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annotate ramclustr.xml @ 8:c043e1fd79d1 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4b8a43b863ff8a0ff1d5a08e516068853adf358d
author recetox
date Tue, 16 Apr 2024 11:30:05 +0000
parents 09cabbc3d12d
children d70dd1d6ac4d
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c043e1fd79d1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4b8a43b863ff8a0ff1d5a08e516068853adf358d
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1 <tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy4" profile="21.09">
2
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2 <description>A feature clustering algorithm for non-targeted mass spectrometric metabolomics data.</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
7
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6 <expand macro='annotation'/>
5
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7 <edam_operations>
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8 <edam_operation>operation_3557</edam_operation>
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9 <edam_operation>operation_3435</edam_operation>
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10 <edam_operation>operation_3432</edam_operation>
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11 <edam_operation>operation_3465</edam_operation>
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12 </edam_operations>
7
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13 <expand macro="refs"/>
0
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14 <expand macro="creator"/>
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16 <requirements>
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17 <requirement type="package" version="@TOOL_VERSION@">r-ramclustr</requirement>
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18 <requirement type="package" version="3.20.0">bioconductor-xcms</requirement>
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19 <requirement type="package" version="9.0.0">r-arrow</requirement>
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20 </requirements>
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21
4
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22 <command detect_errors="exit_code"><![CDATA[
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23 Rscript
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24 -e 'source("${__tool_directory__}/ramclustr_wrapper.R")'
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25 -e 'source("${ramclustr_method}")'
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26 ]]>
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27 </command>
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28 <configfiles>
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29 <configfile name="ramclustr_method">
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30 #if $filetype.type_choice == "xcms":
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31 obj = load("$filetype.xcms.input_xcms")
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32 ramclustObj = RAMClustR::rc.get.xcms.data(
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33 xcmsObj = xdata,
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34 #if $extras.ExpDes:
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35 ExpDes = load_experiment_definition("${$extras.ExpDes}"),
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36 #end if
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37 mzdec = $msp_output_details.mzdec,
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38 ensure.no.na = $extras.replace_zeros
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39 )
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40 #else if $filetype.type_choice == "csv":
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41 ramclustObj = RAMClustR::rc.get.csv.data(
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42 csv = "$filetype.ms_csv.ms",
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43 #if $filetype.ms_csv.idmsms:
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44 idmsms = "$filetype.ms_csv.idmsms",
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45 #end if
4
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46 #if $filetype.ms_csv.csv_phenoData:
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47 phenoData = "$filetype.ms_csv.csv_phenoData",
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48 #end if
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49 #if $extras.ExpDes:
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50 ExpDes = load_experiment_definition("${$extras.ExpDes}"),
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51 #end if
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52 st = $filetype.required.st,
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53 ensure.no.na = $extras.replace_zeros
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54 )
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55 #else if $filetype.type_choice == "recetox-aplcms":
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56 ramclustObj = read_ramclustr_aplcms(
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57 ms1_featuredefinitions = "$filetype.ms_dataframe.ms1_featureDefinitions",
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58 ms1_featurevalues = "$filetype.ms_dataframe.ms1_featureValues",
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59 #if $filetype.ms_dataframe.df_phenoData:
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60 df_phenodata = "$filetype.ms_dataframe.df_phenoData",
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61 phenodata_ext = "${filetype.ms_dataframe.df_phenoData.ext}",
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62 #end if
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63 #if $extras.ExpDes:
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64 exp_des = "${$extras.ExpDes}",
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65 #end if
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66 st = $filetype.required.st,
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67 ensure_no_na = $extras.replace_zeros
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68 )
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69 #end if
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70
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71 #if $extras.replace_zeros == "TRUE":
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72 ramclustObj = RAMClustR::rc.feature.replace.na(ramclustObj = ramclustObj)
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73 #end if
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74
