Mercurial > repos > recetox > matchms_filtering

annotate matchms_filtering.xml @ 5:a177ac3c752c draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
author recetox
date Tue, 27 Jun 2023 14:25:01 +0000
parents 1f2b13dbc0c8
children 13de8005adba
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a177ac3c752c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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1 <tool id="matchms_filtering" name="matchms filtering" version="@TOOL_VERSION@+galaxy0" profile="21.09">
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2 <description>filter and normalize mass spectrometry data</description>
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3
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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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23
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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
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34 -normalise_intensities \
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35 #end if
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36 #if $default_filters.is_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
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40 -clean_metadata \
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41 #end if
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42 #if $relative_intensity.is_true
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43 -relative_intensity \
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44 --from_intensity "$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 $mz_range.is_true
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48 -mz_range \
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49 --from_mz "$mz_range.from_mz" \
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50 --to_mz "$mz_range.to_mz" \
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51 #end if
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52 --output "$output"
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53 </configfile>
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54 </configfiles>
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56 <inputs>
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57 <param label="Spectra file" name="spectra" type="data" format="msp,mgf" help="Mass spectra file to be filtered." />
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59 <conditional name="normalise_intensities">
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60 <param name="is_true" label="Normalize intensities" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
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61 help="Normalize intensities of peaks (and losses) to unit height."/>
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62 </conditional>
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63
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64 <conditional name="default_filters">
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65 <param name="is_true" label="Apply default filters" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
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66 help="Collection of filters that are considered default and that do no require any (factory) arguments."/>
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67 </conditional>
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68
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69 <conditional name="clean_metadata">
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70 <param name="is_true" label="Clean metadata" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
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71 help="Apply all adding and cleaning filters if possible, so that the spectra have canonical metadata." />
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72 </conditional>
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74 <conditional name="relative_intensity">
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75 <param name="is_true" label="Filter relative intensity" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
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76 help="Keep only peaks within set relative intensity range (keep if maximum >= intensity >= minimum)." />
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77 <when value="TRUE">
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78 <param label="Minimum intensity" name="from_intensity" value="0" type="float" help="Lower bound for intensity filter." />
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79 <param label="Maximum intensity" name="to_intensity" value="1" type="float" help="Upper bound for intensity filter." />
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80 </when>
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81 </conditional>
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82
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83 <conditional name="mz_range">
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84 <param name="is_true" label="Filter m/z range" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
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85 help="Keep only peaks between set m/z range (keep if maximum >= m/z >= minimum)." />
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86 <when value="TRUE">
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87 <param label="Minimum m/z" name="from_mz" optional="true" type="float" help="Lower bound for m/z filter." />
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88 <param label="Maximum m/z" name="to_mz" optional="true" type="float" help="Upper bound for m/z filter." />
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89 </when>
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90 </conditional>
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91
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92 </inputs>
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93
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94 <outputs>
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95 <data label="${tool.name} on ${on_string}" name="output" format_source="spectra" />
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96 </outputs>
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97
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98 <tests>
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99 <test>
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100 <param name="spectra" value="filtering/input.msp" ftype="msp"/>
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101 <section name="normalise_intensities">
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102 <param name="is_true" value="TRUE"/>
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103 </section>
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104 <output name="output" file="filtering/normalise_intensities.msp" ftype="msp"/>
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105 </test>
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106 <test>
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107 <param name="spectra" value="filtering/input.msp" ftype="msp"/>
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108 <section name="default_filters">
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109 <param name="is_true" value="TRUE"/>
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110 </section>
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111 <output name="output" file="filtering/default_filters.msp" ftype="msp"/>
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112 </test>
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113 <test>
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114 <param name="spectra" value="filtering/input.msp" ftype="msp"/>
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115 <section name="clean_metadata">
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116 <param name="is_true" value="TRUE"/>
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117 </section>
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118 <output name="output" file="filtering/clean_metadata.msp" ftype="msp"/>
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119 </test>
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120 <test>
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121 <param name="spectra" value="filtering/input.msp" ftype="msp"/>
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122 <section name="relative_intensity">
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123 <param name="is_true" value="TRUE"/>
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124 <param name="from_intensity" value="0.3"/>
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125 <param name="to_intensity" value="0.9"/>
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126 </section>
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127 <output name="output" file="filtering/relative_intensity.msp" ftype="msp"/>
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128 </test>
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129 <test>
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130 <param name="spectra" value="filtering/input.msp" ftype="msp"/>
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131 <section name="mz_range">
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132 <param name="is_true" value="TRUE"/>
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133 <param name="from_mz" value="300"/>
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134 <param name="to_mz" value="800"/>
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135 </section>
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136 <output name="output" file="filtering/mz_range.msp" ftype="msp"/>
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137 </test>
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138 </tests>
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139
5
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140 <help>
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141 @HELP_matchms@
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142 </help>
0
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143
3
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144 <expand macro="citations"/>
0
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145 </tool>