Mercurial > repos > galaxyp > openms_idposteriorerrorprobability
view IDPosteriorErrorProbability.xml @ 6:c69f69d7867a draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
author | galaxyp |
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date | Thu, 11 Jan 2018 18:03:55 -0500 |
parents | a556c14fcd8d |
children | 956891730b67 |
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<?xml version='1.0' encoding='UTF-8'?> <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> <!--Proposed Tool Section: [ID Processing]--> <tool id="IDPosteriorErrorProbability" name="IDPosteriorErrorProbability" version="2.2.0"> <description>Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.</description> <macros> <token name="@EXECUTABLE@">IDPosteriorErrorProbability</token> <import>macros.xml</import> </macros> <expand macro="references"/> <expand macro="stdio"/> <expand macro="requirements"/> <command>IDPosteriorErrorProbability #if $param_in: -in $param_in #end if #if $param_out: -out $param_out #end if #if $param_out_plot: -out_plot $param_out_plot #end if #if $param_split_charge: -split_charge #end if #if $param_top_hits_only: -top_hits_only #end if #if $param_ignore_bad_data: -ignore_bad_data #end if #if $param_prob_correct: -prob_correct #end if #if $adv_opts.adv_opts_selector=='advanced': #if $adv_opts.param_fdr_for_targets_smaller: -fdr_for_targets_smaller $adv_opts.param_fdr_for_targets_smaller #end if #if $adv_opts.param_force: -force #end if #if $adv_opts.param_fit_algorithm_number_of_bins: -fit_algorithm:number_of_bins $adv_opts.param_fit_algorithm_number_of_bins #end if #if $adv_opts.param_fit_algorithm_incorrectly_assigned: -fit_algorithm:incorrectly_assigned #if " " in str($adv_opts.param_fit_algorithm_incorrectly_assigned): "$adv_opts.param_fit_algorithm_incorrectly_assigned" #else $adv_opts.param_fit_algorithm_incorrectly_assigned #end if #end if #if $adv_opts.param_fit_algorithm_max_nr_iterations: -fit_algorithm:max_nr_iterations $adv_opts.param_fit_algorithm_max_nr_iterations #end if #end if </command> <inputs> <param name="param_in" type="data" format="idxml" optional="False" label="input file" help="(-in) "/> <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"/> <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) "/> <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"/> <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) "/> <expand macro="advanced_options"> <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"/> <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> <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"/> <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"> <option value="Gumbel" selected="true">Gumbel</option> <option value="Gauss">Gauss</option> </param> <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) "/> </expand> </inputs> <outputs> <data name="param_out" format="idxml"/> <data name="param_out_plot" format="txt"/> </outputs> <help>Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model. For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDPosteriorErrorProbability.html</help> </tool>