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75 #if $normalisation.normalisation_method.normalize != "none":
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76 ramclustObj = apply_normalisation(
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77 ramclustr_obj = ramclustObj,
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78 #if $normalisation.normalisation_method.normalize == "batch.qc":
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79 metadata_file = "${$normalisation.normalisation_method.batch_order_qc}",
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80 qc_inj_range = $normalisation.normalisation_method.qc_inj_range,
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81 #end if
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82 #if $normalisation.normalisation_method.normalize == "qc":
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83 metadata_file = "${$normalisation.normalisation_method.batch_order_qc}",
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84 p_cut = $normalisation.normalisation_method.p_cut,
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85 rsq_cut = $normalisation.normalisation_method.rsq_cut,
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86 p_adjust = $normalisation.normalisation_method.p_adjust,
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87 #end if
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88 normalize_method = "$normalisation.normalisation_method.normalize"
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89 )
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90 #end if
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91
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92 ramclustObj = RAMClustR::rc.ramclustr(
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93 ramclustObj = ramclustObj,
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94 st = $filetype.required.st,
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95 sr = $filetype.required.sr,
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96 maxt = $filetype.required.maxt,
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97 deepSplit = $clustering.deepSplit,
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98 blocksize = $performance.blocksize,
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99 mult = $performance.mult,
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100 hmax = $clustering.hmax,
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101 minModuleSize = $clustering.minModuleSize,
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102 linkage = "$clustering.linkage",
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103 cor.method = "$filetype.required.cor_method",
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104 rt.only.low.n = $extras.rt_only_low_n,
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105 fftempdir = NULL,
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106 )
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107
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108 store_output(
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109 ramclustr_obj = ramclustObj,
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110 output_merge_msp = $msp_output_details.merge_msp,
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111 output_spec_abundance = "$spec_abundance",
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112 #if $msp_output_details.merge_msp:
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113 msp_file = "$mass_spectra_merged"
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114 #else:
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115 msp_file = NULL
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116 #end if
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117 )
0
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118 </configfile>
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119 </configfiles>
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120 <inputs>
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121 <conditional name="filetype">
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122 <param name="type_choice" type="select" label="Choose input format:">
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123 <option value="xcms" selected="true">XCMS</option>
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124 <option value="csv">CSV</option>
4
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125 <option value="recetox-aplcms">RECETOX-APLCMS</option>
0
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126 </param>
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127 <when value="xcms">
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128 <expand macro="parameters_xcms" />
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129 <section name="required" title="General parameters" expanded="true">
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130 <param label="Sigma t" name="st" type="float" optional="true" help="Retention time similarity (optional).
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131 A recommended starting point is half the value of your average chromatographic peak width at half max (seconds))."/>
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132 <expand macro="parameters_required" />
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133 </section>
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134 </when>
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135 <when value="csv">
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136 <expand macro="parameters_csv" />
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137 <section name="required" title="General parameters" expanded="true">
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138 <param label="Sigma t" name="st" type="float" value="1" help="Retention time similarity.
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139 A recommended starting point is half the value of your average chromatographic peak width at half max (seconds))."/>
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140 <expand macro="parameters_required" />
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141 </section>
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142 </when>
4
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143 <when value="recetox-aplcms">
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144 <expand macro="parameters_recetox_aplcms" />
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145 <section name="required" title="General parameters" expanded="true">
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146 <param label="Sigma t" name="st" type="float" value="1" help="Retention time similarity.
