Mercurial > repos > recetox > matchms_filtering

annotate matchms_filtering.xml @ 17:3370f5b08d19 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f14275bfdc2caa760d71d307ca1803eab1adde76
author recetox
date Wed, 13 Mar 2024 10:15:03 +0000
parents da15e8ea3b28
children 86d265d2a334
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1 <tool id="matchms_filtering" name="matchms filtering" version="@TOOL_VERSION@+galaxy2" profile="21.09">
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2 <description>filter and normalize mass spectrometry data</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_3695</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="exit_code"><![CDATA[
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21 sh ${matchms_python_cli}
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22 ]]> </command>
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24 <environment_variables>
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25 <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable>
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26 </environment_variables>
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28 <configfiles>
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29 <configfile name="matchms_python_cli">
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30 python3 ${__tool_directory__}/matchms_filtering_wrapper.py \
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31 --spectra "$spectra" \
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32 --spectra_format "$spectra.ext" \
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33 #if $normalise_intensities_is_true == "TRUE"
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34 -normalise_intensities \
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35 #end if
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36 #if $default_filters_is_true == "TRUE"
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37 -default_filters \
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38 #end if
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39 #if $clean_metadata_is_true == "TRUE"
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40 -clean_metadata \
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41 #end if
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42 #if $relative_intensity.is_true == "TRUE"
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43 -relative_intensity \
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44 --from_intensity "$relative_intensity.from_intensity" \
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45 --to_intensity "$relative_intensity.to_intensity" \
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46 #end if
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47 #if $mz_range.is_true == "TRUE"
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48 -mz_range \
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49 --from_mz "$mz_range.from_mz" \
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50 --to_mz "$mz_range.to_mz" \
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51 #end if
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52 #if $require_smiles_is_true == "TRUE"
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53 -require_smiles \
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54 #end if
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55 #if $require_inchi_is_true == "TRUE"
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56 -require_inchi \
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57 #end if
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58 #if $derive_precursor_mz_from_parent_mass.is_true == "TRUE"
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59 -derive_precursor_mz_from_parent_mass \
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60 --estimate_from_adduct "${derive_precursor_mz_from_parent_mass.estimate_from_adduct}" \
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61 #end if
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62 #if $reduce_to_top_n_peaks.is_true == "TRUE"
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63 -reduce_to_top_n_peaks \
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64 --n_max "$reduce_to_top_n_peaks.n_max" \
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65 #end if
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66 --output "$output"
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67 </configfile>
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68 </configfiles>
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69
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70 <inputs>
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71 <param label="Spectra file" name="spectra" type="data" format="msp,mgf" help="Mass spectra file to be filtered." />
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72 <param name="normalise_intensities_is_true" label="Normalize intensities" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
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73 help="Normalize intensities of peaks (and losses) to unit height."/>
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74 <param name="default_filters_is_true" label="Apply default filters" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
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75 help="Collection of filters that are considered default and that do no require any (factory) arguments."/>
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76 <param name="clean_metadata_is_true" label="Clean metadata" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
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77 help="Apply all adding and cleaning filters if possible, so that the spectra have canonical metadata." />
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78
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79 <conditional name="relative_intensity">
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80 <param name="is_true" label="Filter relative intensity" type="select"
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81 help="Keep only peaks within set relative intensity range (keep if maximum >= intensity >= minimum).">
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82 <option value="FALSE" selected="true">FALSE</option>
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83 <option value="TRUE">TRUE</option>
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84 </param>
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85 <when value="TRUE">
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86 <param label="Minimum intensity" name="from_intensity" value="0" type="float" help="Lower bound for intensity filter." />
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87 <param label="Maximum intensity" name="to_intensity" value="1" type="float" help="Upper bound for intensity filter." />
0
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88 </when>
6
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89 <when value="FALSE"></when>
0
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90 </conditional>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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91
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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92 <conditional name="mz_range">
6
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93 <param name="is_true" label="Filter m/z range" type="select"
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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94 help="Keep only peaks between set m/z range (keep if maximum >= m/z >= minimum).">
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95 <option value="FALSE" selected="true">FALSE</option>
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96 <option value="TRUE">TRUE</option>
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97 </param>
0
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98 <when value="TRUE">
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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99 <param label="Minimum m/z" name="from_mz" optional="true" type="float" help="Lower bound for m/z filter." />
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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100 <param label="Maximum m/z" name="to_mz" optional="true" type="float" help="Upper bound for m/z filter." />
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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101 </when>
6
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102 <when value="FALSE"></when>
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103 </conditional>
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104
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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105 <param name="require_smiles_is_true" label="Require SMILES" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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106 help="Remove spectra that does not contain SMILES." />
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107
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108 <param name="require_inchi_is_true" label="Require INCHI" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
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109 help="Remove spectra that does not contain INCHI." />
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110
13
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111 <conditional name="derive_precursor_mz_from_parent_mass">
ca5a8db023e1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0
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112 <param name="is_true" label="Derive precursor_mz from parent_mass" type="select"
ca5a8db023e1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0
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113 help="Derives the precursor_mz from the parent mass and adduct or charge.">
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114 <option value="FALSE" selected="true">FALSE</option>
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115 <option value="TRUE">TRUE</option>
ca5a8db023e1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0
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116 </param>
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117 <when value="TRUE">
ca5a8db023e1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0
