Mercurial > repos > recetox > recetox_xmsannotator_advanced

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 8547c5323747595eabbeed29039a1b2363491243
author recetox
date Thu, 20 Jul 2023 06:28:49 +0000
parents a393c4383436
children
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1 <tool id="recetox_xmsannotator_advanced" name="recetox-xMSannotator" version="@TOOL_VERSION@+galaxy0">
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3 <description>annotate peak intensity table including scores and confidence levels</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="creator"/>
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8 <xrefs>
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9 <xref type="bio.tools">recetox-xmsannotator</xref>
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10 </xrefs>
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11 <expand macro="requirements" />
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12 <command detect_errors="aggressive"><![CDATA[
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13 Rscript -e 'source("${__tool_directory__}/utils.R")' -e "n_workers <- \${GALAXY_SLOTS:-1}" -e "source('${wrapper}')"
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14 ]]></command>
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16 <configfiles>
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17 <configfile name="wrapper"><![CDATA[
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18 metadata_table <- load_table("$metadata_table", "$metadata_table.ext")
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19 intensity_table <- load_table("$intensity_table", "$intensity_table.ext")
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20 peak_table <- create_peak_table(metadata_table, intensity_table)
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22 filter_by <- create_filter_by_adducts("$filter_by")
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24 annotation <- advanced_annotation(
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25 peak_table = peak_table,
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26 adduct_table = load_table("$adduct_table", "$adduct_table.ext"),
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27 adduct_weights = load_table("$adduct_weights", "$adduct_weights.ext"),
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28 compound_table = load_table("$compound_table", "$compound_table.ext"),
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29 mass_tolerance = 1e-6 * ${mass_tolerance_ppm},
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30 time_tolerance = $time_tolerance,
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31 correlation_threshold = as.double($clustering.correlation_threshold),
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32 min_cluster_size = as.integer($clustering.min_cluster_size),
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33 deep_split = as.integer($clustering.deep_split),
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34 network_type = "$clustering.network_type",
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35 redundancy_filtering = $scoring.redundancy_filtering,
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36 n_workers = n_workers,
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37 intensity_deviation_tolerance = as.double($intensity_deviation_tolerance),
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38 mass_defect_tolerance = as.double($mass_defect_tolerance),
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39 mass_defect_precision = as.double($mass_defect_precision),
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40 peak_rt_width = as.integer($peak_rt_width),
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41 maximum_isotopes = as.integer($maximum_isotopes),
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42 min_ions_per_chemical = as.integer($min_ions_per_chemical),
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43 filter_by = filter_by
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44 )
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45
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46 save_table(annotation, "$output_file", "$output_file.ext")
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47 ]]></configfile>
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48 </configfiles>
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50 <inputs>
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51 <expand macro="inputs"/>
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52 <expand macro="tolerance">
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53 <param name="time_tolerance" type="float" value="10" min="0">
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54 <label>Retention time tolerance [s]</label>
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55 <help>
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56 Retention time tolerance in seconds for finding peaks derived from the same parent compound.
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57 </help>
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58 </param>
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59 </expand>
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60 <section name="clustering" title="Clustering">
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61 <param name="correlation_threshold" type="float" value="0.7">
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62 <label>Correlation threshold</label>
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63 <help>Correlation threshold between peaks to qualify as adducts/isotopes of the same metabolite.</help>
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64 </param>
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65 <param name="min_cluster_size" type="integer" value="10" min="1">
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66 <label>Minimum cluster size</label>
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67 <help>The minimum number of nodes to be considered as a cluster.</help>
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68 </param>
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69 <param name="deep_split" type="integer" value="2" min="0" max="4">
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70 <label>Deep split</label>
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71 <help>
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72 Deep split provides a rough control over sensitivity to cluster splitting. The higher the value,
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73 the more and smaller clusters will be produced (see WGCNA package documentation).
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74 </help>
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75 </param>
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76 <param name="network_type" type="select" display="radio">
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77 <label>Network type</label>
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78 <help>
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79 Network type parameter affects how the network's adjacency matrix is created from the correlation
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80 matrix (see WGCNA package documentation).
