Mercurial > repos > pieterlukasse > prims_proteomics
comparison quantiline.xml @ 0:d50f079096ee
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| author | pieter.lukasse@wur.nl |
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| date | Wed, 08 Jan 2014 11:39:16 +0100 |
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| -1:000000000000 | 0:d50f079096ee |
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| 1 <tool name="Quantiline" id="quantiline1" version="1.0.2"> | |
| 2 <description>Labeled ms/ms data pre-processing for Protein Quantification (and Inference) pipelines</description> | |
| 3 <!-- | |
| 4 For remote debugging start you listener on port 8000 and use the following as command interpreter: | |
| 5 java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000 | |
| 6 ////////////////////////// | |
| 7 --> | |
| 8 <command interpreter="java -jar "> | |
| 9 Quantiline.jar | |
| 10 -ppidsFileName $ppidsFileName | |
| 11 -spectraDataFile $spectraDataFile | |
| 12 -ppidsInputFormat MZID | |
| 13 -labelMzValues "$labelMzValues" | |
| 14 -labelmTol $labelmTol | |
| 15 -outputFile $outputFile | |
| 16 -outReport $outReport | |
| 17 </command> | |
| 18 <inputs> | |
| 19 | |
| 20 <param name="ppidsFileName" type="data" format="prims.fileset.zip" label="MS/MS peptide identifications fileSet (N mzidentml files)"/> | |
| 21 <param name="spectraDataFile" type="data" format="prims.fileset.zip" label="MS/MS spectra fileSet (N mzml files)"/> | |
| 22 | |
| 23 <param name="labelMzValues" type="text" size="20" label="Label m/z values" | |
| 24 help="e.g. for 4plexed iTRAQ : 114.0,115.0,116.0,117.0"/> | |
| 25 | |
| 26 <param name="labelmTol" type="float" size="10" value="0.5" label="Label detection tolerance (Da)" | |
| 27 help="Tolerance in daltons for label detection."/> | |
| 28 | |
| 29 </inputs> | |
| 30 <outputs> | |
| 31 <data name="outputFile" format="apml" label="${tool.name} on ${on_string}: Peptides quantification (APML)" /> | |
| 32 <data name="outReport" format="html" label="${tool.name} on ${on_string}: Peptides quantification report (HTML)"/> | |
| 33 </outputs> | |
| 34 <tests> | |
| 35 </tests> | |
| 36 <help> | |
| 37 | |
| 38 .. class:: infomark | |
| 39 | |
| 40 This tool can read spectra files (mzML) and their respective identification files (mzIdentML) and based | |
| 41 on the configured label masses produce a file that contains the merged information: | |
| 42 peptides and their quantification based on label fragment intensity values read from the spectrum in which they | |
| 43 were identified. | |
| 44 | |
| 45 In other words, it produces the peptide (relative) quantification file. This file can subsequently be used | |
| 46 by other tools for protein inference and protein quantification (e.g. Quantifere). | |
| 47 | |
| 48 | |
| 49 ----- | |
| 50 | |
| 51 **Output details** | |
| 52 | |
| 53 *Peptide quantification file (APML)* | |
| 54 | |
| 55 This is the list of peptides with their (relative) quantification based on the labels and their | |
| 56 intensities found in the label peaks of the corresponding spectrum. | |
| 57 | |
| 58 | |
| 59 | |
| 60 | |
| 61 </help> | |
| 62 </tool> |