Mercurial > repos > recetox > matchms_convert

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a57d984a9850c1faa44b6948981eb1303881ba9c
author recetox
date Thu, 14 Aug 2025 12:43:17 +0000
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1 <tool id="matchms_convert" name="matchms convert" version="@TOOL_VERSION@+galaxy2" profile="23.0" license="MIT">
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2 <description>convert between mass spectral library formats (.mgf/.msp/.json) using matchms</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 <import>help.xml</import>
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7 </macros>
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9 <expand macro="creator"/>
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11 <edam_operations>
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12 <edam_operation>operation_3434</edam_operation>
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13 </edam_operations>
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14 <expand macro="bio.tools"/>
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16 <requirements>
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17 <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
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18 </requirements>
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20 <command detect_errors='aggressive'><![CDATA[
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21 python ${matchms_python_cli}
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22 #if $output_file.output_format == "msp":
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23 #if $output_file.export_style == "ms_lima":
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24 &&
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25 sh ${ms_lima_output}
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26 #end if
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27 #end if
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28 ]]></command>
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30 <configfiles>
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31 <configfile name="matchms_python_cli">
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32 @init_logger@
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33
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34 from matchms.importing import load_from_msp, load_from_mgf, load_from_json
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35 from matchms.exporting import save_as_msp, save_as_mgf, save_as_json
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36 spectra = list(load_from_${spectral_library.ext}("${spectral_library}", ${harmonization_metadata}))
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37 #if $output_file.output_format == "msp"
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38 #if $output_file.export_style == "ms_lima"
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39 save_as_msp(spectra, "${converted_library}", write_peak_comments = ${output_file.export_peak_comments}, style = "riken")
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40 #else
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41 save_as_msp(spectra, "${converted_library}", write_peak_comments = ${output_file.export_peak_comments}, style = "${output_file.export_style}")
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42 #end if
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43 #else
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44 save_as_${output_file.output_format}(spectra, "${converted_library}")
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45 #end if
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46 </configfile>
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47 <configfile name="ms_lima_output">
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48 sed -E "s,[[:space:]]+, ,g" ${converted_library} > ${converted_library}.tmp
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50 grep -rl 'CHARGE' . | xargs sed '/CHARGE/d' ${converted_library}.tmp > ${converted_library}.tmp1
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51 grep -rl 'COMPOUND_NAME' . | xargs sed 's/COMPOUND_NAME/NAME/g' ${converted_library}.tmp1 > ${converted_library}.tmp2
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52
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53 mv ${converted_library}.tmp2 ${converted_library}
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54 rm -f ${converted_library}.tmp1 ${converted_library}.tmp2 ${converted_library}.tmp
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55 </configfile>
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56 </configfiles>
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58 <inputs>
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59 <param label="Spectra file" name="spectral_library" type="data" format="msp,mgf,json"
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60 help="Mass spectral library file to convert." />
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61
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62 <param label="Harmonization metadata" name="harmonization_metadata" type="boolean" truevalue="True" falsevalue="False"
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63 checked="true"
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64 help="Apply metadata harmonization, parsing certain keys required by additional filters or initializing other attributes. The default is True." />
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65
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66 <conditional name="output_file">
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67 <param label="Spectral library format" name="output_format" type="select"
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68 help="Output format to convert the spectral library into.">
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69 <option value="msp" selected="true">msp</option>
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70 <option value="mgf">mgf</option>
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71 <option value="json">json</option>
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72 </param>
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73 <when value="msp">
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74 <param label="Export peak comments" name="export_peak_comments" type="boolean"
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75 truevalue="True" falsevalue="False" checked="true"
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76 help="Retain peak comments from individual peaks after the respective mz and intensity pairs when selected." />
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77 <param label="Export style" name="export_style" type="select"
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78 help="Converts the keys to a specific style - see [1] for details.. One of ['matchms', 'massbank', 'nist', 'riken', 'gnps']. Default is 'matchms'.">
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79 <option value="matchms" selected="true">matchms</option>
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80 <option value="massbank">massbank</option>
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81 <option value="nist">nist</option>
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82 <option value="riken">riken</option>
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83 <option value="gnps">gnps</option>
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84 <option value="ms_lima">ms-lima</option>
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85 </param>
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86 </when>
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87 <when value="mgf" />
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88 <when value="json" />
2
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89 </conditional>
0
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90 </inputs>
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91
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92 <outputs>
2
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93 <data label="${tool.name} from ${spectral_library.ext} to ${output_file.output_format} on ${on_string}" name="converted_library" format="msp">
0
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94 <change_format>
