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annotate ramclustr.xml @ 9:d70dd1d6ac4d draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e
author recetox
date Wed, 17 Apr 2024 07:51:23 +0000
parents c043e1fd79d1
children 2d94da58904b
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d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e
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1 <tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy5" 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>
0
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20 </requirements>
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21
4
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22 <command detect_errors="exit_code"><![CDATA[
0
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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")
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
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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
4
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74
9
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75 #if $filtering.feature_filter_blanks.filter_blanks == "TRUE":
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76 ramclustObj = RAMClustR::rc.feature.filter.blanks(
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77 ramclustObj = ramclustObj,
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78 qc.tag = "${filtering.feature_filter_blanks.qc_tag}",
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79 blank.tag = "${filtering.feature_filter_blanks.blank_tag}",
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80 sn = $filtering.feature_filter_blanks.sn,
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81 remove.blanks = $filtering.feature_filter_blanks.remove_blanks
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82 )
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83 #end if
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84
4
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85 #if $normalisation.normalisation_method.normalize != "none":
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86 ramclustObj = apply_normalisation(
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87 ramclustr_obj = ramclustObj,
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88 #if $normalisation.normalisation_method.normalize == "batch.qc":
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89 metadata_file = "${$normalisation.normalisation_method.batch_order_qc}",
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90 qc_inj_range = $normalisation.normalisation_method.qc_inj_range,
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91 #end if
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92 #if $normalisation.normalisation_method.normalize == "qc":
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93 metadata_file = "${$normalisation.normalisation_method.batch_order_qc}",
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94 p_cut = $normalisation.normalisation_method.p_cut,
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95 rsq_cut = $normalisation.normalisation_method.rsq_cut,
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96 p_adjust = $normalisation.normalisation_method.p_adjust,
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97 #end if
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98 normalize_method = "$normalisation.normalisation_method.normalize"
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99 )
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100 #end if
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101
9
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102 #if $filtering.feature_filter_cv.filter_cv == "TRUE":
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103 ramclustObj = RAMClustR::rc.feature.filter.cv(
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104 ramclustObj = ramclustObj,
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105 qc.tag = "${filtering.feature_filter_cv.qc_tag}",
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106 max.cv = $filtering.feature_filter_cv.max_cv
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107 )
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108 #end if
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109
4
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110 ramclustObj = RAMClustR::rc.ramclustr(
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111 ramclustObj = ramclustObj,
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112 st = $filetype.required.st,
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113 sr = $filetype.required.sr,
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114 maxt = $filetype.required.maxt,
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115 deepSplit = $clustering.deepSplit,
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116 blocksize = $performance.blocksize,
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117 mult = $performance.mult,
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118 hmax = $clustering.hmax,
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119 minModuleSize = $clustering.minModuleSize,
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120 linkage = "$clustering.linkage",
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121 cor.method = "$filetype.required.cor_method",
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122 rt.only.low.n = $extras.rt_only_low_n,
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123 fftempdir = NULL,
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124 )
9
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125
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126 #if $extras.quality_control == "TRUE":
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127 ramclustObj = RAMClustR::rc.qc(ramclustObj = ramclustObj)
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128 #end if
4
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129
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130 store_output(
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131 ramclustr_obj = ramclustObj,
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132 output_merge_msp = $msp_output_details.merge_msp,
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133 output_spec_abundance = "$spec_abundance",
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134 #if $msp_output_details.merge_msp:
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135 msp_file = "$mass_spectra_merged"
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136 #else:
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137 msp_file = NULL
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138 #end if
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139 )
0
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140 </configfile>
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141 </configfiles>
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142 <inputs>
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143 <conditional name="filetype">
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144 <param name="type_choice" type="select" label="Choose input format:">
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145 <option value="xcms" selected="true">XCMS</option>
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146 <option value="csv">CSV</option>
4
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147 <option value="recetox-aplcms">RECETOX-APLCMS</option>
0
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148 </param>
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149 <when value="xcms">
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150 <expand macro="parameters_xcms" />
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151 <section name="required" title="General parameters" expanded="true">
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152 <param label="Sigma t" name="st" type="float" optional="true" help="Retention time similarity (optional).
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153 A recommended starting point is half the value of your average chromatographic peak width at half max (seconds))."/>
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154 <expand macro="parameters_required" />
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155 </section>
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156 </when>
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157 <when value="csv">
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158 <expand macro="parameters_csv" />
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159 <section name="required" title="General parameters" expanded="true">
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160 <param label="Sigma t" name="st" type="float" value="1" help="Retention time similarity.
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161 A recommended starting point is half the value of your average chromatographic peak width at half max (seconds))."/>
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162 <expand macro="parameters_required" />
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163 </section>
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164 </when>
4
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165 <when value="recetox-aplcms">
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166 <expand macro="parameters_recetox_aplcms" />
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167 <section name="required" title="General parameters" expanded="true">
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168 <param label="Sigma t" name="st" type="float" value="1" help="Retention time similarity.
