('--filter_table_column', default=None)
+    parser.add_option('--filter_table_file_column', default=None)
+    parser.add_option('--debug', dest='debug', action='store_true', default=False)
+
+    (options, args) = parser.parse_args()
+    if len(options.inputs) < 1:
+        stop_err("No input files to msconvert specified")
+    if len(options.input_names) > 0 and len(options.input_names) != len(options.inputs):
+        stop_err("Number(s) of supplied input names and input files do not match")
+    if not options.output:
+        stop_err("Must specify output location")
+    input_files = []
+    for i, input in enumerate(options.inputs):
+        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('.%s' % options.fromextension.lower()) and input not in options.implicits:
+            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)
+        if input in options.implicits:
+            continue
+        input_files.append(input_file)
+
+    cmd = _build_base_cmd(options)
+    file_column = options.filter_table_file_column
+    if not file_column:
+        # Apply same filters to all files, just create a unviersal filter files
+        # and run msconvert once.
+        filters_file_path = _create_filters_file(options, debug=options.debug)
+        cmd = "%s -c %s" % (cmd, filters_file_path)
+    else:
+        # Dispatching on a column to filter different files differently, need to filter
+        # each input once with msconvert and then merge once.
+        filtered_files = []
+        for index, input_file in enumerate(input_files):
+            filters_file_path = _create_filters_file(options, index + 1, debug=options.debug)
+            filter_cmd = "%s -c %s" % (cmd, filters_file_path)
+            filtered_output_file = _run(filter_cmd, output_dir='output%d' % index, inputs=[input_file], debug=options.debug)
+            filtered_files.append(filtered_output_file)
+        input_files = filtered_files
+    if len(input_files) > 1:
+        cmd = "%s --merge" % cmd
+    output_file = _run(cmd, output_dir='output', inputs=input_files, debug=options.debug)
+    shutil.copy(output_file, options.output)
+
+
+if __name__ == '__main__':
+    __main__()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML	Thu Oct 22 14:00:58 2015 -0400
@@ -0,0 +1,4759 @@
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+  <mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" id="D100930_yeast_SCX10S_rak_ft8E_pc_01" version="1.1.0">
+    <cvList count="2">
+      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="3.74.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>
+      <cv id="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>
+    </cvList>
+    <fileDescription>
+      <fileContent>
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+        <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>
+      </fileContent>
+      <sourceFileList count="1">
+        <sourceFile id="RAW1" name="D100930_yeast_SCX10S_rak_ft8E_pc_01.RAW" location="file:///D:\test\iPRG_2011">
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+      </software>
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+      </software>
+    </softwareList>
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+        <componentList count="3">
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+          <cvParam cvRef="MS" accession="MS:1000505" name="base peak intensity" value="606.315307617188" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
+          <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="8762.4814453125"/>
+          <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="197.148773193359" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+          <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="1968.756469726563" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+          <scanList count="1">
+            <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>
+            <scan instrumentConfigurationRef="IC2">
+              <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="60.807293333333" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>
+              <cvParam cvRef="MS" accession="MS:1000512" name="filter string" value="ITMS + c NSI d sa Full ms2 655.97@etd66.67 [50.00-1980.00]"/>
+              <cvParam cvRef="MS" accession="MS:1000616" name="preset scan configuration" value="8"/>
+              <cvParam cvRef="MS" accession="MS:1000927" name="ion injection time" value="100.0" unitCvRef="UO" unitAccession="UO:0000028" unitName="millisecond"/>
+              <userParam name="[Thermo Trailer Extra]Monoisotopic M/Z:" value="655.9720458984375" type="xsd:float"/>
+              <scanWindowList count="1">
+                <scanWindow>
+                  <cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="50.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+                  <cvParam cvRef="MS" accession="MS:1000500" name="scan window upper limit" value="1980.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+                </scanWindow>
+              </scanWindowList>
+            </scan>
+          </scanList>
+          <precursorList count="1">
+            <precursor>
+              <isolationWindow>
+                <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="655.97" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+                <cvParam cvRef="MS" accession="MS:1000828" name="i