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1 <tool id="proteomics_search_peptide_prophet_1" name="Peptide Prophet" version="1.1.0">
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2 <requirements>
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3 <container type="docker">iracooke/protk-1.4.1</container>
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4 <requirement type="package" version="1.4">protk</requirement>
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5 <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
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6 </requirements>
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7
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8 <description>Calculate Peptide Prophet statistics on search results</description>
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9
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10 <command>
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11 peptide_prophet.rb --galaxy $input_file -o peptide_prophet_output.pep.xml
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12
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13 -r
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14 $glyco
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15 $useicat
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16 $phospho
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17 $usepi
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18 $usert
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19 $accurate_mass
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20 $no_ntt
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21 $no_nmc
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22 $use_gamma
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23 $use_only_expect
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24 $force_fit
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25 $allow_alt_instruments
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26 $maldi
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27 $usedecoys
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28 --decoy-prefix $decoy_prefix_string
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29
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30 #if $experiment_label
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31 --experiment-label $experiment_label
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32 #end if
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33
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34 --p-thresh $p_thresh
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35
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36 --threads $threads
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37
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38 </command>
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39
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40 <inputs>
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41
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42 <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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43
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44 <param name="glyco" type="boolean" label="Expect true positives to have a glycocapture motif" truevalue="--glyco" falsevalue=""/>
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45 <param name="useicat" type="boolean" label="Use icat information" truevalue="--useicat" falsevalue=""/>
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46 <param name="phospho" type="boolean" label="Use phospho information" truevalue="--phospho" falsevalue=""/>
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47 <param name="usepi" type="boolean" label="Use pI information" truevalue="--usepi" falsevalue=""/>
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48 <param name="usert" type="boolean" label="Use hydrophobicity / RT information" truevalue="--usert" falsevalue=""/>
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49 <param name="accurate_mass" type="boolean" label="Use accurate mass binning" truevalue="--accurate-mass" falsevalue=""/>
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50 <param name="no_ntt" type="boolean" label="Don't use NTT model" truevalue="--no-ntt" falsevalue=""/>
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51 <param name="no_nmc" type="boolean" label="Don't use NMC model" truevalue="--no-nmc" falsevalue=""/>
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52 <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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53 <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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54 Helpful for data with homologous top hits e.g. phospho or glyco" truevalue="--use-only-expect" falsevalue=""/>
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55 <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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56 <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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57 <param name="maldi" type="boolean" label="Maldi data" truevalue="-l" falsevalue=""/>
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58 <param name="usedecoys" type="boolean" label="Use decoys to pin down the negative distribution" truevalue="" falsevalue="--no-decoy"/>
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59 <param name="decoy_prefix_string" help="Prefix string for decoy ids" type="text" value="decoy_" label="Decoy Prefix String" size="20"/>
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60 <param name="experiment_label" help="Used to commonly label all spectra from one experiment" type="text" value="" label="Experiment Label" size="20"/>
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61 <param name="p_thresh" help="Peptides scoring less than this value are discarded" type="float" value="0.05" min="0" max="1" label="Probability Threshold"/>
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62 <param name="threads" type="integer" value="1" min="0" label="Threads" help="Number of threads to use"/>
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63
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64 </inputs>
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65 <outputs>
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66 <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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67 </outputs>
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68
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69
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70 <help>
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71
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72 **What it does**
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73
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74 Given raw search engine scores as inputs this tool estimates the accuracy of peptide assignments.
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75
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76 ----
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77
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78 **Citation**
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79
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80 If you use this tool please read and cite the paper describing the statistical model implemented by Peptide Prophet
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81
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82 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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83
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84
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85 </help>
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86
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87
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88 <!--PeptideProphet options [following the 'O']:
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89 i [use icat information in PeptideProphet]
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90 f [do not use icat information in PeptideProphet]
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91 g [use N-glyc motif information in PeptideProphet]
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92 H [use Phospho information in PeptideProphet]
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93 m [maldi data]
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94 I [use pI information in PeptideProphet]
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95 R [use Hydrophobicity / RT information in PeptideProphet]
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96 F [force the fitting of the mixture model, bypass automatic mixture model checks]
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97 A [use accurate mass binning in PeptideProphet]
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98 w [warning instead of exit with error if instrument types between runs is different]
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99 x [exclude all entries with asterisked score values in PeptideProphet]
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100 l [leave alone all entries with asterisked score values in PeptideProphet]
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101 n [use hardcoded default initialization parameters of the distributions]
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102 P [use Non-parametric model, can only be used with decoy option]
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103 N [do not use the NTT model]
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104 M [do not use the NMC model]
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105 G [use Gamma Distribution to model the Negatives (applies only to X!Tandem data)]
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106 E [only use Expect Score as the Discriminant(applies only to X!Tandem data,
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107 helpful for data with homologous top hits e.g. phospho or glyco)]
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108 d [report decoy hits with a computed probability based on the model learned]
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109 p [run ProteinProphet afterwards]
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110 t [do not create png data plot]
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111 u [do not assemble protein groups in ProteinProphet analysis]
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112 s [do not use Occam's Razor in ProteinProphet analysis to
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113 derive the simplest protein list to explain observed peptides]
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114 -->
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115
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116 </tool>
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