Mercurial > repos > galaxyp > openms_idposteriorerrorprobability

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:40:19 +0000
parents 986e03d3201e
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1 <!--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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2 <!--Proposed Tool Section: [Identification Processing]-->
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3 <tool id="IDPosteriorErrorProbability" name="IDPosteriorErrorProbability" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">IDPosteriorErrorProbability</token>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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11 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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12 @EXT_FOO@
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13 #import re
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14
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15 ## Preprocessing
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16 mkdir in &&
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17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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18 mkdir out &&
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19 #if "out_plot_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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20 mkdir out_plot &&
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21 #end if
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23 ## Main program call
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25 set -o pipefail &&
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26 @EXECUTABLE@ -write_ctd ./ &&
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27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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29 -in
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30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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31 -out
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32 'out/output.${gxy2omsext("idxml")}'
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33 #if "out_plot_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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34 -out_plot
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35 'out_plot/output.${gxy2omsext("txt")}'
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36 #end if
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37 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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38 | tee '$stdout'
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39 #end if
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41 ## Postprocessing
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42 && mv 'out/output.${gxy2omsext("idxml")}' '$out'
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43 #if "out_plot_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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44 && mv 'out_plot/output.${gxy2omsext("txt")}' '$out_plot'
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45 #end if
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46 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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47 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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48 #end if]]></command>
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49 <configfiles>
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50 <inputs name="args_json" data_style="paths"/>
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51 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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52 </configfiles>
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53 <inputs>
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54 <param argument="-in" type="data" format="idxml" label="input file" help=" select idxml data sets(s)"/>
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55 <param argument="-split_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="The search engine scores are split by charge if this flag is set" help="Thus, for each charge state a new model will be computed"/>
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56 <param argument="-top_hits_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set only the top hits of every PeptideIdentification will be used" help=""/>
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57 <param argument="-ignore_bad_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set errors will be written but ignored" help="Useful for pipelines with many datasets where only a few are bad, but the pipeline should run through"/>
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58 <param argument="-prob_correct" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set scores will be calculated as '1 - ErrorProbabilities' and can be interpreted as probabilities for correct identifications" help=""/>
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59 <section name="fit_algorithm" title="Algorithm parameter subsection" help="" expanded="false">
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60 <param name="number_of_bins" argument="-fit_algorithm:number_of_bins" type="integer" value="100" label="Number of bins used for visualization" help="Only needed if each iteration step of the EM-Algorithm will be visualized"/>
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61 <param name="incorrectly_assigned" argument="-fit_algorithm:incorrectly_assigned" type="select" label="for 'Gumbel', the Gumbel distribution is used to plot incorrectly assigned sequences" help="For 'Gauss', the Gauss distribution is used">
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62 <option value="Gumbel" selected="true">Gumbel</option>
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63 <option value="Gauss">Gauss</option>
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64 <expand macro="list_string_san" name="incorrectly_assigned"/>
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65 </param>
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66 <param name="max_nr_iterations" argument="-fit_algorithm:max_nr_iterations" type="integer" value="1000" label="Bounds the number of iterations for the EM algorithm when convergence is slow" help=""/>
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67 <param name="neg_log_delta" argument="-fit_algorithm:neg_log_delta" type="integer" value="6" label="The negative logarithm of the convergence threshold for the likelihood increase" help=""/>
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68 <param name="outlier_handling" argument="-fit_algorithm:outlier_handling" type="select" label="What to do with outliers:" help="- ignore_iqr_outliers: ignore outliers outside of 3*IQR from Q1/Q3 for fitting. - set_iqr_to_closest_valid: set IQR-based outliers to the last valid value for fitting. - ignore_extreme_percentiles: ignore everything outside 99th and 1st percentile (also removes equal values like potential censored max values in XTandem). - none: do nothing">
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69 <option value="ignore_iqr_outliers" selected="true">ignore_iqr_outliers</option>
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70 <option value="set_iqr_to_closest_valid">set_iqr_to_closest_valid</option>
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71 <option value="ignore_extreme_percentiles">ignore_extreme_percentiles</option>
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72 <option value="none">none</option>
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73 <expand macro="list_string_san" name="outlier_handling"/>
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74 </param>
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75 </section>
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76 <expand macro="adv_opts_macro">
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77 <param argument="-fdr_for_targets_smaller" type="float" value="0.05" label="Only used, when top_hits_only set" help="Additionally, target/decoy information should be available. The score_type must be q-value from an previous False Discovery Rate run"/>
