Mercurial > repos > iracooke > protk

comparison peptide_prophet.xml @ 0:a929e27eb203 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author iracooke
date Thu, 21 Jun 2012 22:30:48 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:a929e27eb203
1 <tool id="proteomics_search_peptide_prophet_1" name="Peptide Prophet" version="1.0.0">
2 <requirements><requirement type="package">protk</requirement></requirements>
3 <description>Calculate Peptide Prophet statistics on search results</description>
4
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
6 </command>
7
8 <inputs>
9
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"/>
11
12 <param name="glyco" type="boolean" label="Expect true positives to have a glycocapture motif" truevalue="--glyco" falsevalue=""/>
13 <param name="useicat" type="boolean" label="Use icat information" truevalue="--useicat" falsevalue="--no-useicat"/>
14 <param name="phospho" type="boolean" label="Use phospho information" truevalue="--phospho" falsevalue=""/>
15 <param name="usepi" type="boolean" label="Use pI information" truevalue="--usepi" falsevalue=""/>
16 <param name="usert" type="boolean" label="Use hydrophobicity / RT information" truevalue="--usert" falsevalue=""/>
17 <param name="accurate_mass" type="boolean" label="Use accurate mass binning" truevalue="--accurate-mass" falsevalue=""/>
18 <param name="no_ntt" type="boolean" label="Don't use NTT model" truevalue="--no-ntt" falsevalue=""/>
19 <param name="no_nmc" type="boolean" label="Don't use NMC model" truevalue="--no-nmc" falsevalue=""/>
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=""/>
21 <param name="use_only_expect" type="boolean" label="Only use Expect Score as the discriminant" help="Applies only to X!Tandem results.
22 Helpful for data with homologous top hits e.g. phospho or glyco" truevalue="--use-only-expect" falsevalue=""/>
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=""/>
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=""/>
25 <param name="maldi" type="boolean" label="Maldi data" truevalue="-l" falsevalue=""/>
26
27
28 </inputs>
29 <outputs>
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"/>
31 </outputs>
32
33 <help>
34 Run Peptide Prophet
35 </help>
36
37
38 <!--PeptideProphet options [following the 'O']:
39 i [use icat information in PeptideProphet]
40 f [do not use icat information in PeptideProphet]
41 g [use N-glyc motif information in PeptideProphet]
42 H [use Phospho information in PeptideProphet]
43 m [maldi data]
44 I [use pI information in PeptideProphet]
45 R [use Hydrophobicity / RT information in PeptideProphet]
46 F [force the fitting of the mixture model, bypass automatic mixture model checks]
47 A [use accurate mass binning in PeptideProphet]
48 w [warning instead of exit with error if instrument types between runs is different]
49 x [exclude all entries with asterisked score values in PeptideProphet]
50 l [leave alone all entries with asterisked score values in PeptideProphet]
51 n [use hardcoded default initialization parameters of the distributions]
52 P [use Non-parametric model, can only be used with decoy option]
53 N [do not use the NTT model]
54 M [do not use the NMC model]
55 G [use Gamma Distribution to model the Negatives (applies only to X!Tandem data)]
56 E [only use Expect Score as the Discriminant(applies only to X!Tandem data,
57 helpful for data with homologous top hits e.g. phospho or glyco)]
58 d [report decoy hits with a computed probability based on the model learned]
59 p [run ProteinProphet afterwards]
60 t [do not create png data plot]
61 u [do not assemble protein groups in ProteinProphet analysis]
62 s [do not use Occam's Razor in ProteinProphet analysis to
63 derive the simplest protein list to explain observed peptides]
64 -->
65
66 </tool>