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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit aec90552d259748822d040248a9e1265759cc198
author recetox
date Tue, 01 Jul 2025 09:28:32 +0000
parents f0fe957df1cc
children
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7
06f2d0d6d107 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit aec90552d259748822d040248a9e1265759cc198
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1 <tool id="isolib" name="isolib" version="2.6+galaxy3" profile="23.0" license="MIT">
4
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2 <description>create an isotopic pattern library for given compounds and adducts based on enviPat</description>
0
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3 <creator>
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4 <person
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5 givenName="Helge"
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6 familyName="Hecht"
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7 url="https://github.com/hechth"
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8 identifier="0000-0001-6744-996X" />
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9 <organization
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10 url="https://www.recetox.muni.cz/"
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11 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
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12 name="RECETOX MUNI" />
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13 </creator>
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14 <edam_operations>
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15 <edam_operation>operation_3632</edam_operation>
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16 </edam_operations>
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17 <requirements>
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18 <requirement type="package" version="1.10.0">bioconductor-metabocoreutils</requirement>
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19 <requirement type="package" version="1.12.0">bioconductor-spectra</requirement>
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20 <requirement type="package" version="1.6.0">bioconductor-msbackendmsp</requirement>
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21 <requirement type="package" version="2.6">r-envipat</requirement>
2
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22 <requirement type="package" version="2.1.5">r-readr</requirement>
4
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23 <requirement type="package" version="1.3.1">r-tidyr</requirement>
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24 <requirement type="package" version="1.5.1">r-stringr</requirement>
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25 <requirement type="package" version="1.0.2">r-purrr</requirement>
0
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26 </requirements>
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27 <command detect_errors="exit_code"><![CDATA[
4
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28 Rscript '${__tool_directory__}/isolib.R'
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29 '${input_file}'
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30 '${ionization.adducts}'
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31 '${threshold}'
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32 '${append_adduct}'
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33 #if $formatting.out_format == "tabular"
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34 '${formatting.append_isotopes}'
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35 #else
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36 'FALSE'
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37 #end if
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38 '${formatting.out_format}'
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39 '${isotope_library}'
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40 '${rel_to.value}'
0
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41 ]]></command>
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42 <inputs>
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43 <param name="input_file" type="data" format="tabular" label="Table with input compounds"/>
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44 <conditional name="ionization">
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45 <param name="ionization" type="select" label="Ionization mode" help="Ionization mode used in the experiment">
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46 <option value="negative" selected="true">negative</option>
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47 <option value="positive">positive</option>
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48 </param>
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49 <when value="positive">
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50 <param name="adducts" type="select" label="Adducts" multiple="true" help="Adducts to use">
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51 <option value="M+H" selected="true">M+H</option>
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52 </param>
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53 </when>
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54 <when value="negative">
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55 <param name="adducts" type="select" label="Adducts" multiple="true" help="Adducts to use">
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56 <option value="M-H" selected="true">M-H</option>
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57 <option value="M-2H">M-2H</option>
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58 <option value="2M-H">2M-H</option>
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59 </param>
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60 </when>
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61 </conditional>
5
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62 <conditional name="rel_to">
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63 <param name="value" type="select" label="Intensity normalization mode">
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64 <option value="0" selected="true">0 - Relative to most intense peak</option>
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65 <option value="1">1 - Relative to monoisotopic peak</option>
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66 <option value="2">2 - No normalization (absolute probabilities)</option>
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67 <option value="3">3 - Prune by most intense peak (%), output absolute</option>
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68 <option value="4">4 - Prune by mono peak (%), output absolute</option>
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69 </param>
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70
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71 <when value="0">
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72 <param name="threshold" type="float" label="Threshold (% of base peak)" value="1.0" min="0" max="100"
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73 help="Remove peaks below this % of the most intense peak"/>
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74 </when>
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75 <when value="1">
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76 <param name="threshold" type="float" label="Threshold (% of monoisotopic peak)" value="1.0" min="0" max="100"
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77 help="Remove peaks below this % of the monoisotopic peak"/>
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78 </when>
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79 <when value="2">
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80 <param name="threshold" type="float" label="Threshold (absolute probability)" value="0.0001" min="0" max="1"
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81 help="Remove peaks with probability below this absolute value"/>
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82 </when>
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83 <when value="3">
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84 <param name="threshold" type="float" label="Threshold (% of base peak)" value="1.0" min="0" max="100"
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85 help="Remove peaks below this % of the most intense peak (output is not normalized)"/>
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86 </when>
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87 <when value="4">
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88 <param name="threshold" type="float" label="Threshold (% of monoisotopic peak)" value="1.0" min="0" max="100"
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89 help="Remove peaks below this % of the monoisotopic peak (output is not normalized)"/>
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90 </when>
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91 </conditional>
0
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92 <param name="append_adduct" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Append adduct to compound name" help="Append the adduct string to the compound name for easy identification." />
4
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93 <conditional name="formatting">
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94 <param name="out_format" type="select" label="Output Format" help="Choose the output format, either MSP or Tabular">
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95 <option value="tabular">tabular</option>
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96 <option value="msp" selected="true">msp</option>
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97 </param>
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98 <when value="tabular">
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99 <param name="append_isotopes" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Append isotopes to formula" help="Append the isotopic composition to the formula for easy identification." />
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100 </when>
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101 <when value="msp">
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102 </when>
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103 </conditional>
0
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104 </inputs>
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105 <outputs>
4
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106 <data format="msp" name="isotope_library">
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107 <change_format>
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108 <when input="formatting.out_format" value="msp" format="msp" />
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109 <when input="formatting.out_format" value="tabular" format="tabular" />
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110 </change_format>
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111 </data>
0