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78 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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79 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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80 <expand macro="list_string_san" name="test"/>
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81 </param>
0
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82 </expand>
12
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83 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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84 <option value="out_plot_FLAG">out_plot (txt file (if gnuplot is available, a corresponding PDF will be created as well.))</option>
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85 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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86 </param>
0
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87 </inputs>
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88 <outputs>
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89 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
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90 <data name="out_plot" label="${tool.name} on ${on_string}: out_plot" format="txt">
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91 <filter>OPTIONAL_OUTPUTS is not None and "out_plot_FLAG" in OPTIONAL_OUTPUTS</filter>
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92 </data>
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93 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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94 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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95 </data>
0
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96 </outputs>
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97 <tests>
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98 <!-- TOPP_IDPosteriorErrorProbability_1 -->
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99 <test expect_num_outputs="2">
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100 <section name="adv_opts">
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101 <param name="fdr_for_targets_smaller" value="0.05"/>
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102 <param name="force" value="false"/>
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103 <param name="test" value="true"/>
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104 </section>
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105 <param name="in" value="IDPosteriorErrorProbability_Mascot_input.idXML"/>
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106 <output name="out" value="IDPosteriorErrorProbability_Mascot_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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107 <param name="split_charge" value="false"/>
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108 <param name="top_hits_only" value="false"/>
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109 <param name="ignore_bad_data" value="false"/>
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110 <param name="prob_correct" value="false"/>
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111 <section name="fit_algorithm">
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112 <param name="number_of_bins" value="100"/>
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113 <param name="incorrectly_assigned" value="Gumbel"/>
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114 <param name="max_nr_iterations" value="1000"/>
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115 <param name="neg_log_delta" value="6"/>
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116 <param name="outlier_handling" value="ignore_iqr_outliers"/>
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117 </section>
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118 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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119 <output name="ctd_out" ftype="xml">
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120 <assert_contents>
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121 <is_valid_xml/>
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122 </assert_contents>
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123 </output>
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124 <assert_stdout>
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125 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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126 </assert_stdout>
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127 </test>
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128 <!-- TOPP_IDPosteriorErrorProbability_2 -->
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129 <test expect_num_outputs="2">
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130 <section name="adv_opts">
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131 <param name="fdr_for_targets_smaller" value="0.05"/>
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132 <param name="force" value="false"/>
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133 <param name="test" value="true"/>
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134 </section>
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135 <param name="in" value="IDPosteriorErrorProbability_XTandem_input.idXML"/>
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136 <output name="out" value="IDPosteriorErrorProbability_XTandem_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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137 <param name="split_charge" value="false"/>
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138 <param name="top_hits_only" value="false"/>
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139 <param name="ignore_bad_data" value="false"/>
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140 <param name="prob_correct" value="false"/>
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141 <section name="fit_algorithm">
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142 <param name="number_of_bins" value="100"/>
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143 <param name="incorrectly_assigned" value="Gumbel"/>
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144 <param name="max_nr_iterations" value="1000"/>
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145 <param name="neg_log_delta" value="6"/>
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146 <param name="outlier_handling" value="ignore_iqr_outliers"/>
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147 </section>
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148 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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149 <output name="ctd_out" ftype="xml">
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150 <assert_contents>
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151 <is_valid_xml/>
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152 </assert_contents>
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153 </output>
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154 <assert_stdout>
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155 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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156 </assert_stdout>
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157 </test>
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158 <!-- TOPP_IDPosteriorErrorProbability_3 -->
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159 <test expect_num_outputs="2">
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160 <section name="adv_opts">
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161 <param name="fdr_for_targets_smaller" value="0.05"/>
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162 <param name="force" value="false"/>
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163 <param name="test" value="true"/>
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164 </section>
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165 <param name="in" value="IDPosteriorErrorProbability_OMSSA_input.idXML"/>
