Mercurial > repos > galaxyp > openms_rtmodel

annotate RTModel.xml @ 10:654e2bf18e82 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 20:15:37 +0000
parents a9ece00a3e54
children 0fc4aa40badb
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8480765683cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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1 <?xml version='1.0' encoding='UTF-8'?>
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c3da4387e137 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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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 CTDConverter.-->
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3 <!--Proposed Tool Section: [Peptide property prediction]-->
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4 <tool id="RTModel" name="RTModel" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Trains a model for the retention time prediction of peptides from a training set.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">RTModel</token>
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8 <import>macros.xml</import>
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9 <import>macros_autotest.xml</import>
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10 <import>macros_test.xml</import>
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11 </macros>
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12 <expand macro="requirements"/>
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13 <expand macro="stdio"/>
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14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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15 @EXT_FOO@
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16 #import re
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17
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18 ## Preprocessing
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19 #if $in:
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20 mkdir in &&
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21 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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22 #end if
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23 #if $in_positive:
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24 mkdir in_positive &&
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25 ln -s '$in_positive' 'in_positive/${re.sub("[^\w\-_]", "_", $in_positive.element_identifier)}.$gxy2omsext($in_positive.ext)' &&
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26 #end if
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27 #if $in_negative:
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28 mkdir in_negative &&
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29 ln -s '$in_negative' 'in_negative/${re.sub("[^\w\-_]", "_", $in_negative.element_identifier)}.$gxy2omsext($in_negative.ext)' &&
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30 #end if
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31 mkdir out &&
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32 #if "out_oligo_params_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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33 mkdir out_oligo_params &&
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34 #end if
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35 #if "out_oligo_trainset_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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36 mkdir out_oligo_trainset &&
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37 #end if
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38
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39 ## Main program call
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41 set -o pipefail &&
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42 @EXECUTABLE@ -write_ctd ./ &&
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43 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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44 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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45 #if $in:
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46 -in
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47 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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48 #end if
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49 #if $in_positive:
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50 -in_positive
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51 'in_positive/${re.sub("[^\w\-_]", "_", $in_positive.element_identifier)}.$gxy2omsext($in_positive.ext)'
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52 #end if
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53 #if $in_negative:
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54 -in_negative
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55 'in_negative/${re.sub("[^\w\-_]", "_", $in_negative.element_identifier)}.$gxy2omsext($in_negative.ext)'
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56 #end if
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57 -out
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58 'out/output.${gxy2omsext("txt")}'
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59 #if "out_oligo_params_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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60 -out_oligo_params
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61 'out_oligo_params/output.${gxy2omsext("paramxml")}'
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62 #end if
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63 #if "out_oligo_trainset_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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64 -out_oligo_trainset
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65 'out_oligo_trainset/output.${gxy2omsext("txt")}'
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66 #end if
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67 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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68 | tee '$stdout'
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69 #end if
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70
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71 ## Postprocessing
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72 && mv 'out/output.${gxy2omsext("txt")}' '$out'
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73 #if "out_oligo_params_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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74 && mv 'out_oligo_params/output.${gxy2omsext("paramxml")}' '$out_oligo_params'
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75 #end if
8
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76 #if "out_oligo_trainset_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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77 && mv 'out_oligo_trainset/output.${gxy2omsext("txt")}' '$out_oligo_trainset'
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78 #end if
8
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79 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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80 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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81 #end if]]></command>
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82 <configfiles>
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83 <inputs name="args_json" data_style="paths"/>
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84 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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85 </configfiles>
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86 <inputs>
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87 <param name="in" argument="-in" type="data" format="idxml,txt" optional="true" label="This is the name of the input file (RT prediction)" help="It is assumed that the file type is idXML. Alternatively you can provide a .txt file having a sequence and the corresponding rt per line.. select idxml,txt data sets(s)"/>
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88 <param name="in_positive" argument="-in_positive" type="data" format="idxml" optional="true" label="input file with positive examples (peptide separation prediction)" help=" select idxml data sets(s)"/>
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89 <param name="in_negative" argument="-in_negative" type="data" format="idxml" optional="true" label="input file with negative examples (peptide separation prediction)" help=" select idxml data sets(s)"/>
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90 <param name="svm_type" argument="-svm_type" display="radio" type="select" optional="false" label="the type of the svm (NU_SVR or EPSILON_SVR for RT prediction, automatically set" help="to C_SVC for separation prediction). ">
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91 <option value="NU_SVR" selected="true">NU_SVR</option>
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92 <option value="NU_SVC">NU_SVC</option>
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93 <option value="EPSILON_SVR">EPSILON_SVR</option>
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94 <option value="C_SVC">C_SVC</option>
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95 <expand macro="list_string_san"/>
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96 </param>
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97 <param name="nu" argument="-nu" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="the nu parameter [0..1] of the svm (for nu-SVR)" help=""/>
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98 <param name="p" argument="-p" type="float" optional="true" value="0.1" label="the epsilon parameter of the svm (for epsilon-SVR)" help=""/>
