|
0
|
1 <?xml version='1.0' encoding='UTF-8'?>
|
|
|
2 <tool id="IDPosteriorErrorProbability" name="IDPosteriorErrorProbability" version="2.0.0">
|
|
|
3 <description>Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.</description>
|
|
|
4 <macros>
|
|
|
5 <token name="@EXECUTABLE@">IDPosteriorErrorProbability</token>
|
|
|
6 <import>macros.xml</import>
|
|
|
7 </macros>
|
|
|
8 <expand macro="stdio"/>
|
|
|
9 <expand macro="requirements"/>
|
|
|
10 <command>IDPosteriorErrorProbability
|
|
|
11
|
|
|
12 #if $param_in:
|
|
|
13 -in $param_in
|
|
|
14 #end if
|
|
|
15 #if $param_out:
|
|
|
16 -out $param_out
|
|
|
17 #end if
|
|
|
18 #if $param_out_plot:
|
|
|
19 -out_plot $param_out_plot
|
|
|
20 #end if
|
|
|
21 #if $param_split_charge:
|
|
|
22 -split_charge
|
|
|
23 #end if
|
|
|
24 #if $param_top_hits_only:
|
|
|
25 -top_hits_only
|
|
|
26 #end if
|
|
|
27 #if $param_ignore_bad_data:
|
|
|
28 -ignore_bad_data
|
|
|
29 #end if
|
|
|
30 #if $param_prob_correct:
|
|
|
31 -prob_correct
|
|
|
32 #end if
|
|
|
33 -threads \${GALAXY_SLOTS:-24}
|
|
|
34 #if $adv_opts.adv_opts_selector=='advanced':
|
|
|
35 #if $adv_opts.param_smallest_e_value:
|
|
|
36 -smallest_e_value $adv_opts.param_smallest_e_value
|
|
|
37 #end if
|
|
|
38 #if $adv_opts.param_fdr_for_targets_smaller:
|
|
|
39 -fdr_for_targets_smaller $adv_opts.param_fdr_for_targets_smaller
|
|
|
40 #end if
|
|
|
41 #if $adv_opts.param_force:
|
|
|
42 -force
|
|
|
43 #end if
|
|
|
44 #if $adv_opts.param_fit_algorithm_number_of_bins:
|
|
|
45 -fit_algorithm:number_of_bins $adv_opts.param_fit_algorithm_number_of_bins
|
|
|
46 #end if
|
|
|
47 #if $adv_opts.param_fit_algorithm_incorrectly_assigned:
|
|
|
48 -fit_algorithm:incorrectly_assigned
|
|
|
49 #if " " in str($adv_opts.param_fit_algorithm_incorrectly_assigned):
|
|
|
50 "$adv_opts.param_fit_algorithm_incorrectly_assigned"
|
|
|
51 #else
|
|
|
52 $adv_opts.param_fit_algorithm_incorrectly_assigned
|
|
|
53 #end if
|
|
|
54 #end if
|
|
|
55 #end if
|
|
|
56 </command>
|
|
|
57 <inputs>
|
|
|
58 <param name="param_in" type="data" format="idxml" optional="False" label="input file" help="(-in) "/>
|
|
|
59 <param name="param_split_charge" type="boolean" truevalue="-split_charge" falsevalue="" checked="false" optional="True" label="The search engine scores are split by charge if this flag is set" help="(-split_charge) Thus, for each charge state a new model will be computed"/>
|
|
|
60 <param name="param_top_hits_only" type="boolean" truevalue="-top_hits_only" falsevalue="" checked="false" optional="True" label="If set only the top hits of every PeptideIdentification will be used" help="(-top_hits_only) "/>
|
|
|
61 <param name="param_ignore_bad_data" type="boolean" truevalue="-ignore_bad_data" falsevalue="" checked="false" optional="True" label="If set errors will be written but ignored" help="(-ignore_bad_data) Useful for pipelines with many datasets where only a few are bad, but the pipeline should run through"/>
|
|
|
62 <param name="param_prob_correct" type="boolean" truevalue="-prob_correct" falsevalue="" checked="false" optional="True" label="If set scores will be calculated as 1-ErrorProbabilities and can be interpreted as probabilities for correct identifications" help="(-prob_correct) "/>
|
|
|
63 <expand macro="advanced_options">
|
|
|
64 <param name="param_smallest_e_value" type="float" value="1e-19" label="This value gives a lower bound to E-Values" help="(-smallest_e_value) It should not be 0, as transformation in a real number (log of E-value) is not possible for certain values then"/>
|
|
|
65 <param name="param_fdr_for_targets_smaller" type="float" value="0.05" label="Only used, when top_hits_only set" help="(-fdr_for_targets_smaller) Additionally, target_decoy information should be available. The score_type must be q-value from an previous False Discovery Rate run"/>
|
|
|
66 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
|
|
|
67 <param name="param_fit_algorithm_number_of_bins" type="integer" value="100" label="Number of bins used for visualization" help="(-number_of_bins) Only needed if each iteration step of the EM-Algorithm will be visualized"/>
|
|
|
68 <param name="param_fit_algorithm_incorrectly_assigned" type="select" optional="True" value="Gumbel" label="for 'Gumbel', the Gumbel distribution is used to plot incorrectly assigned sequences" help="(-incorrectly_assigned) For 'Gauss', the Gauss distribution is used">
|
|
|
69 <option value="Gumbel">Gumbel</option>
|
|
|
70 <option value="Gauss">Gauss</option>
|
|
|
71 </param>
|
|
|
72 </expand>
|
|
|
73 </inputs>
|
|
|
74 <outputs>
|
|
|
75 <data name="param_out" format="idxml"/>
|
|
|
76 <data name="param_out_plot" format="txt"/>
|
|
|
77 </outputs>
|
|
|
78 <help>**What it does**
|
|
|
79
|
|
|
80 Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.
|
|
|
81
|
|
|
82
|
|
|
83 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDPosteriorErrorProbability.html</help>
|
|
|
84 <expand macro="references"/>
|
|
|
85 </tool>
|