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166 <output name="out" value="IDPosteriorErrorProbability_OMSSA_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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167 <param name="split_charge" value="false"/>
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168 <param name="top_hits_only" value="false"/>
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169 <param name="ignore_bad_data" value="false"/>
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170 <param name="prob_correct" value="false"/>
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171 <section name="fit_algorithm">
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172 <param name="number_of_bins" value="100"/>
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173 <param name="incorrectly_assigned" value="Gumbel"/>
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174 <param name="max_nr_iterations" value="1000"/>
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175 <param name="neg_log_delta" value="6"/>
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176 <param name="outlier_handling" value="ignore_iqr_outliers"/>
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177 </section>
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178 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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179 <output name="ctd_out" ftype="xml">
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180 <assert_contents>
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181 <is_valid_xml/>
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182 </assert_contents>
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183 </output>
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184 <assert_stdout>
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185 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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186 </assert_stdout>
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187 </test>
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188 <!-- TOPP_IDPosteriorErrorProbability_4 -->
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189 <test expect_num_outputs="2">
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190 <section name="adv_opts">
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191 <param name="fdr_for_targets_smaller" value="0.05"/>
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192 <param name="force" value="false"/>
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193 <param name="test" value="true"/>
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194 </section>
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195 <param name="in" value="IDPosteriorErrorProbability_OMSSA_input2.idXML"/>
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196 <output name="out" value="IDPosteriorErrorProbability_OMSSA_output2.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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197 <param name="split_charge" value="true"/>
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198 <param name="top_hits_only" value="false"/>
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199 <param name="ignore_bad_data" value="false"/>
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200 <param name="prob_correct" value="false"/>
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201 <section name="fit_algorithm">
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202 <param name="number_of_bins" value="100"/>
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203 <param name="incorrectly_assigned" value="Gumbel"/>
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204 <param name="max_nr_iterations" value="1000"/>
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205 <param name="neg_log_delta" value="6"/>
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206 <param name="outlier_handling" value="ignore_iqr_outliers"/>
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207 </section>
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208 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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209 <output name="ctd_out" ftype="xml">
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210 <assert_contents>
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211 <is_valid_xml/>
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212 </assert_contents>
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213 </output>
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214 <assert_stdout>
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215 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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216 </assert_stdout>
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217 </test>
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218 <!-- TOPP_IDPosteriorErrorProbability_5 -->
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219 <test expect_num_outputs="2">
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220 <section name="adv_opts">
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221 <param name="fdr_for_targets_smaller" value="0.05"/>
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222 <param name="force" value="false"/>
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223 <param name="test" value="true"/>
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224 </section>
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225 <param name="in" value="IDPosteriorErrorProbability_XTandem_input2.idXML"/>
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226 <output name="out" value="IDPosteriorErrorProbability_XTandem_output2.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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227 <param name="split_charge" value="true"/>
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228 <param name="top_hits_only" value="false"/>
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229 <param name="ignore_bad_data" value="false"/>
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230 <param name="prob_correct" value="false"/>
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231 <section name="fit_algorithm">
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232 <param name="number_of_bins" value="100"/>
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233 <param name="incorrectly_assigned" value="Gumbel"/>
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234 <param name="max_nr_iterations" value="1000"/>
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235 <param name="neg_log_delta" value="6"/>
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236 <param name="outlier_handling" value="ignore_iqr_outliers"/>
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237 </section>
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238 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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239 <output name="ctd_out" ftype="xml">
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240 <assert_contents>
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241 <is_valid_xml/>
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242 </assert_contents>
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243 </output>
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244 <assert_stdout>
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245 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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246 </assert_stdout>
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247 </test>
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248 <!-- TOPP_IDPosteriorErrorProbability_6 -->
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249 <test expect_num_outputs="2">
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250 <section name="adv_opts">
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251 <param name="fdr_for_targets_smaller" value="0.05"/>
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252 <param name="force" value="false"/>
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253 <param name="test" value="true"/>
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254 </section>
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255 <param name="in" value="IDPosteriorErrorProbability_Mascot_input2.idXML"/>
