Mercurial > repos > galaxyp > openms_idposteriorerrorprobability

comparison IDPosteriorErrorProbability.xml @ 0:377d4fcad44e draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:44:11 -0500
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children e3c7e3d5a171
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-1:000000000000 0:377d4fcad44e
1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [ID Processing]-->
4 <tool id="IDPosteriorErrorProbability" name="IDPosteriorErrorProbability" version="2.1.0">
5 <description>Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.</description>
6 <macros>
7 <token name="@EXECUTABLE@">IDPosteriorErrorProbability</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>IDPosteriorErrorProbability
14
15 #if $param_in:
16 -in $param_in
17 #end if
18 #if $param_out:
19 -out $param_out
20 #end if
21 #if $param_out_plot:
22 -out_plot $param_out_plot
23 #end if
24 #if $param_split_charge:
25 -split_charge
26 #end if
27 #if $param_top_hits_only:
28 -top_hits_only
29 #end if
30 #if $param_ignore_bad_data:
31 -ignore_bad_data
32 #end if
33 #if $param_prob_correct:
34 -prob_correct
35 #end if
36 #if $adv_opts.adv_opts_selector=='advanced':
37 #if $adv_opts.param_fdr_for_targets_smaller:
38 -fdr_for_targets_smaller $adv_opts.param_fdr_for_targets_smaller
39 #end if
40 #if $adv_opts.param_force:
41 -force
42 #end if
43 #if $adv_opts.param_fit_algorithm_number_of_bins:
44 -fit_algorithm:number_of_bins $adv_opts.param_fit_algorithm_number_of_bins
45 #end if
46 #if $adv_opts.param_fit_algorithm_incorrectly_assigned:
47 -fit_algorithm:incorrectly_assigned $adv_opts.param_fit_algorithm_incorrectly_assigned
48 #end if
49 #if $adv_opts.param_fit_algorithm_max_nr_iterations:
50 -fit_algorithm:max_nr_iterations $adv_opts.param_fit_algorithm_max_nr_iterations
51 #end if
52 #end if
53 </command>
54 <inputs>
55 <param name="param_in" type="data" format="idxml" optional="False" label="input file" help="(-in) "/>
56 <param name="param_split_charge" display="radio" 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"/>
57 <param name="param_top_hits_only" display="radio" 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) "/>
58 <param name="param_ignore_bad_data" display="radio" 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"/>
59 <param name="param_prob_correct" display="radio" 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) "/>
60 <expand macro="advanced_options">
61 <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"/>
62 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
63 <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"/>
64 <param name="param_fit_algorithm_incorrectly_assigned" display="radio" type="select" optional="False" 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">
65 <option value="Gumbel" selected="true">Gumbel</option>
66 <option value="Gauss">Gauss</option>
67 </param>
68 <param name="param_fit_algorithm_max_nr_iterations" type="integer" value="1000" label="Bounds the number of iterations for the EM algorithm when convergence is slow" help="(-max_nr_iterations) "/>
69 </expand>
70 </inputs>
71 <outputs>
72 <data name="param_out" format="idxml"/>
73 <data name="param_out_plot" format="txt"/>
74 </outputs>
75 <help>Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.
76
77
78 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDPosteriorErrorProbability.html</help>
79 </tool>