annotate IDPosteriorErrorProbability.xml @ 3:a556c14fcd8d draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14

<?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>