<?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: [Peptide property prediction]-->
  <tool id="RTPredict" name="RTPredict" version="2.0.0">
    <description>Predicts retention times for peptides using a model trained by RTModel.</description>
    <macros>
      <token name="@EXECUTABLE@">RTPredict</token>
      <import>macros.xml</import>
    </macros>
    <expand macro="references"/>
    <expand macro="stdio"/>
    <expand macro="requirements"/>
    <command>RTPredict

#if $param_in_id:
  -in_id $param_in_id
#end if
#if $param_in_text:
  -in_text $param_in_text
#end if
#if $param_svm_model:
  -svm_model $param_svm_model
#end if
#if $param_total_gradient_time:
  -total_gradient_time $param_total_gradient_time
#end if
-threads \${GALAXY_SLOTS:-24}
#if $param_out_id_file:
  -out_id:file $param_out_id_file
#end if
#if $param_out_id_positive:
  -out_id:positive $param_out_id_positive
#end if
#if $param_out_id_negative:
  -out_id:negative $param_out_id_negative
#end if
#if $param_out_text_file:
  -out_text:file $param_out_text_file
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_max_number_of_peptides:
  -max_number_of_peptides $adv_opts.param_max_number_of_peptides
#end if
    #if $adv_opts.param_force:
  -force
#end if
    #if $adv_opts.param_out_id_rewrite_peptideidentification_rtmz:
  -out_id:rewrite_peptideidentification_rtmz
#end if
#end if
</command>
    <inputs>
      <param format="xml" help="(-in_id) " label="Peptides with precursor information" name="param_in_id" optional="True" type="data"/>
      <param format="txt" help="(-in_text) " label="Peptides as text-based file" name="param_in_text" optional="True" type="data"/>
      <param format="txt" help="(-svm_model) " label="svm model in libsvm format (can be produced by RTModel)" name="param_svm_model" optional="False" type="data"/>
      <param help="(-total_gradient_time) " label="The time (in seconds) of the gradient (peptide RT prediction)" min="1e-05" name="param_total_gradient_time" optional="True" type="float" value="1.0"/>
      <expand macro="advanced_options">
        <param help="(-max_number_of_peptides) " label="The maximum number of peptides considered at once (bigger number will lead to faster results but needs more memory)" name="param_max_number_of_peptides" type="integer" value="100000"/>
        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
        <param checked="false" falsevalue="" help="(-rewrite_peptideidentification_rtmz) " label="Rewrites each peptideidentification's rt and mz from prediction and calculation (according to the best hit)" name="param_out_id_rewrite_peptideidentification_rtmz" optional="True" truevalue="-out_id:rewrite_peptideidentification_rtmz" type="boolean"/>
      </expand>
    </inputs>
    <outputs>
      <data format="xml" name="param_out_id_file"/>
      <data format="xml" name="param_out_id_positive"/>
      <data format="xml" name="param_out_id_negative"/>
      <data format="tabular" name="param_out_text_file"/>
    </outputs>
    <help>Predicts retention times for peptides using a model trained by RTModel.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_RTPredict.html</help>
  </tool>