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1 <tool id="ms2preproc" name="ms2preproc" version="0.1.0">
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2 <description>preprocess and filter MS/MS spectra</description>
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3
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4 <command>
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5 #if $window:
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6 #set $window_arg = "-Z %s" % $window
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7 #else
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8 #set $window_arg = ""
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9 #end if
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10 ms2preproc --infile ${input} --outfile ${output} --informat mgf --top ${top} ${window_arg}; sed -i -e 's/,SCAN\(.*\)$/\nSCANS=\1/' ${output}
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11 </command>
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12
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13 <inputs>
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14 <param format="mgf" name="input" type="data" label="Input MGF" />
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15 <param name="top" type="integer" label="Number of top peaks to keep" value="200" help="" />
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16 <param name="window" type="float" label="m/z Window" value="" optional="true" help="m/z Windows (+/-Z) around high-intensity peaks in which the number specified above are selected. (Optional)" />
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17 </inputs>
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18 <outputs>
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19 <data format="mgf" name="output" label="ms2preproc on ${on_string}"/>
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20 </outputs>
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21
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22 <requirements>
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23 <requirement type="package">ms2preproc</requirement>
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24 </requirements>
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25
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26 <help>
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27 **What it does**
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28
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29 ms2preproc is a software tool to preprocess MS/MS spectra, please see the citation below for more information.
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30
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31 **Inputs and Parameters**
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32
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33 ms2preproc is very specific about the formatting of the MGF file it parses. Therefore it is recommended that the MGF Formatter tool is used to create a MGF file specifically for ms2preproc prior to the use of this tool.
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34
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35 The authors of this software recommend running ms2preproc with the following settings:
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36
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37 Mascot:
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38 Select top 200 peaks globally.
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39
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40 Sequest:
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41 Select top 6 peaks in windows of size 30 m/z.
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42
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43 ProteinPilot:
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44 Select top 6 peaks in windows of size 30 m/z.
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45
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46 ------
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47
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48 **Citation**
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49
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50 For the underlying tool, please cite `Renard BY, Kirchner M, Monigatti F, Invanov AR, Rappsilber J, Winter D, Steen JAJ, Hamprecht FA, Steen H. When Less Can Yield More - Computational Preprocessing of MS/MS Spectra for Peptide Identification, Proteomics (2009).`
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51
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52 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-ms2preproc
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53 </help>
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54 </tool>
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