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147 A recommended starting point is half the value of your average chromatographic peak width at half max (seconds))."/>
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148 <expand macro="parameters_required" />
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149 </section>
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150 </when>
0
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151 </conditional>
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152 <expand macro="main_parameters" />
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153 </inputs>
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154
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155 <outputs>
8
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156 <data label="Spec Abundance of ${on_string}" name="spec_abundance" format="tsv" />
0
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157 <expand macro="output_msp"/>
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158 </outputs>
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159
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160 <tests>
7
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161 <test expect_num_outputs="2"><!-- TEST 1 -->
0
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162 <section name="filetype">
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163 <param name="type_choice" value="xcms"/>
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164 <section name="xcms">
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165 <param name="input_xcms" value="test1_xcmsObj_1.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
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166 </section>
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167 <section name="required">
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168 <param name="maxt" value="259.8"/>
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169 </section>
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170 </section>
4
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171 <section name="msp_output_details">
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172 <param name="mzdec" value="4"/>
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173 </section>
0
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174 <section name="extras">
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175 <param name="ExpDes" value="lc-ramclustr-define-experiment.csv" ftype="csv"/>
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176 </section>
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177 <output name="mass_spectra_merged" file="test1_fill_xcms_1.msp" ftype="msp"/>
8
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178 <output name="spec_abundance" file="test1_spec_abundance_xcms_1.tsv" ftype="tsv" compare="sim_size" delta="100"/>
0
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179 </test>
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180 <test expect_num_outputs="2"><!-- TEST 2 -->
0
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181 <section name="filetype">
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182 <param name="type_choice" value="xcms"/>
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183 <section name="xcms">
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184 <param name="input_xcms" value="test2_xcmsObj_2.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
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185 </section>
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186 <section name="required">
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187 <param name="maxt" value="78.4"/>
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188 </section>
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189 </section>
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190 <section name="msp_output_details">
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191 <param name="mzdec" value="4"/>
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192 </section>
0
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193 <section name="normalisation">
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194 <section name="normalisation_method">
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195 <param name="batch_order_qc" value="test2_sample_metadata_xcms_2.csv" ftype="csv" />
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196 </section>
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197 </section>
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198 <output name="mass_spectra_merged" file="test2_fill_xcms_2.msp" ftype="msp" compare="sim_size" delta="100"/>
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199 <output name="spec_abundance" file="test2_spec_abundance_xcms_2.tsv" ftype="tsv" compare="sim_size" delta="100"/>
0
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200 </test>
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201 <test expect_num_outputs="2"><!-- TEST 3 -->
0
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202 <section name="filetype">
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203 <param name="type_choice" value="csv"/>
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204 <section name="ms_csv">
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205 <param name="ms" value="test3_csv_test-input_1_2.csv" ftype="csv"/>
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206 </section>
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207 <section name="required">
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208 <param name="st" value="5.0"/>
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209 <param name="maxt" value="1"/>
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210 </section>
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211 </section>
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212 <section name="performance">
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213 <param name="blocksize" value="1000"/>
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214 <param name="mult" value="1"/>
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215 </section>
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216 <output name="mass_spectra_merged" file="test3_spectra_csv_1.msp" ftype="msp"/>
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217 <output name="spec_abundance" file="test3_spec_abundance_csv_1.tsv" ftype="tsv"/>
0
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218 </test>
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219 <test expect_num_outputs="2"><!-- TEST 4 -->
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220 <section name="filetype">
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221 <param name="type_choice" value="csv"/>
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222 <section name="ms_csv">
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223 <param name="ms" value="test3_csv_test-input_1_2.csv" ftype="csv"/>
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224 </section>
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225 </section>
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226 <output name="mass_spectra_merged" file="test4_spectra_csv_2.msp" ftype="msp" lines_diff="10"/>
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227 </test>
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228 <test expect_num_outputs="2"><!-- TEST 5 -->
4
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229 <section name="filetype">
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230 <param name="type_choice" value="recetox-aplcms"/>
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231 <section name="ms_dataframe">
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232 <param name="ms1_featureDefinitions" value="test5_df_featureDefinitions_input.parquet" ftype="parquet"/>
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233 <param name="ms1_featureValues" value="test5_df_featureValues_input.parquet" ftype="parquet"/>
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234 </section>
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235 </section>
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236 <output name="mass_spectra_merged" file="test5_spectra.msp" ftype="msp" lines_diff="10"/>
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237 </test>
0
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238 </tests>
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239
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240 <help>
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241 <![CDATA[
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242 @HELP@
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243
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244 .. rubric:: **Footnotes**
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245 .. [1] Correlation, Variance and Covariance - `stats::cor <https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/cor>`_
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246 .. [2] Hierarchical Clustering - `stats::hclust <https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/hclust>`_
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247 .. [3] Dynamic Dendrogram Pruning Based on Dendrogram Only - `dynamicTreeCut::cutreeDynamicTree <https://www.rdocumentation.org/packages/dynamicTreeCut/versions/1.63-1/topics/cutreeDynamicTree>`_
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248 ]]>
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249 </help>
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250
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251 <expand macro="citations" />
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252 </tool>