2
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95 <when input="output_file.output_format" value="mgf" format="mgf" />
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96 <when input="output_file.output_format" value="json" format="json" />
0
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97 </change_format>
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98 </data>
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99 </outputs>
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100
22
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101 <tests>
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102 <!-- Test 1: Convert to MGF -->
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103 <test>
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104 <conditional name="output_file">
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105 <param name="output_format" value="mgf"/>
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106 </conditional>
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107 <param name="spectral_library" value="similarity/RECETOX_Exposome_pesticides_HR_MS_20220323.msp" ftype="msp"/>
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108 <param name="harmonization_metadata" value="False"/>
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109 <output name="converted_library" file="convert/mgf_out.mgf" ftype="mgf"/>
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110 </test>
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111
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112 <!-- Test 2: Convert to JSON -->
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113 <test>
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114 <conditional name="output_file">
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115 <param name="output_format" value="json"/>
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116 </conditional>
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117 <param name="spectral_library" value="similarity/RECETOX_Exposome_pesticides_HR_MS_20220323.msp" ftype="msp"/>
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118 <param name="harmonization_metadata" value="False"/>
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119 <output name="converted_library" file="convert/json_out.json" ftype="json"/>
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120 </test>
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121
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122 <!-- Test 3: Convert to MSP with matchms style -->
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123 <test>
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124 <conditional name="output_file">
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125 <param name="output_format" value="msp"/>
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126 <param name="export_peak_comments" value="False"/>
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127 <param name="export_style" value="matchms"/>
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128 </conditional>
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129 <param name="spectral_library" value="convert/mgf_out.mgf" ftype="mgf"/>
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130 <param name="harmonization_metadata" value="False"/>
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131 <output name="converted_library" file="convert/msp_out.msp" ftype="msp"/>
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132 </test>
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133
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134 <!-- Test 4: Convert to MSP with harmonization -->
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135 <test>
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136 <conditional name="output_file">
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137 <param name="output_format" value="msp"/>
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138 <param name="export_peak_comments" value="False"/>
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139 <param name="export_style" value="matchms"/>
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140 </conditional>
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141 <param name="spectral_library" value="convert/mgf_out.mgf" ftype="mgf"/>
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142 <param name="harmonization_metadata" value="True"/>
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143 <output name="converted_library" file="convert/harmonized_msp_out.msp" ftype="msp"/>
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144 </test>
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145
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146 <!-- Test 5: Convert to MSP with peak comments -->
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147 <test>
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148 <conditional name="output_file">
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149 <param name="output_format" value="msp"/>
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150 <param name="export_peak_comments" value="True"/>
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151 <param name="export_style" value="matchms"/>
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152 </conditional>
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153 <param name="spectral_library" value="convert/mgf_out.mgf" ftype="mgf"/>
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154 <param name="harmonization_metadata" value="True"/>
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155 <output name="converted_library" file="convert/harmonized_msp_peakcomments_out.msp" ftype="msp"/>
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156 </test>
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157
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158 <!-- Test 6: Convert to MSP with ms-lima style -->
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159 <test>
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160 <conditional name="output_file">
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161 <param name="output_format" value="msp"/>
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162 <param name="export_peak_comments" value="False"/>
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163 <param name="export_style" value="ms_lima"/>
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164 </conditional>
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165 <param name="spectral_library" value="convert/mgf_out.mgf" ftype="mgf"/>
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166 <param name="harmonization_metadata" value="True"/>
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167 <output name="converted_library" file="convert/ms_lima_output.msp" ftype="msp"/>
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168 </test>
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169 </tests>
0
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170
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171
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172 <help><![CDATA[
3
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173 Description
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174 Mass spectral libraries are often stored in various formats, such as `msp`, `mgf` or `json`.
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175 This tool can be used to convert from one library format to another.
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176 Some of the metadata keywords might change during the conversion process, as they are harmonized internally with matchms.
0
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177
3
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178 .. rubric:: **Footnotes**
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179 .. [1] Export styles - see the 'export\_key\_conversions' file in the matchms GitHub repository for supported key conversions and detailed description of the export styles.
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180
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181 @HELP_matchms@
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182 ]]></help>
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185 <expand macro="citations"/>
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186 </tool>