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1 <tool id="proteomics_search_peptide_prophet_1" name="Peptide Prophet" version="1.0.0">
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2 <requirements><requirement type="package">protk</requirement></requirements>
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3 <description>Calculate Peptide Prophet statistics on search results</description>
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4
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5 <command interpreter="ruby">peptide_prophet_wrapper.rb ${output} ${input_file} -r $glyco $useicat $phospho $usepi $usert $accurate_mass $no_ntt $no_nmc $use_gamma $use_only_expect $force_fit $allow_alt_instruments $maldi
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6 </command>
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7
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8 <inputs>
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9
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10 <param name="input_file" type="data" format="raw_pepxml" multiple="false" label="Raw Search Results" help="These files will typically be outputs from omssa or xtandem search tools"/>
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11
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12 <param name="glyco" type="boolean" label="Expect true positives to have a glycocapture motif" truevalue="--glyco" falsevalue=""/>
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13 <param name="useicat" type="boolean" label="Use icat information" truevalue="--useicat" falsevalue="--no-useicat"/>
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14 <param name="phospho" type="boolean" label="Use phospho information" truevalue="--phospho" falsevalue=""/>
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15 <param name="usepi" type="boolean" label="Use pI information" truevalue="--usepi" falsevalue=""/>
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16 <param name="usert" type="boolean" label="Use hydrophobicity / RT information" truevalue="--usert" falsevalue=""/>
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17 <param name="accurate_mass" type="boolean" label="Use accurate mass binning" truevalue="--accurate-mass" falsevalue=""/>
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18 <param name="no_ntt" type="boolean" label="Don't use NTT model" truevalue="--no-ntt" falsevalue=""/>
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19 <param name="no_nmc" type="boolean" label="Don't use NMC model" truevalue="--no-nmc" falsevalue=""/>
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20 <param name="use_gamma" type="boolean" label="Use Gamma distribution to model the negatives" help="Applies only to X!Tandem results" truevalue="--usegamma" falsevalue=""/>
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21 <param name="use_only_expect" type="boolean" label="Only use Expect Score as the discriminant" help="Applies only to X!Tandem results.
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22 Helpful for data with homologous top hits e.g. phospho or glyco" truevalue="--use-only-expect" falsevalue=""/>
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23 <param name="force_fit" type="boolean" label="Force fitting" help="Bypasses automatic mixture model checks and forces fitting of a mixture model" truevalue="--force-fit" falsevalue=""/>
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24 <param name="allow_alt_instruments" type="boolean" label="Allow multiple instrument types" help="Warning instead of exit with error if instrument types between runs is different" truevalue="--allow-alt-instruments" falsevalue=""/>
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25 <param name="maldi" type="boolean" label="Maldi data" truevalue="-l" falsevalue=""/>
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26
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27
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28 </inputs>
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29 <outputs>
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30 <data format="peptideprophet_pepxml" name="output" metadata_source="input_file" label="peptide_prophet.${input_file.display_name}.pep.xml" from_work_dir="peptide_prophet_output.pep.xml"/>
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31 </outputs>
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32
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33 <help>
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34
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35 **What it does**
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36
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37 Given raw search engine scores as inputs this tool estimates the accuracy of peptide assignments. From a practical perspective it estimates the probability that each peptide assignment is correct (providing probabilities as outputs), given raw scores (possibly on some arbitrary scale) as inputs.
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38
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39 ----
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40
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41 **Citation**
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42
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43 If you use this tool please read and cite the paper describing the statistical model implemented by Peptide Prophet
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44
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45 Keller A., et al. “Empirical Statistical Model to Estimate the Accuracy of Peptide Identifications Made by MS/MS and Database Search” *Anal. Chem.* 74, 5383-5392 (2002).
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46
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47
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48 </help>
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49
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50
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51 <!--PeptideProphet options [following the 'O']:
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52 i [use icat information in PeptideProphet]
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53 f [do not use icat information in PeptideProphet]
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54 g [use N-glyc motif information in PeptideProphet]
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55 H [use Phospho information in PeptideProphet]
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56 m [maldi data]
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57 I [use pI information in PeptideProphet]
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58 R [use Hydrophobicity / RT information in PeptideProphet]
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59 F [force the fitting of the mixture model, bypass automatic mixture model checks]
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60 A [use accurate mass binning in PeptideProphet]
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61 w [warning instead of exit with error if instrument types between runs is different]
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62 x [exclude all entries with asterisked score values in PeptideProphet]
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63 l [leave alone all entries with asterisked score values in PeptideProphet]
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64 n [use hardcoded default initialization parameters of the distributions]
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65 P [use Non-parametric model, can only be used with decoy option]
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66 N [do not use the NTT model]
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67 M [do not use the NMC model]
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68 G [use Gamma Distribution to model the Negatives (applies only to X!Tandem data)]
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69 E [only use Expect Score as the Discriminant(applies only to X!Tandem data,
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70 helpful for data with homologous top hits e.g. phospho or glyco)]
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71 d [report decoy hits with a computed probability based on the model learned]
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72 p [run ProteinProphet afterwards]
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73 t [do not create png data plot]
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74 u [do not assemble protein groups in ProteinProphet analysis]
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75 s [do not use Occam's Razor in ProteinProphet analysis to
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76 derive the simplest protein list to explain observed peptides]
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77 -->
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78
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79 </tool>
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