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112 </outputs>
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113
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114 <tests>
5
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115 <!-- Test 1: Default settings with rel_to = 0 -->
0
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116 <test>
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117 <param name="input_file" value="lc_markers_neg.tsv"/>
5
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118 <conditional name="rel_to">
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119 <param name="value" value="0"/>
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120 <param name="threshold" value="1.0"/>
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121 </conditional>
0
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122 <output name="isotope_library" file="test0.msp"/>
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123 </test>
5
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124
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125 <!-- Test 2: rel_to = 1 (Relative to monoisotopic peak) -->
2
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126 <test>
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127 <param name="input_file" value="markers_no_rt.tsv"/>
5
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128 <conditional name="rel_to">
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129 <param name="value" value="1"/>
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130 <param name="threshold" value="1.0"/>
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131 </conditional>
2
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132 <output name="isotope_library" file="test1.msp"/>
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133 </test>
5
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134
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135 <!-- Test 3: rel_to = 2 (No normalization, absolute probabilities) -->
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136 <test>
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137 <param name="input_file" value="lc_markers_neg.tsv"/>
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138 <conditional name="rel_to">
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139 <param name="value" value="2"/>
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140 <param name="threshold" value="0.0001"/>
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141 </conditional>
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142 <output name="isotope_library" file="test2.msp"/>
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143 </test>
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144
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145 <!-- Test 4: rel_to = 3 (Prune by most intense peak, output absolute) -->
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146 <test>
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147 <param name="input_file" value="lc_markers_neg.tsv"/>
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148 <conditional name="rel_to">
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149 <param name="value" value="3"/>
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150 <param name="threshold" value="5.0"/>
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151 </conditional>
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152 <output name="isotope_library" file="test3.msp"/>
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153 </test>
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154
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155 <!-- Test 5: rel_to = 4 (Prune by monoisotopic peak, output absolute) -->
4
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156 <test>
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157 <param name="input_file" value="lc_markers_neg.tsv"/>
5
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158 <conditional name="rel_to">
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159 <param name="value" value="4"/>
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160 <param name="threshold" value="2.0"/>
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161 </conditional>
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162 <output name="isotope_library" file="test4.msp"/>
4
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163 </test>
5
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164
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165 <!-- Test 6: Tabular output with rel_to = 2 and append_isotopes = TRUE -->
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166 <test>
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167 <param name="input_file" value="lc_markers_neg.tsv"/>
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168 <conditional name="formatting">
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169 <param name="out_format" value="tabular"/>
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170 <param name="append_isotopes" value="TRUE"/>
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171 </conditional>
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172 <conditional name="rel_to">
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173 <param name="value" value="2"/>
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174 <param name="threshold" value="0.01"/>
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175 </conditional>
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176 <output name="isotope_library" file="test5.tabular"/>
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177 </test>
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178
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179 <!-- Test 7: Tabular output with rel_to = 3 and custom adducts -->
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180 <test>
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181 <param name="input_file" value="lc_markers_neg.tsv"/>
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182 <conditional name="formatting">
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183 <param name="out_format" value="tabular"/>
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184 <param name="append_isotopes" value="FALSE"/>
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185 </conditional>
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186 <conditional name="ionization">
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187 <param name="ionization" value="negative"/>
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188 <param name="adducts" value="M-H,2M-H"/>
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189 </conditional>
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190 <conditional name="rel_to">
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191 <param name="value" value="3"/>
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192 <param name="threshold" value="1.0"/>
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193 </conditional>
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194 <output name="isotope_library" file="test6.tabular"/>
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195 </test>
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196
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197 <!-- Test 8: Positive ionization mode with rel_to = 0 -->
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198 <test>
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199 <param name="input_file" value="lc_markers_neg.tsv"/>
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200 <conditional name="ionization">
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201 <param name="ionization" value="positive"/>
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202 <param name="adducts" value="M+H"/>
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203 </conditional>
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204 <conditional name="rel_to">
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205 <param name="value" value="0"/>
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206 <param name="threshold" value="1.0"/>
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207 </conditional>
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208 <output name="isotope_library" file="test7.msp"/>
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209 </test>
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210 <!-- Test 9: Positive ionization mode with custom adducts -->
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211 <test>
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212 <param name="input_file" value="edge_case.tabular"/>
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213 <conditional name="ionization">
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214 <param name="ionization" value="positive"/>
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215 <param name="adducts" value="M+H"/>
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216 </conditional>
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217 <conditional name="rel_to">
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218 <param name="value" value="0"/>
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219 <param name="threshold" value="10"/>
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220 </conditional>
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221 <output name="isotope_library" file="test8.msp"/>
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222 </test>
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223 <!-- Test 10: Positive ionization mode with custom adducts, tabular output -->
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224 <test>
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225 <param name="input_file" value="edge_case.tabular"/>
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226 <conditional name="ionization">
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227 <param name="ionization" value="positive"/>
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228 <param name="adducts" value="M+H"/>
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229 </conditional>
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230 <conditional name="formatting">
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231 <param name="out_format" value="tabular"/>
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232 </conditional>
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233 <conditional name="rel_to">
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234 <param name="value" value="0"/>
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235 <param name="threshold" value="10"/>
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236 </conditional>
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237 <output name="isotope_library" file="test9.tsv" ftype="tabular"/>
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238 </test>
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239 </tests>
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240 <help><![CDATA[
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241 This tool computes isotopic patterns for given compounds and adduct forms.