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256 <output name="out" value="IDPosteriorErrorProbability_Mascot_output2.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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257 <param name="split_charge" value="true"/>
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258 <param name="top_hits_only" value="false"/>
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259 <param name="ignore_bad_data" value="false"/>
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260 <param name="prob_correct" value="false"/>
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261 <section name="fit_algorithm">
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262 <param name="number_of_bins" value="100"/>
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263 <param name="incorrectly_assigned" value="Gumbel"/>
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264 <param name="max_nr_iterations" value="1000"/>
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265 <param name="neg_log_delta" value="6"/>
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266 <param name="outlier_handling" value="ignore_iqr_outliers"/>
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267 </section>
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268 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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269 <output name="ctd_out" ftype="xml">
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270 <assert_contents>
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271 <is_valid_xml/>
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272 </assert_contents>
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273 </output>
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274 <assert_stdout>
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275 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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276 </assert_stdout>
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277 </test>
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278 <!-- TOPP_IDPosteriorErrorProbability_7 -->
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279 <test expect_num_outputs="2">
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280 <section name="adv_opts">
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281 <param name="fdr_for_targets_smaller" value="0.05"/>
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282 <param name="force" value="false"/>
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283 <param name="test" value="true"/>
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284 </section>
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285 <param name="in" value="IDPosteriorErrorProbability_bad_data.idXML"/>
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286 <output name="out" value="IDPosteriorErrorProbability_bad_data_output.tmp" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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287 <param name="split_charge" value="false"/>
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288 <param name="top_hits_only" value="false"/>
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289 <param name="ignore_bad_data" value="true"/>
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290 <param name="prob_correct" value="false"/>
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291 <section name="fit_algorithm">
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292 <param name="number_of_bins" value="100"/>
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293 <param name="incorrectly_assigned" value="Gumbel"/>
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294 <param name="max_nr_iterations" value="1000"/>
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295 <param name="neg_log_delta" value="6"/>
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296 <param name="outlier_handling" value="ignore_iqr_outliers"/>
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297 </section>
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298 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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299 <output name="ctd_out" ftype="xml">
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300 <assert_contents>
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301 <is_valid_xml/>
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302 </assert_contents>
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303 </output>
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304 <assert_stdout>
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305 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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306 </assert_stdout>
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307 </test>
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308 <!-- TOPP_IDPosteriorErrorProbability_8 -->
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309 <test expect_num_outputs="2">
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310 <section name="adv_opts">
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311 <param name="fdr_for_targets_smaller" value="0.05"/>
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312 <param name="force" value="false"/>
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313 <param name="test" value="true"/>
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314 </section>
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315 <param name="in" value="IDPosteriorErrorProbability_OMSSA_input.idXML"/>
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316 <output name="out" value="IDPosteriorErrorProbability_prob_correct_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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317 <param name="split_charge" value="false"/>
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318 <param name="top_hits_only" value="false"/>
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319 <param name="ignore_bad_data" value="false"/>
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320 <param name="prob_correct" value="true"/>
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321 <section name="fit_algorithm">
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322 <param name="number_of_bins" value="100"/>
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323 <param name="incorrectly_assigned" value="Gumbel"/>
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324 <param name="max_nr_iterations" value="1000"/>
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325 <param name="neg_log_delta" value="6"/>
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326 <param name="outlier_handling" value="ignore_iqr_outliers"/>
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327 </section>
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328 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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329 <output name="ctd_out" ftype="xml">
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330 <assert_contents>
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331 <is_valid_xml/>
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332 </assert_contents>
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333 </output>
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334 <assert_stdout>
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335 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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336 </assert_stdout>
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337 </test>
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338 </tests>
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339 <help><![CDATA[Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.
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340
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341
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342 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IDPosteriorErrorProbability.html]]></help>
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343 <expand macro="references"/>
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344 </tool>