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1 <tool id="iquant" name="iQuant" version="0.2.0">
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2 <description>Perform quantitation on data labeled with isobaric tags.</description>
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3 <command>
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4 LTQ-iQuant-cli --report_type ${peptide_report.report_type} --group_type ${group_type} --report ${peptide_report.report} --type ${quant_type} --output $output
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5 #for $input in $inputs:
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6 "${input}"
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7 #end for
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8 </command>
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9 <inputs>
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10 <conditional name="peptide_report">
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11 <param name="report_type" type="select" label="Identification Report Type">
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12 <option value="PEPXML">PepXML</option>
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13 <option value="SCAFFOLD">Scaffold Spectrum Report</option>
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14 <option value="PROTEIN_PILOT">ProteinPilot Peptide Report</option>
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15 <option value="MAX_QUANT">MaxQuant MSMS Export</option>
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16 </param>
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17 <when value="PEPXML">
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18 <param format="pepxml" name="report" type="data" label="Input PepXML"/>
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19 </when>
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20 <when value="SCAFFOLD">
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21 <param format="text" name="report" type="data" label="Input Scaffold Report"/>
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22 </when>
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23 <when value="PROTEIN_PILOT">
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24 <param format="text" name="report" type="data" label="Input ProteinPilot Peptide Report"/>
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25 </when>
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26 <when value="MAX_QUANT">
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27 <param format="text" name="report" type="data" label="Input MaxQuant MSMS Export"/>
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28 </when>
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29 </conditional>
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30 <param name="inputs" multiple="true" type="data" format="mzxml,mzml" label="Peaklist(s)" help=""/>
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31 <param name="quant_type" type="select" label="Quantification type">
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32 <option value="FOUR_PLEX">iTRAQ 4-plex</option>
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33 <option value="EIGHT_PLEX">iTRAQ 8-plex</option>
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34 <option value="TMT_TWO_PLEX">TMT 2-plex</option>
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35 <option value="TMT_SIX_PLEX">TMT 6-plex</option>
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36 </param>
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37 <param name="group_type" type="select" label="Quantify based on grouping of">
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38 <option value="PROTEIN">Proteins</option>
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39 <option value="PEPTIDE">Peptides</option>
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40 <option value="PEPTIDE_WITH_MODIFICATIONS">Peptides with modifications</option>
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41 <option value="PEPTIDE_WITH_UNIQUE_MODIFICATION">Peptide with an identified modification</option>
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42 </param>
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43 </inputs>
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44
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45 <outputs>
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46 <data format="tabular" name="output" />
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47 </outputs>
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48
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49 <requirements>
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50 <requirement type="package" version="1.19.19">tint_proteomics_scripts</requirement><!-- Version 1.19.19 or higher -->
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51 </requirements>
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52
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53 <help>
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54 **What it does**
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55
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56 iQuant is a tool that performs tag based isobaric quantification by implementing a technique assigning collective reporter ion intensity-based weights to each peptide abundance ratio and calculating a protein's weighted average abundance ratio and p-value.
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57
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58 iQuant requires identification results from an upstream identification pipeline along with XML peak lists for the data (mzXML is well supported and an mzML option has been provided for testing).
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59
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60 ------
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61
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62 **Citation**
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63
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64 For the underlying tool, please cite ``Onsongo G, Stone MD, Van Riper SK, Chilton J, Wu B, Higgins L, Lund TC, Carlis JV, Griffin TJ, 2010. LTQ-iQuant: A freely available software pipeline for automated and accurate protein quantification of isobaric tagged peptide data from LTQ instruments. Proteomics. 10(19). doi: 10.1002/pmic.201000189.``
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65
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66 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-iquant
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67
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68 </help>
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69 </tool>
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