Mercurial > repos > galaxyp > iquant
comparison iquant.xml @ 0:44077d92c836 draft
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author | galaxyp |
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date | Thu, 09 May 2013 17:14:17 -0400 |
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1 <tool id="iquant" name="iQuant" version="0.2.0"> | |
2 <description>Perform quantitation on data labeled with isobaric tags.</description> | |
3 <command> | |
4 LTQ-iQuant-cli --report_type ${peptide_report.report_type} --group_type ${group_type} --report ${peptide_report.report} --type ${quant_type} --output $output | |
5 #for $input in $inputs: | |
6 "${input}" | |
7 #end for | |
8 </command> | |
9 <inputs> | |
10 <conditional name="peptide_report"> | |
11 <param name="report_type" type="select" label="Identification Report Type"> | |
12 <option value="PEPXML">PepXML</option> | |
13 <option value="SCAFFOLD">Scaffold Spectrum Report</option> | |
14 <option value="PROTEIN_PILOT">ProteinPilot Peptide Report</option> | |
15 <option value="MAX_QUANT">MaxQuant MSMS Export</option> | |
16 </param> | |
17 <when value="PEPXML"> | |
18 <param format="pepxml" name="report" type="data" label="Input PepXML"/> | |
19 </when> | |
20 <when value="SCAFFOLD"> | |
21 <param format="text" name="report" type="data" label="Input Scaffold Report"/> | |
22 </when> | |
23 <when value="PROTEIN_PILOT"> | |
24 <param format="text" name="report" type="data" label="Input ProteinPilot Peptide Report"/> | |
25 </when> | |
26 <when value="MAX_QUANT"> | |
27 <param format="text" name="report" type="data" label="Input MaxQuant MSMS Export"/> | |
28 </when> | |
29 </conditional> | |
30 <param name="inputs" multiple="true" type="data" format="mzxml,mzml" label="Peaklist(s)" help=""/> | |
31 <param name="quant_type" type="select" label="Quantification type"> | |
32 <option value="FOUR_PLEX">iTRAQ 4-plex</option> | |
33 <option value="EIGHT_PLEX">iTRAQ 8-plex</option> | |
34 <option value="TMT_TWO_PLEX">TMT 2-plex</option> | |
35 <option value="TMT_SIX_PLEX">TMT 6-plex</option> | |
36 </param> | |
37 <param name="group_type" type="select" label="Quantify based on grouping of"> | |
38 <option value="PROTEIN">Proteins</option> | |
39 <option value="PEPTIDE">Peptides</option> | |
40 <option value="PEPTIDE_WITH_MODIFICATIONS">Peptides with modifications</option> | |
41 <option value="PEPTIDE_WITH_UNIQUE_MODIFICATION">Peptide with an identified modification</option> | |
42 </param> | |
43 </inputs> | |
44 | |
45 <outputs> | |
46 <data format="tabular" name="output" /> | |
47 </outputs> | |
48 | |
49 <requirements> | |
50 <requirement type="package" version="1.19.19">tint_proteomics_scripts</requirement><!-- Version 1.19.19 or higher --> | |
51 </requirements> | |
52 | |
53 <help> | |
54 **What it does** | |
55 | |
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. | |
57 | |
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). | |
59 | |
60 ------ | |
61 | |
62 **Citation** | |
63 | |
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.`` | |
65 | |
66 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-iquant | |
67 | |
68 </help> | |
69 </tool> |