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99 <param name="c" argument="-c" type="float" optional="true" value="1.0" label="the penalty parameter of the svm" help=""/>
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100 <param name="kernel_type" argument="-kernel_type" display="radio" type="select" optional="false" label="the kernel type of the svm" help="">
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101 <option value="LINEAR">LINEAR</option>
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102 <option value="RBF">RBF</option>
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103 <option value="POLY">POLY</option>
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104 <option value="OLIGO" selected="true">OLIGO</option>
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105 <expand macro="list_string_san"/>
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106 </param>
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107 <param name="degree" argument="-degree" type="integer" optional="true" min="1" value="1" label="the degree parameter of the kernel function of the svm (POLY kernel)" help=""/>
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108 <param name="border_length" argument="-border_length" type="integer" optional="true" min="1" value="22" label="length of the POBK" help=""/>
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109 <param name="max_std" argument="-max_std" type="float" optional="true" min="0.0" value="10.0" label="max standard deviation for a peptide to be included (if there are several ones for one peptide string)(median is taken)" help=""/>
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110 <param name="k_mer_length" argument="-k_mer_length" type="integer" optional="true" min="1" value="1" label="k_mer length of the POBK" help=""/>
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111 <param name="sigma" argument="-sigma" type="float" optional="true" value="5.0" label="sigma of the POBK" help=""/>
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112 <param name="total_gradient_time" argument="-total_gradient_time" type="float" optional="true" min="1e-05" value="1.0" label="the time (in seconds) of the gradient (only for RT prediction)" help=""/>
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113 <param name="first_dim_rt" argument="-first_dim_rt" type="boolean" truevalue="true" falsevalue="false" checked="false" label="if set the model will be built for first_dim_rt" help=""/>
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114 <param name="additive_cv" argument="-additive_cv" type="boolean" truevalue="true" falsevalue="false" checked="false" label="if the step sizes should be interpreted additively (otherwise the actual value is multiplied" help="with the step size to get the new value"/>
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115 <section name="cv" title="Parameters for the grid search / cross validation:" help="" expanded="false">
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116 <param name="skip_cv" argument="-cv:skip_cv" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set to enable Cross-Validation or set to true if the model should just be trained with 1 set of specified parameters" help=""/>
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117 <param name="number_of_runs" argument="-cv:number_of_runs" type="integer" optional="true" min="1" value="1" label="number of runs for the CV (each run creates a new random partition of the data)" help=""/>
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118 <param name="number_of_partitions" argument="-cv:number_of_partitions" type="integer" optional="true" min="2" value="10" label="number of CV partitions" help=""/>
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119 <param name="degree_start" argument="-cv:degree_start" type="integer" optional="true" min="1" value="1" label="starting point of degree" help=""/>
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120 <param name="degree_step_size" argument="-cv:degree_step_size" type="integer" optional="true" value="2" label="step size point of degree" help=""/>
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121 <param name="degree_stop" argument="-cv:degree_stop" type="integer" optional="true" value="4" label="stopping point of degree" help=""/>
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122 <param name="p_start" argument="-cv:p_start" type="float" optional="true" value="1.0" label="starting point of p" help=""/>
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123 <param name="p_step_size" argument="-cv:p_step_size" type="float" optional="true" value="10.0" label="step size point of p" help=""/>
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124 <param name="p_stop" argument="-cv:p_stop" type="float" optional="true" value="1000.0" label="stopping point of p" help=""/>
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125 <param name="c_start" argument="-cv:c_start" type="float" optional="true" value="1.0" label="starting point of c" help=""/>
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126 <param name="c_step_size" argument="-cv:c_step_size" type="float" optional="true" value="10.0" label="step size of c" help=""/>
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127 <param name="c_stop" argument="-cv:c_stop" type="float" optional="true" value="1000.0" label="stopping point of c" help=""/>
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128 <param name="nu_start" argument="-cv:nu_start" type="float" optional="true" min="0.0" max="1.0" value="0.3" label="starting point of nu" help=""/>
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129 <param name="nu_step_size" argument="-cv:nu_step_size" type="float" optional="true" value="1.2" label="step size of nu" help=""/>
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130 <param name="nu_stop" argument="-cv:nu_stop" type="float" optional="true" min="0.0" max="1.0" value="0.7" label="stopping point of nu" help=""/>
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131 <param name="sigma_start" argument="-cv:sigma_start" type="float" optional="true" value="1.0" label="starting point of sigma" help=""/>
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132 <param name="sigma_step_size" argument="-cv:sigma_step_size" type="float" optional="true" value="1.3" label="step size of sigma" help=""/>
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133 <param name="sigma_stop" argument="-cv:sigma_stop" type="float" optional="true" value="15.0" label="stopping point of sigma" help=""/>
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134 </section>
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135 <expand macro="adv_opts_macro">
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136 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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137 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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138 <expand macro="list_string_san"/>
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139 </param>
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140 </expand>
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141 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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142 <option value="out_oligo_params_FLAG">out_oligo_params (output file with additional model parameters when using the OLIGO kernel)</option>
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143 <option value="out_oligo_trainset_FLAG">out_oligo_trainset (output file with the used training dataset when using the OLIGO kernel)</option>
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144 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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145 </param>
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146 </inputs>
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147 <outputs>
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148 <data name="out" label="${tool.name} on ${on_string}: out" format="txt"/>
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149 <data name="out_oligo_params" label="${tool.name} on ${on_string}: out_oligo_params" format="paramxml">
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150 <filter>OPTIONAL_OUTPUTS is not None and "out_oligo_params_FLAG" in OPTIONAL_OUTPUTS</filter>
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151 </data>
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152 <data name="out_oligo_trainset" label="${tool.name} on ${on_string}: out_oligo_trainset" format="txt">
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153 <filter>OPTIONAL_OUTPUTS is not None and "out_oligo_trainset_FLAG" in OPTIONAL_OUTPUTS</filter>
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154 </data>
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155 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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156 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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157 </data>
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158 </outputs>
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159 <tests>
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160 <expand macro="autotest_RTModel"/>
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161 <expand macro="manutest_RTModel"/>
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162 </tests>
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163 <help><![CDATA[Trains a model for the retention time prediction of peptides from a training set.
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164
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165
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166 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_RTModel.html]]></help>
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167 <expand macro="references"/>
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168 </tool>