Mercurial > repos > galaxyp > openms_noisefiltergaussian

annotate NoiseFilterGaussian.xml @ 14:464f7877215b draft default tip

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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 21:37:30 +0000
parents 47982606f542
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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: [Spectrum processing: peak smoothing / normalization]-->
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3 <tool id="NoiseFilterGaussian" name="NoiseFilterGaussian" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data)</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">NoiseFilterGaussian</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 &&
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17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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18 mkdir out &&
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20 ## Main program call
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21
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22 set -o pipefail &&
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23 @EXECUTABLE@ -write_ctd ./ &&
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24 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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25 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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26 -in
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27 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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28 -out
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29 'out/output.${gxy2omsext("mzml")}'
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31 ## Postprocessing
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32 && mv 'out/output.${gxy2omsext("mzml")}' '$out'
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33 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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34 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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35 #end if]]></command>
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36 <configfiles>
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37 <inputs name="args_json" data_style="paths"/>
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38 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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39 </configfiles>
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40 <inputs>
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41 <param argument="-in" type="data" format="mzml" label="input raw data file" help=" select mzml data sets(s)"/>
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42 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
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43 <param name="gaussian_width" argument="-algorithm:gaussian_width" type="float" value="0.2" label="Use a gaussian filter width which has approximately the same width as your mass peaks (FWHM in m/z)" help=""/>
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44 <param name="ppm_tolerance" argument="-algorithm:ppm_tolerance" type="float" value="10.0" label="Gaussian width, depending on the m/z position" help="The higher the value, the wider the peak and therefore the wider the gaussian"/>
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45 <param name="use_ppm_tolerance" argument="-algorithm:use_ppm_tolerance" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If true, instead of the gaussian_width value, the ppm_tolerance is used" help="The gaussian is calculated in each step anew, so this is much slower"/>
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46 <param name="write_log_messages" argument="-algorithm:write_log_messages" type="boolean" truevalue="true" falsevalue="false" checked="false" label="true: Warn if no signal was found by the Gauss filter algorithm" help=""/>
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47 </section>
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48 <expand macro="adv_opts_macro">
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49 <param argument="-processOption" type="select" label="Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first" help="">
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50 <option value="inmemory" selected="true">inmemory</option>
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51 <option value="lowmemory">lowmemory</option>
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52 <expand macro="list_string_san" name="processOption"/>
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53 </param>
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54 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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55 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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56 <expand macro="list_string_san" name="test"/>
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57 </param>
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58 </expand>
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59 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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60 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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61 </param>
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62 </inputs>
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63 <outputs>
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64 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
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65 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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66 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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67 </data>
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68 </outputs>
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69 <tests>
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70 <!-- TOPP_NoiseFilterGaussian_1 -->
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71 <test expect_num_outputs="2">
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72 <section name="adv_opts">
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73 <param name="processOption" value="inmemory"/>
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74 <param name="force" value="false"/>
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75 <param name="test" value="true"/>
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76 </section>
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77 <param name="in" value="NoiseFilterGaussian_1_input.mzML"/>
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78 <output name="out" value="NoiseFilterGaussian_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
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79 <section name="algorithm">
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80 <param name="gaussian_width" value="1.0"/>
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81 <param name="ppm_tolerance" value="10.0"/>
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82 <param name="use_ppm_tolerance" value="false"/>
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83 <param name="write_log_messages" value="false"/>
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84 </section>
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85 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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86 <output name="ctd_out" ftype="xml">
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87 <assert_contents>
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88 <is_valid_xml/>
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89 </assert_contents>
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90 </output>
14
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91 <assert_stdout>
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92 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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93 </assert_stdout>
13
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94 </test>
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95 <!-- TOPP_NoiseFilterGaussian_2 -->
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96 <test expect_num_outputs="2">
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97 <section name="adv_opts">
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98 <param name="processOption" value="inmemory"/>
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99 <param name="force" value="false"/>
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100 <param name="test" value="true"/>
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101 </section>
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102 <param name="in" value="NoiseFilterGaussian_2_input.chrom.mzML"/>
14
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103 <output name="out" value="NoiseFilterGaussian_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
13
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104 <section name="algorithm">
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105 <param name="gaussian_width" value="50.0"/>
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106 <param name="ppm_tolerance" value="10.0"/>
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107 <param name="use_ppm_tolerance" value="false"/>
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108 <param name="write_log_messages" value="false"/>
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109 </section>
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110 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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111 <output name="ctd_out" ftype="xml">
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112 <assert_contents>
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113 <is_valid_xml/>
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114 </assert_contents>
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115 </output>
14
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116 <assert_stdout>
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117 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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118 </assert_stdout>
13
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119 </test>
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120 <!-- TOPP_NoiseFilterGaussian_3 -->
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121 <test expect_num_outputs="2">
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122 <section name="adv_opts">
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123 <param name="processOption" value="lowmemory"/>
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124 <param name="force" value="false"/>
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125 <param name="test" value="true"/>
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126 </section>
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127 <param name="in" value="NoiseFilterGaussian_1_input.mzML"/>
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128 <output name="out" value="NoiseFilterGaussian_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
13
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129 <section name="algorithm">
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130 <param name="gaussian_width" value="1.0"/>
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131 <param name="ppm_tolerance" value="10.0"/>
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132 <param name="use_ppm_tolerance" value="false"/>
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133 <param name="write_log_messages" value="false"/>
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134 </section>
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135 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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136 <output name="ctd_out" ftype="xml">
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137 <assert_contents>
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138 <is_valid_xml/>
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139 </assert_contents>
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140 </output>
14
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141 <assert_stdout>
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142 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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143 </assert_stdout>
13
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144 </test>
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145 <!-- TOPP_NoiseFilterGaussian_4 -->
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146 <test expect_num_outputs="2">
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147 <section name="adv_opts">
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148 <param name="processOption" value="lowmemory"/>
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149 <param name="force" value="false"/>
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150 <param name="test" value="true"/>
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151 </section>
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152 <param name="in" value="NoiseFilterGaussian_2_input.chrom.mzML"/>
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153 <output name="out" value="NoiseFilterGaussian_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
13
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154 <section name="algorithm">
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155 <param name="gaussian_width" value="50.0"/>
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156 <param name="ppm_tolerance" value="10.0"/>
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157 <param name="use_ppm_tolerance" value="false"/>
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158 <param name="write_log_messages" value="false"/>
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159 </section>
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160 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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161 <output name="ctd_out" ftype="xml">
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162 <assert_contents>
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163 <is_valid_xml/>
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164 </assert_contents>
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165 </output>
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166 <assert_stdout>
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167 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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168 </assert_stdout>
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169 </test>
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170 </tests>
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171 <help><![CDATA[Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data).
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172
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173
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174 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_NoiseFilterGaussian.html]]></help>
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175 <expand macro="references"/>
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176 </tool>