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comparison IDPosteriorErrorProbability.xml @ 0:3070d71e0e5c draft

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author bgruening
date Thu, 16 Apr 2015 08:37:04 -0400
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-1:000000000000 0:3070d71e0e5c
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>