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1 <tool name="Quantiline" id="quantiline1" version="1.0.2">
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2 <description>Labeled ms/ms data pre-processing for Protein Quantification (and Inference) pipelines</description>
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3 <!--
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4 For remote debugging start you listener on port 8000 and use the following as command interpreter:
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5 java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000
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6 //////////////////////////
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7 -->
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8 <command interpreter="java -jar ">
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9 Quantiline.jar
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10 -ppidsFileName $ppidsFileName
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11 -spectraDataFile $spectraDataFile
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12 -ppidsInputFormat MZID
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13 -labelMzValues "$labelMzValues"
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14 -labelmTol $labelmTol
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15 -outputFile $outputFile
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16 -outReport $outReport
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17 </command>
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18 <inputs>
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19
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20 <param name="ppidsFileName" type="data" format="prims.fileset.zip" label="MS/MS peptide identifications fileSet (N mzidentml files)"/>
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21 <param name="spectraDataFile" type="data" format="prims.fileset.zip" label="MS/MS spectra fileSet (N mzml files)"/>
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22
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23 <param name="labelMzValues" type="text" size="20" label="Label m/z values"
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24 help="e.g. for 4plexed iTRAQ : 114.0,115.0,116.0,117.0"/>
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25
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26 <param name="labelmTol" type="float" size="10" value="0.5" label="Label detection tolerance (Da)"
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27 help="Tolerance in daltons for label detection."/>
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28
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29 </inputs>
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30 <outputs>
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31 <data name="outputFile" format="apml" label="${tool.name} on ${on_string}: Peptides quantification (APML)" />
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32 <data name="outReport" format="html" label="${tool.name} on ${on_string}: Peptides quantification report (HTML)"/>
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33 </outputs>
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34 <tests>
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35 </tests>
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36 <help>
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37
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38 .. class:: infomark
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39
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40 This tool can read spectra files (mzML) and their respective identification files (mzIdentML) and based
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41 on the configured label masses produce a file that contains the merged information:
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42 peptides and their quantification based on label fragment intensity values read from the spectrum in which they
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43 were identified.
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44
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45 In other words, it produces the peptide (relative) quantification file. This file can subsequently be used
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46 by other tools for protein inference and protein quantification (e.g. Quantifere).
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47
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48
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49 -----
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50
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51 **Output details**
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52
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53 *Peptide quantification file (APML)*
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54
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55 This is the list of peptides with their (relative) quantification based on the labels and their
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56 intensities found in the label peaks of the corresponding spectrum.
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57
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58
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59
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60
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61 </help>
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62 </tool>
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