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242
0
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243 The compound table input file should contain the following columns:
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244
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245 - **name**: Compound name.
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246 - **formula**: Compound formula.
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247 - **rt** (optional): Retention time.
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248
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249 The output is a spectral library in the MSP format.
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250
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251 Parameters:
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252
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253 **rel_to Modes**:
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254
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255 - **0**: Normalize to the most intense peak (threshold in percentage).
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256 - **1**: Normalize to the monoisotopic peak (threshold in percentage).
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257 - **2**: No normalization (threshold is an absolute probability).
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258 - **3**: Prune by percentage of most intense peak, output absolute intensities.
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259 - **4**: Prune by percentage of monoisotopic peak, output absolute intensities.
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260
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261 **Threshold Behavior**:
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262
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263 The threshold's units and behavior change based on the selected **rel_to** mode. Use this to tailor output to your downstream needs.
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264
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265 **Threshold for Modes 0, 1, 3, 4 (Percentage of Peak Intensity)**:
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266
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267 - The threshold is a **percentage** of the most intense or monoisotopic peak.
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268 - Example 1: To remove isotopes with a probability of less than 1% of the most intense peak, set the threshold to `1` and select **rel_to = 0**.
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269 - Example 2: To remove isotopes with a probability of less than 1% of the monoisotopic peak, set the threshold to `1` and select **rel_to = 1**.
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270 - Example 3: To remove isotopes with a probability of less than 1% of the most intense peak but output absolute intensities, set the threshold to `1` and select **rel_to = 3**.
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271 - Example 4: To remove isotopes with a probability of less than 1% of the monoisotopic peak but output absolute intensities, set the threshold to `1` and select **rel_to = 4**.
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272
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273 **Threshold for Mode 2 (Absolute Probability)**:
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274
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275 - The threshold is an **absolute probability** (e.g., `0.01`, `0.0005`, etc.).
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276 - Example 1: To remove isotopes with a probability of less than `0.01`, set the threshold to `0.01` and select **rel_to = 2**.
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277 - **Important**: Be cautious with very small threshold values in **rel_to = 2**. If the threshold is too low (e.g., `0.0001`), it may prune almost all peaks, resulting in a sparse or empty output. Similarly, a threshold that is too high may result in no isotopes being removed.
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278 - Consider using threshold values like `0.01`, `0.1`, or `0.5` depending on your data.
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279
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280 **General Guidance**:
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281
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282 - **Threshold Selection**:
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283
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284 - For **modes 0, 1, 3, and 4**: The threshold is **relative** to the most intense or monoisotopic peak, and a **percentage** threshold works well for most data sets.
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285 - For **mode 2**: The threshold is **absolute**, and users must be careful not to choose a value that’s too small or too large.
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287 Example Scenarios:
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288
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289 1. **Scenario 1**: You have a dataset with peaks that vary significantly in intensity. You want to keep isotopes that are at least 1% of the most intense peak. Set the threshold to `1` and use **rel_to = 0** or **rel_to = 3**.
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290 2. **Scenario 2**: You want to remove isotopes with an absolute probability below `0.005` regardless of peak intensity. Set the threshold to `0.005` and use **rel_to = 2**.
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291
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292 ]]></help>
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293 <citations>
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294 <citation type="doi">10.1021/acs.analchem.5b00941</citation>
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295 <citation type="doi">10.3390/metabo12020173</citation>
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296 </citations>
1
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297 </tool>