Mercurial > repos > galaxyp > openms_psmfeatureextractor

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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 21:40:34 +0000
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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="PSMFeatureExtractor" name="PSMFeatureExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Computes extra features for each input PSM</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">PSMFeatureExtractor</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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15 ## Preprocessing
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16 mkdir in_cond.in &&
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17 #if $in_cond.in_select == "no"
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18 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
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19 ${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
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20 #else
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21 cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
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22 #end if
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23 mkdir out &&
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25 ## Main program call
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27 set -o pipefail &&
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28 @EXECUTABLE@ -write_ctd ./ &&
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29 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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30 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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31 -in
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32 #if $in_cond.in_select == "no"
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33 ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
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34 #else
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35 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
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36 #end if
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37 -out
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38 'out/output.${out_type}'
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39
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40 ## Postprocessing
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41 && mv 'out/output.${out_type}' '$out'
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42 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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43 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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44 #end if]]></command>
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45 <configfiles>
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46 <inputs name="args_json" data_style="paths"/>
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47 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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48 </configfiles>
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49 <inputs>
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50 <conditional name="in_cond">
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51 <param name="in_select" type="select" label="Run tool in batch mode for -in">
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52 <option value="no">No: process all datasets jointly</option>
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53 <option value="yes">Yes: process each dataset in an independent job</option>
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54 </param>
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55 <when value="no">
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56 <param argument="-in" type="data" format="idxml,mzid" multiple="true" label="Input file(s)" help=" select idxml,mzid data sets(s)"/>
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57 </when>
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58 <when value="yes">
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59 <param argument="-in" type="data" format="idxml,mzid" label="Input file(s)" help=" select idxml,mzid data sets(s)"/>
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60 </when>
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61 </conditional>
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62 <param argument="-out_type" type="select" label="Output file type -- default: determined from file extension or content" help="">
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63 <option value="idXML">idxml</option>
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64 <option value="mzid">mzid</option>
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65 <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
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66 <expand macro="list_string_san" name="out_type"/>
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67 </param>
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68 <param argument="-extra" type="text" optional="true" value="" label="List of the MetaData parameters to be included in a feature set for precolato" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
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69 <expand macro="list_string_val" name="extra"/>
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70 <expand macro="list_string_san" name="extra"/>
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71 </param>
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72 <param argument="-multiple_search_engines" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Combine PSMs from different search engines by merging on scan level" help=""/>
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73 <expand macro="adv_opts_macro">
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74 <param argument="-skip_db_check" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Manual override to skip the check if same settings for multiple search engines were applied" help="Only valid together with -multiple_search_engines flag"/>
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75 <param argument="-concat" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Naive merging of PSMs from different search engines: concatenate multiple search results instead of merging on scan level" help="Only valid together with -multiple_search_engines flag"/>
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76 <param argument="-impute" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Will instead of discarding all PSM not unanimously detected by all SE, impute missing values by their respective scores min/max observed" help="Only valid together with -multiple_search_engines flag"/>
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77 <param argument="-limit_imputation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Will impute missing scores with the worst numerical limit (instead of min/max observed) of the respective score" help="Only valid together with -multiple_search_engines flag"/>
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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">
10
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80 <expand macro="list_string_san" name="test"/>
0
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81 </param>
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82 </expand>
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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="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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85 </param>
0
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86 </inputs>
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87 <outputs>
10
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88 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml">
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89 <change_format>
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90 <when input="out_type" value="mzid" format="mzid"/>
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91 </change_format>
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92 </data>
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93 <data name="ctd_out" format="xml" label="${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_PSMFeatureExtractor_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="skip_db_check" value="true"/>
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102 <param name="concat" value="false"/>
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103 <param name="impute" value="false"/>
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104 <param name="limit_imputation" value="false"/>
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105 <param name="force" value="false"/>
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106 <param name="test" value="true"/>
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107 </section>
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108 <conditional name="in_cond">
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109 <param name="in" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/>
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110 </conditional>
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111 <output name="out" value="PSMFeatureExtractor_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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112 <param name="out_type" value="idXML"/>
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113 <param name="multiple_search_engines" value="true"/>
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114 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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115 <output name="ctd_out" ftype="xml">
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116 <assert_contents>
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117 <is_valid_xml/>
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118 </assert_contents>
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119 </output>
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120 <assert_stdout>
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121 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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122 </assert_stdout>
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123 </test>
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124 <!-- TOPP_PSMFeatureExtractor_2 -->
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125 <test expect_num_outputs="2">
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126 <section name="adv_opts">
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127 <param name="skip_db_check" value="true"/>
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128 <param name="concat" value="false"/>
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129 <param name="impute" value="false"/>
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130 <param name="limit_imputation" value="false"/>
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131 <param name="force" value="false"/>
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132 <param name="test" value="true"/>
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133 </section>
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134 <conditional name="in_cond">
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135 <param name="in" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/>
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136 </conditional>
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137 <output name="out" value="PSMFeatureExtractor_2_out.mzid" compare="sim_size" delta_frac="0.7" ftype="mzid"/>
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138 <param name="out_type" value="mzid"/>
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139 <param name="multiple_search_engines" value="true"/>
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140 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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141 <output name="ctd_out" ftype="xml">
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142 <assert_contents>
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143 <is_valid_xml/>
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144 </assert_contents>
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145 </output>
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146 <assert_stdout>
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147 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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148 </assert_stdout>
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149 </test>
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150 <!-- TOPP_PSMFeatureExtractor_3 -->
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151 <test expect_num_outputs="2">
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152 <section name="adv_opts">
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153 <param name="skip_db_check" value="false"/>
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154 <param name="concat" value="false"/>
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155 <param name="impute" value="false"/>
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156 <param name="limit_imputation" value="false"/>
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157 <param name="force" value="false"/>
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158 <param name="test" value="true"/>
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159 </section>
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160 <conditional name="in_cond">
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161 <param name="in" value="MSGFPlusAdapter_1_out.idXML"/>
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162 </conditional>
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163 <output name="out" value="PSMFeatureExtractor_3_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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164 <param name="out_type" value="idXML"/>
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165 <param name="multiple_search_engines" value="false"/>
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166 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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167 <output name="ctd_out" ftype="xml">
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168 <assert_contents>
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169 <is_valid_xml/>
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170 </assert_contents>
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171 </output>
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172 <assert_stdout>
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173 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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174 </assert_stdout>
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175 </test>
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176 </tests>
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177 <help><![CDATA[Computes extra features for each input PSM.
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178
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179
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180 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_PSMFeatureExtractor.html]]></help>
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181 <expand macro="references"/>
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182 </tool>