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118 <param label="Estimate from adduct" name="estimate_from_adduct" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" />
ca5a8db023e1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0
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119 </when>
ca5a8db023e1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0
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120 <when value="FALSE"></when>
ca5a8db023e1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0
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121 </conditional>
ca5a8db023e1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0
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122
6
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123 <conditional name="reduce_to_top_n_peaks">
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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124 <param name="is_true" label="Reduce to top n peaks" type="select"
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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125 help="Lowest intensity peaks will be removed when it has more peaks than desired.">
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126 <option value="FALSE" selected="true">FALSE</option>
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127 <option value="TRUE">TRUE</option>
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128 </param>
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129 <when value="TRUE">
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130 <param label="Maximum number of peaks" name="n_max" value="5" type="integer" help="Maximum number of peaks. Remove peaks if more peaks are found." />
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131 </when>
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132 <when value="FALSE"></when>
0
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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133 </conditional>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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134
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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135 </inputs>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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136
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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137 <outputs>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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138 <data label="${tool.name} on ${on_string}" name="output" format_source="spectra" />
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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139 </outputs>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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140
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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141 <tests>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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142 <test>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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143 <param name="spectra" value="filtering/input.msp" ftype="msp"/>
6
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144 <param name="normalise_intensities_is_true" value="TRUE"/>
0
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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145 <output name="output" file="filtering/normalise_intensities.msp" ftype="msp"/>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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146 </test>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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147 <test>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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148 <param name="spectra" value="filtering/input.msp" ftype="msp"/>
6
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149 <param name="default_filters_is_true" value="TRUE"/>
0
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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150 <output name="output" file="filtering/default_filters.msp" ftype="msp"/>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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151 </test>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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152 <test>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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153 <param name="spectra" value="filtering/input.msp" ftype="msp"/>
6
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154 <param name="clean_metadata_is_true" value="TRUE"/>
0
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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155 <output name="output" file="filtering/clean_metadata.msp" ftype="msp"/>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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156 </test>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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157 <test>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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158 <param name="spectra" value="filtering/input.msp" ftype="msp"/>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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159 <section name="relative_intensity">
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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160 <param name="is_true" value="TRUE"/>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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161 <param name="from_intensity" value="0.3"/>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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162 <param name="to_intensity" value="0.9"/>
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163 </section>
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164 <output name="output" file="filtering/relative_intensity.msp" ftype="msp"/>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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165 </test>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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166 <test>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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167 <param name="spectra" value="filtering/input.msp" ftype="msp"/>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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168 <section name="mz_range">
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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169 <param name="is_true" value="TRUE"/>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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170 <param name="from_mz" value="300"/>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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171 <param name="to_mz" value="800"/>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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172 </section>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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173 <output name="output" file="filtering/mz_range.msp" ftype="msp"/>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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174 </test>
6
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175 <test>
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176 <param name="spectra" value="filtering/require_filter.msp" ftype="msp"/>
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177 <param name="require_smiles_is_true" value="TRUE"/>
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178 <output name="output" file="filtering/require_out.msp" ftype="msp"/>
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179 </test>
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180 <test>
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181 <param name="spectra" value="filtering/require_filter.msp" ftype="msp"/>
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182 <param name="require_inchi_is_true" value="TRUE"/>
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183 <output name="output" file="filtering/require_out.msp" ftype="msp"/>
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184 </test>
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185 <test>
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186 <param name="spectra" value="filtering/input.msp" ftype="msp"/>
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187 <section name="reduce_to_top_n_peaks">
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188 <param name="is_true" value="TRUE"/>
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189 <param name="n_max" value="5"/>
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190 </section>
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191 <output name="output" file="filtering/reduce_to_top_n_peaks.msp" ftype="msp"/>
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192 </test>
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193 <test>
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194 <param name="spectra" value="filtering/derive_precursor_mz.msp" ftype="msp"/>
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195 <section name="derive_precursor_mz_from_parent_mass">
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196 <param name="is_true" value="TRUE"/>
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197 <param name="estimate_from_adduct" value="TRUE"/>
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198 </section>
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199 <output name="output" file="filtering/derive_precursor_mz_out.msp" ftype="msp"/>
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200 </test>
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201 </tests>
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202
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203 <help>
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204 @HELP_matchms@
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205 </help>
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206
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207 <expand macro="citations"/>
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208 </tool>