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81 </help>
5
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82 <option value="signed">Signed</option>
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83 <option value="unsigned" selected="true">Unsigned</option>
2
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84 </param>
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85 </section>
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86 <section name="scoring" title="Scoring" expanded="true">
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87 <param name="strict_boosting" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE">
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88 <label>Strict boosting</label>
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89 <help>
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90 Boost the scores of metabolites that not only belongs to the same pathway but also to the same
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91 cluster. Otherwise, do not account for cluster membership.
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92 </help>
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93 </param>
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94 <param name="min_isp" type="integer" min="0" value="1">
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95 <label>Minimum number of expected isotopes</label>
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96 <help>
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97 Minimum number of adducts/isotopes to be present for a match to be considered as a high confidence match.
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98 </help>
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99 </param>
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100 <param name="max_isp" type="integer" min="0" value="5">
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101 <label>Maximum number of expected isotopes</label>
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102 <help>
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103 Maximum number of adducts/isotopes to be present for a match to be considered as a high confidence match.
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104 </help>
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105 </param>
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106 <param name="redundancy_filtering" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE">
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107 <label>Redundancy filtering</label>
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108 <help>Whether to filter out low-scored multiple matcher or not.</help>
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109 </param>
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110 </section>
5
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111 <param name="intensity_deviation_tolerance" type="float" value="0.1">
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112 <label>Tolerance of intensity deviation</label>
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113 <help>A numeric threshold by which an intensity ratio of two isotopic peaks may differ from their actual abundance ratio.</help>
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114 </param>
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115 <param name="mass_defect_tolerance" type="float" value="0.1">
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116 <label>Tolerance of mass defect</label>
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117 <help>Maximum difference in mass defect between two peaks of the same compound.</help>
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118 </param>
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119 <param name="mass_defect_precision" type="float" value="0.01">
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120 <label>Precision for computing mass defect</label>
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121 </param>
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122 <param name="peak_rt_width" type="integer" value="1">
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123 <label>Estimated chromatographic peak width</label>
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124 </param>
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125 <param name="maximum_isotopes" type="integer" value="10">
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126 <label>Maximum isotopes</label>
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127 </param>
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128 <param name="min_ions_per_chemical" type="integer" value="2">
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129 <label>Minimum ions per chemical</label>
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130 </param>
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131 <param name="filter_by" type="select" label="Adducts to filter by" multiple="true" optional="true">
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132 <option value="M-H" selected="true">M-H</option>
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133 <option value="M+H" selected="true">M+H</option>
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134 <option value="2M-H">2M-H</option>
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135 <option value="M-2H">M-2H</option>
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136 </param>
2
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137 </inputs>
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138
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139 <outputs>
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140 <expand macro="outputs"/>
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141 </outputs>
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142
5
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143 <tests>
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144 <test>
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145 <param name="metadata_table" value="metadata_table.parquet" ftype="parquet" />
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146 <param name="intensity_table" value="intensity_table.parquet" ftype="parquet" />
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147 <param name="compound_table" value="database.parquet" ftype="parquet" />
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148 <param name="adduct_table" value="adduct_table.parquet" ftype="parquet" />
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149 <output name="output_file" file="expected_output.parquet" ftype="parquet"/>
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150 </test>
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151 <test>
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152 <param name="metadata_table" value="metadata_table.csv" ftype="csv" />
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153 <param name="intensity_table" value="intensity_table.csv" ftype="csv" />
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154 <param name="compound_table" value="database.csv" ftype="csv" />
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155 <param name="adduct_table" value="adduct_table.csv" ftype="csv" />
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156 <output name="output_file" file="expected_output.csv" ftype="csv"/>
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157 </test>
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158 </tests>
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159
2
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160 <help>
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161 <![CDATA[
5
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162 @HELP@
2
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163 ]]>
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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164 </help>
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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165
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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166 <citations>
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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167 <expand macro="citations"/>
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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168 </citations>
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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169 </tool>