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author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [ID Processing]-->
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4 <tool id="IDPosteriorErrorProbability" name="IDPosteriorErrorProbability" version="2.0.0">
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5 <description>Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">IDPosteriorErrorProbability</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
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12 <expand macro="requirements"/>
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13 <command>IDPosteriorErrorProbability
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14
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15 #if $param_in:
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16 -in $param_in
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17 #end if
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18 #if $param_out:
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19 -out $param_out
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20 #end if
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21 #if $param_out_plot:
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22 -out_plot $param_out_plot
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23 #end if
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24 #if $param_split_charge:
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25 -split_charge
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26 #end if
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27 #if $param_top_hits_only:
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28 -top_hits_only
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29 #end if
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30 #if $param_ignore_bad_data:
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31 -ignore_bad_data
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32 #end if
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33 #if $param_prob_correct:
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34 -prob_correct
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35 #end if
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36 -threads \${GALAXY_SLOTS:-24}
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37 #if $adv_opts.adv_opts_selector=='advanced':
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38 #if $adv_opts.param_fdr_for_targets_smaller:
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39 -fdr_for_targets_smaller $adv_opts.param_fdr_for_targets_smaller
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40 #end if
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41 #if $adv_opts.param_force:
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42 -force
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43 #end if
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44 #if $adv_opts.param_fit_algorithm_number_of_bins:
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45 -fit_algorithm:number_of_bins $adv_opts.param_fit_algorithm_number_of_bins
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46 #end if
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47 #if $adv_opts.param_fit_algorithm_incorrectly_assigned:
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48 -fit_algorithm:incorrectly_assigned
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49 #if &quot; &quot; in str($adv_opts.param_fit_algorithm_incorrectly_assigned):
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50 &quot;$adv_opts.param_fit_algorithm_incorrectly_assigned&quot;
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51 #else
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52 $adv_opts.param_fit_algorithm_incorrectly_assigned
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53 #end if
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54 #end if
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55 #if $adv_opts.param_fit_algorithm_max_nr_iterations:
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56 -fit_algorithm:max_nr_iterations $adv_opts.param_fit_algorithm_max_nr_iterations
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57 #end if
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58 #end if
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59 </command>
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60 <inputs>
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61 <param format="xml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
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62 <param checked="false" falsevalue="" help="(-split_charge) Thus, for each charge state a new model will be computed" label="The search engine scores are split by charge if this flag is set" name="param_split_charge" optional="True" truevalue="-split_charge" type="boolean"/>
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63 <param checked="false" falsevalue="" help="(-top_hits_only) " label="If set only the top hits of every PeptideIdentification will be used" name="param_top_hits_only" optional="True" truevalue="-top_hits_only" type="boolean"/>
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64 <param checked="false" falsevalue="" help="(-ignore_bad_data) Useful for pipelines with many datasets where only a few are bad, but the pipeline should run through" label="If set errors will be written but ignored" name="param_ignore_bad_data" optional="True" truevalue="-ignore_bad_data" type="boolean"/>
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65 <param checked="false" falsevalue="" help="(-prob_correct) " label="If set scores will be calculated as '1 - ErrorProbabilities' and can be interpreted as probabilities for correct identifications" name="param_prob_correct" optional="True" truevalue="-prob_correct" type="boolean"/>
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66 <expand macro="advanced_options">
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67 <param 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" label="Only used, when top_hits_only set" name="param_fdr_for_targets_smaller" type="float" value="0.05"/>
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68 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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69 <param help="(-number_of_bins) Only needed if each iteration step of the EM-Algorithm will be visualized" label="Number of bins used for visualization" name="param_fit_algorithm_number_of_bins" type="integer" value="100"/>
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70 <param help="(-incorrectly_assigned) For 'Gauss', the Gauss distribution is used" label="for 'Gumbel', the Gumbel distribution is used to plot incorrectly assigned sequences" name="param_fit_algorithm_incorrectly_assigned" optional="True" type="select" value="Gumbel">
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71 <option value="Gumbel">Gumbel</option>
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72 <option value="Gauss">Gauss</option>
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73 </param>
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74 <param help="(-max_nr_iterations) " label="Bounds the number of iterations for the EM algorithm when convergence is slow" name="param_fit_algorithm_max_nr_iterations" type="integer" value="1000"/>
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75 </expand>
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76 </inputs>
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77 <outputs>
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78 <data format="xml" name="param_out"/>
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79 <data format="txt" name="param_out_plot"/>
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80 </outputs>
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81 <help>Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.
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83
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84 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDPosteriorErrorProbability.html</help>
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85 </tool>