Mercurial > repos > iracooke > tpp_prophets

comparison peptide_prophet.xml @ 14:d90c8bc10a9c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Docker support and update for protk 1.4
author iracooke
date Thu, 26 Mar 2015 19:55:19 -0400
parents b793fe628648
children 0746a2ae9e04
comparison
equal deleted inserted replaced
13:b793fe628648 14:d90c8bc10a9c
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="1.1.0">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="1.3">protk</requirement> 3 <container type="docker">iracooke/protk-1.4.1</container>
4 <requirement type="package" version="4.6.3">trans_proteomic_pipeline</requirement> 4 <requirement type="package" version="1.4">protk</requirement>
5 <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
5 </requirements> 6 </requirements>
6 7
7 <description>Calculate Peptide Prophet statistics on search results</description> 8 <description>Calculate Peptide Prophet statistics on search results</description>
8 9
9 <command> 10 <command>
21 $use_gamma 22 $use_gamma
22 $use_only_expect 23 $use_only_expect
23 $force_fit 24 $force_fit
24 $allow_alt_instruments 25 $allow_alt_instruments
25 $maldi 26 $maldi
27 $usedecoys
28 --decoy-prefix $decoy_prefix_string
29
30 #if $experiment_label
31 --experiment-label $experiment_label
32 #end if
33
34 --p-thresh $p_thresh
35
36 --threads $threads
26 37
27 </command> 38 </command>
28 39
29 <inputs> 40 <inputs>
30 41
42 <param name="use_only_expect" type="boolean" label="Only use Expect Score as the discriminant" help="Applies only to X!Tandem results. 53 <param name="use_only_expect" type="boolean" label="Only use Expect Score as the discriminant" help="Applies only to X!Tandem results.
43 Helpful for data with homologous top hits e.g. phospho or glyco" truevalue="--use-only-expect" falsevalue=""/> 54 Helpful for data with homologous top hits e.g. phospho or glyco" truevalue="--use-only-expect" falsevalue=""/>
44 <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=""/> 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=""/>
45 <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=""/> 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=""/>
46 <param name="maldi" type="boolean" label="Maldi data" truevalue="-l" falsevalue=""/> 57 <param name="maldi" type="boolean" label="Maldi data" truevalue="-l" falsevalue=""/>
47 58 <param name="usedecoys" type="boolean" label="Use decoys to pin down the negative distribution" truevalue="" falsevalue="--no-decoy"/>
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"/>
48 63
49 </inputs> 64 </inputs>
50 <outputs> 65 <outputs>
51 <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"/> 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"/>
52 </outputs> 67 </outputs>
53 68
69
54 <help> 70 <help>
55 71
56 **What it does** 72 **What it does**
57 73
58 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. 74 Given raw search engine scores as inputs this tool estimates the accuracy of peptide assignments.
59 75
60 ---- 76 ----
61 77
62 **Citation** 78 **Citation**
63 79