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comparison peptide_prophet.xml @ 18:84b47300a4c8 draft default tip

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planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
author iracooke
date Tue, 20 Oct 2015 20:46:16 -0400
parents b68f292b2904
children
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17:b68f292b2904 18:84b47300a4c8
1 <tool id="proteomics_search_peptide_prophet_1" name="Peptide Prophet" version="1.0.1"> 1 <tool id="proteomics_search_peptide_prophet_1" name="Peptide Prophet" version="1.1.1">
2 <description>Calculate Peptide Prophet statistics on search results</description>
2 <requirements> 3 <requirements>
3 <container type="docker">simonalpha/protk:1.4.0</container> 4 <container type="docker">iracooke/protk-1.4.3</container>
4 <requirement type="package" version="1.3">protk</requirement> 5 <requirement type="package" version="1.4.3">protk</requirement>
5 <requirement type="package" version="4.6.3">trans_proteomic_pipeline</requirement> 6 <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
6 </requirements> 7 </requirements>
7 8 <command>
8 <description>Calculate Peptide Prophet statistics on search results</description> 9 peptide_prophet.rb
10 --galaxy $input_file
11 -o peptide_prophet_output.pep.xml
12 -r
13 $glyco
14 $useicat
15 $phospho
16 $usepi
17 $usert
18 $accurate_mass
19 $no_ntt
20 $no_nmc
21 $use_gamma
22 $use_only_expect
23 $force_fit
24 $allow_alt_instruments
25 $maldi
26 $usedecoys
27 --decoy-prefix $decoy_prefix_string
9 28
10 <command> 29 #if $experiment_label
11 peptide_prophet.rb --galaxy $input_file -o peptide_prophet_output.pep.xml 30 --experiment-label $experiment_label
31 #end if
12 32
13 -r 33 --p-thresh $p_thresh
14 $glyco 34 --threads "\${GALAXY_SLOTS:-12}"
15 $useicat
16 $phospho
17 $usepi
18 $usert
19 $accurate_mass
20 $no_ntt
21 $no_nmc
22 $use_gamma
23 $use_only_expect
24 $force_fit
25 $allow_alt_instruments
26 $maldi
27 $usedecoys
28 --decoy-prefix $decoy_prefix_string
29 35
30 #if $experiment_label
31 --experiment-label $experiment_label
32 #end if
33 36
34 --p-thresh $p_thresh 37 </command>
38 <inputs>
39 <param name="input_file" type="data" format="pepxml,raw_pepxml" multiple="false" label="Raw Search Results" help="These files will typically be outputs from omssa or xtandem search tools"/>
35 40
36 --threads $threads 41 <param name="glyco" type="boolean" label="Expect true positives to have a glycocapture motif" truevalue="--glyco" falsevalue=""/>
37 42 <param name="useicat" type="boolean" label="Use icat information" truevalue="--useicat" falsevalue=""/>
38 </command> 43 <param name="phospho" type="boolean" label="Use phospho information" truevalue="--phospho" falsevalue=""/>
39 44 <param name="usepi" type="boolean" label="Use pI information" truevalue="--usepi" falsevalue=""/>
40 <inputs> 45 <param name="usert" type="boolean" label="Use hydrophobicity / RT information" truevalue="--usert" falsevalue=""/>
41 46 <param name="accurate_mass" type="boolean" label="Use accurate mass binning" truevalue="--accurate-mass" falsevalue=""/>
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"/> 47 <param name="no_ntt" type="boolean" label="Don't use NTT model" truevalue="--no-ntt" falsevalue=""/>
43 48 <param name="no_nmc" type="boolean" label="Don't use NMC model" truevalue="--no-nmc" falsevalue=""/>
44 <param name="glyco" type="boolean" label="Expect true positives to have a glycocapture motif" truevalue="--glyco" falsevalue=""/> 49 <param name="use_gamma" type="boolean" label="Use Gamma distribution to model the negatives" help="Applies only to X!Tandem results" truevalue="--usegamma" falsevalue=""/>
45 <param name="useicat" type="boolean" label="Use icat information" truevalue="--useicat" falsevalue=""/> 50 <param name="use_only_expect" type="boolean" label="Only use Expect Score as the discriminant" help="Applies only to X!Tandem results.
46 <param name="phospho" type="boolean" label="Use phospho information" truevalue="--phospho" falsevalue=""/> 51 Helpful for data with homologous top hits e.g. phospho or glyco" truevalue="--use-only-expect" falsevalue=""/>
47 <param name="usepi" type="boolean" label="Use pI information" truevalue="--usepi" falsevalue=""/> 52 <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=""/>
48 <param name="usert" type="boolean" label="Use hydrophobicity / RT information" truevalue="--usert" falsevalue=""/> 53 <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=""/>
49 <param name="accurate_mass" type="boolean" label="Use accurate mass binning" truevalue="--accurate-mass" falsevalue=""/> 54 <param name="maldi" type="boolean" label="Maldi data" truevalue="-l" falsevalue=""/>
50 <param name="no_ntt" type="boolean" label="Don't use NTT model" truevalue="--no-ntt" falsevalue=""/> 55 <param name="usedecoys" type="boolean" label="Use decoys to pin down the negative distribution" truevalue="" falsevalue="--no-decoy"/>
51 <param name="no_nmc" type="boolean" label="Don't use NMC model" truevalue="--no-nmc" falsevalue=""/> 56 <param name="decoy_prefix_string" help="Prefix string for decoy ids" type="text" value="decoy_" label="Decoy Prefix String" size="20"/>
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=""/> 57 <param name="experiment_label" help="Used to commonly label all spectra from one experiment" type="text" value="" label="Experiment Label" size="20"/>
53 <param name="use_only_expect" type="boolean" label="Only use Expect Score as the discriminant" help="Applies only to X!Tandem results. 58 <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"/>
54 Helpful for data with homologous top hits e.g. phospho or glyco" truevalue="--use-only-expect" falsevalue=""/> 59 </inputs>
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=""/> 60 <outputs>
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=""/> 61 <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"/>
57 <param name="maldi" type="boolean" label="Maldi data" truevalue="-l" falsevalue=""/> 62 </outputs>
58 <param name="usedecoys" type="boolean" label="Use decoys to pin down the negative distribution" truevalue="" falsevalue="--no-decoy"/> 63 <help>
59 <param name="decoy_prefix_string" help="Prefix string for decoy ids" type="text" value="decoy_" label="Decoy Prefix String" size="20"/>
60 <param name="experiment_label" help="Used to commonly label all spectra from one experiment" type="text" value="" label="Experiment Label" size="20"/>
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"/>
62 <param name="threads" type="integer" value="1" min="0" label="Threads" help="Number of threads to use"/>
63
64 </inputs>
65 <outputs>
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"/>
67 </outputs>
68
69 <help>
70 64
71 **What it does** 65 **What it does**
72 66
73 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. 67 Given raw search engine scores as inputs this tool estimates the accuracy of peptide assignments.
74 68
75 ---- 69 ----
76 70
77 **Citation** 71 **Citation**
78 72
79 If you use this tool please read and cite the paper describing the statistical model implemented by Peptide Prophet 73 If you use this tool please read and cite the paper describing the statistical model implemented by Peptide Prophet
80 74
81 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). 75 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).
82 76
83 77
84 </help> 78 </help>
85 79
86 80
87 <!--PeptideProphet options [following the 'O']: 81 <!--PeptideProphet options [following the 'O']:
88 i [use icat information in PeptideProphet] 82 i [use icat information in PeptideProphet]
89 f [do not use icat information in PeptideProphet] 83 f [do not use icat information in PeptideProphet]