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169 A recommended starting point is half the value of your average chromatographic peak width at half max (seconds))."/>
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170 <expand macro="parameters_required" />
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171 </section>
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172 </when>
0
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173 </conditional>
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174 <expand macro="main_parameters" />
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175 </inputs>
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176
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177 <outputs>
8
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178 <data label="Spec Abundance of ${on_string}" name="spec_abundance" format="tsv" />
0
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179 <expand macro="output_msp"/>
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180 </outputs>
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181
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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182 <tests>
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183 <test expect_num_outputs="2"><!-- TEST 1 -->
0
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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184 <section name="filetype">
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185 <param name="type_choice" value="xcms"/>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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186 <section name="xcms">
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187 <param name="input_xcms" value="test1_xcmsObj_1.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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188 </section>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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189 <section name="required">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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190 <param name="maxt" value="259.8"/>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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191 </section>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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192 </section>
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193 <section name="msp_output_details">
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194 <param name="mzdec" value="4"/>
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195 </section>
0
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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196 <section name="extras">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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197 <param name="ExpDes" value="lc-ramclustr-define-experiment.csv" ftype="csv"/>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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198 </section>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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199 <output name="mass_spectra_merged" file="test1_fill_xcms_1.msp" ftype="msp"/>
8
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200 <output name="spec_abundance" file="test1_spec_abundance_xcms_1.tsv" ftype="tsv" compare="sim_size" delta="100"/>
0
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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201 </test>
7
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202 <test expect_num_outputs="2"><!-- TEST 2 -->
0
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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203 <section name="filetype">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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204 <param name="type_choice" value="xcms"/>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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205 <section name="xcms">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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206 <param name="input_xcms" value="test2_xcmsObj_2.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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207 </section>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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208 <section name="required">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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209 <param name="maxt" value="78.4"/>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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210 </section>
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211 </section>
4
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212 <section name="msp_output_details">
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213 <param name="mzdec" value="4"/>
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214 </section>
0
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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215 <section name="normalisation">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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216 <section name="normalisation_method">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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217 <param name="batch_order_qc" value="test2_sample_metadata_xcms_2.csv" ftype="csv" />
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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218 </section>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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219 </section>
4
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220 <output name="mass_spectra_merged" file="test2_fill_xcms_2.msp" ftype="msp" compare="sim_size" delta="100"/>
8
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221 <output name="spec_abundance" file="test2_spec_abundance_xcms_2.tsv" ftype="tsv" compare="sim_size" delta="100"/>
0
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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222 </test>
7
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223 <test expect_num_outputs="2"><!-- TEST 3 -->
0
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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224 <section name="filetype">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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225 <param name="type_choice" value="csv"/>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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226 <section name="ms_csv">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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227 <param name="ms" value="test3_csv_test-input_1_2.csv" ftype="csv"/>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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228 </section>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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229 <section name="required">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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230 <param name="st" value="5.0"/>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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231 <param name="maxt" value="1"/>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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232 </section>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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233 </section>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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234 <section name="performance">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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235 <param name="blocksize" value="1000"/>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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236 <param name="mult" value="1"/>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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237 </section>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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238 <output name="mass_spectra_merged" file="test3_spectra_csv_1.msp" ftype="msp"/>
8
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239 <output name="spec_abundance" file="test3_spec_abundance_csv_1.tsv" ftype="tsv"/>
0
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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240 </test>
7
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241 <test expect_num_outputs="2"><!-- TEST 4 -->
0
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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242 <section name="filetype">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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243 <param name="type_choice" value="csv"/>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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244 <section name="ms_csv">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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245 <param name="ms" value="test3_csv_test-input_1_2.csv" ftype="csv"/>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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246 </section>
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247 </section>
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248 <output name="mass_spectra_merged" file="test4_spectra_csv_2.msp" ftype="msp" lines_diff="10"/>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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249 </test>
7
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250 <test expect_num_outputs="2"><!-- TEST 5 -->
4
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251 <section name="filetype">
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252 <param name="type_choice" value="recetox-aplcms"/>
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253 <section name="ms_dataframe">
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254 <param name="ms1_featureDefinitions" value="test5_df_featureDefinitions_input.parquet" ftype="parquet"/>
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255 <param name="ms1_featureValues" value="test5_df_featureValues_input.parquet" ftype="parquet"/>
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256 </section>
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257 </section>
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258 <output name="mass_spectra_merged" file="test5_spectra.msp" ftype="msp" lines_diff="10"/>
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259 </test>
9
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260 <test expect_num_outputs="3"><!-- TEST 6 -->
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261 <section name="filetype">
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262 <param name="type_choice" value="xcms"/>
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263 <section name="xcms">
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264 <param name="input_xcms" value="test6.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
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265 </section>
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266 </section>
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267 <section name="msp_output_details">
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268 <param name="mzdec" value="4"/>
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269 </section>
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270 <section name="extras">
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271 <param name="quality_control" value="TRUE"/>
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272 </section>
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273 <section name="filtering">
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274 <section name="feature_filter_blanks">
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275 <param name="filter_blanks" value="TRUE"/>
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276 <param name="blank_tag" value="Blanc"/>
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277 </section>
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278 <section name="feature_filter_cv">
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279 <param name="filter_cv" value="TRUE"/>
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280 </section>
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281 </section>
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282 <output name="mass_spectra_merged" file="test6_out.msp" ftype="msp"/>
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283 <output name="spec_abundance">
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284 <assert_contents>
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285 <has_size value="309" delta="10"/>
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286 </assert_contents>
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287 </output>
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288 <output name="pdf_plot">
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289 <assert_contents>
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290 <has_size value="6842" delta="100"/>
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291 </assert_contents>
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292 </output>
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293 </test>
0
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294 </tests>
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295
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296 <help>
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297 <![CDATA[
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298 @HELP@
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299
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300 .. rubric:: **Footnotes**
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301 .. [1] Correlation, Variance and Covariance - `stats::cor <https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/cor>`_
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302 .. [2] Hierarchical Clustering - `stats::hclust <https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/hclust>`_
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303 .. [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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304 ]]>
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305 </help>
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306
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307 <expand macro="citations" />
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308 </tool>