Mercurial > repos > recetox > matchms_filtering

annotate matchms_filtering.xml @ 1:b8e9a7c7add2 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit ca44513d50b29a4706e2a2db96c23ef6688b7c2d
author recetox
date Fri, 22 Jul 2022 16:48:44 +0000
parents 3d275fbdf741
children f814052fbdc5
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b8e9a7c7add2 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit ca44513d50b29a4706e2a2db96c23ef6688b7c2d
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1 <tool id="matchms_filtering" name="matchMS filtering" version="@TOOL_VERSION@+galaxy0">
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2 <description>filter and normalize mass spectrometry data</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="creator"/>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
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9 <requirement type="package" version="1.1.4">pandas</requirement>
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10 </requirements>
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12 <environment_variables>
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13 <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable>
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14 </environment_variables>
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3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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16 <command detect_errors="exit_code"><![CDATA[
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17 sh ${matchms_python_cli}
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18 ]]> </command>
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20 <configfiles>
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21 <configfile name="matchms_python_cli">
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22 python3 ${__tool_directory__}/matchms_filtering_wrapper.py \
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23 --spectra "$spectra" \
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24 --spectra_format "$spectra.ext" \
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25 #if $normalise_intensities.is_true
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26 -normalise_intensities \
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27 #end if
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28 #if $default_filters.is_true
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29 -default_filters \
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30 #end if
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31 #if $clean_metadata.is_true
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32 -clean_metadata \
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33 #end if
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34 #if $relative_intensity.is_true
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35 -relative_intensity \
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36 --from_intensity "$relative_intensity.from_intensity" \
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37 --to_intensity "$relative_intensity.to_intensity" \
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38 #end if
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39 #if $mz_range.is_true
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40 -mz_range \
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41 --from_mz "$mz_range.from_mz" \
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42 --to_mz "$mz_range.to_mz" \
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43 #end if
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44 --output "$output"
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45 </configfile>
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46 </configfiles>
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47
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48 <inputs>
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49 <param label="Spectra file" name="spectra" type="data" format="msp,mgf" help="Mass spectra file to be filtered." />
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50
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51 <conditional name="normalise_intensities">
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52 <param name="is_true" label="Normalize intensities" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
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53 help="Normalize intensities of peaks (and losses) to unit height."/>
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54 </conditional>
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55
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56 <conditional name="default_filters">
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57 <param name="is_true" label="Apply default filters" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
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58 help="Collection of filters that are considered default and that do no require any (factory) arguments."/>
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59 </conditional>
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60
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61 <conditional name="clean_metadata">
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62 <param name="is_true" label="Clean metadata" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
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63 help="Apply all adding and cleaning filters if possible, so that the spectra have canonical metadata." />
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64 </conditional>
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65
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66 <conditional name="relative_intensity">
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67 <param name="is_true" label="Filter relative intensity" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
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68 help="Keep only peaks within set relative intensity range (keep if maximum >= intensity >= minimum)." />
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69 <when value="TRUE">
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70 <param label="Minimum intensity" name="from_intensity" optional="true" type="float" help="Lower bound for intensity filter." />
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71 <param label="Maximum intensity" name="to_intensity" optional="true" type="float" help="Upper bound for intensity filter." />
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72 </when>
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73 </conditional>
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74
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75 <conditional name="mz_range">
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76 <param name="is_true" label="Filter m/z range" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
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77 help="Keep only peaks between set m/z range (keep if maximum >= m/z >= minimum)." />
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78 <when value="TRUE">
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79 <param label="Minimum m/z" name="from_mz" optional="true" type="float" help="Lower bound for m/z filter." />
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80 <param label="Maximum m/z" name="to_mz" optional="true" type="float" help="Upper bound for m/z filter." />
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81 </when>
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82 </conditional>
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83
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84 </inputs>
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85
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86 <outputs>
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87 <data label="${tool.name} on ${on_string}" name="output" format_source="spectra" />
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88 </outputs>
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89
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90 <tests>
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91 <test>
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92 <param name="spectra" value="filtering/input.msp" ftype="msp"/>
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93 <section name="normalise_intensities">
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94 <param name="is_true" value="TRUE"/>
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95 </section>
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96 <output name="output" file="filtering/normalise_intensities.msp" ftype="msp"/>
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97 </test>
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98 <test>
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99 <param name="spectra" value="filtering/input.msp" ftype="msp"/>
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100 <section name="default_filters">
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101 <param name="is_true" value="TRUE"/>
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102 </section>
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103 <output name="output" file="filtering/default_filters.msp" ftype="msp"/>
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104 </test>
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105 <test>
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106 <param name="spectra" value="filtering/input.msp" ftype="msp"/>
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107 <section name="clean_metadata">
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108 <param name="is_true" value="TRUE"/>
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109 </section>
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110 <output name="output" file="filtering/clean_metadata.msp" ftype="msp"/>
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111 </test>
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112 <test>
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113 <param name="spectra" value="filtering/input.msp" ftype="msp"/>
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114 <section name="relative_intensity">
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115 <param name="is_true" value="TRUE"/>
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116 <param name="from_intensity" value="0.3"/>
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117 <param name="to_intensity" value="0.9"/>
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118 </section>
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119 <output name="output" file="filtering/relative_intensity.msp" ftype="msp"/>
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120 </test>
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121 <test>
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122 <param name="spectra" value="filtering/input.msp" ftype="msp"/>
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123 <section name="mz_range">
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124 <param name="is_true" value="TRUE"/>
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125 <param name="from_mz" value="300"/>
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126 <param name="to_mz" value="800"/>
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127 </section>
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128 <output name="output" file="filtering/mz_range.msp" ftype="msp"/>
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129 </test>
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130 </tests>
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131
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132 <help><![CDATA[
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133 Documentation
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134 For documentation on the tool see https://github.com/matchms/matchms/blob/master/README.rst and https://matchms.readthedocs.io/en/latest/.
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135
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136 Upstream Tools
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137 +-----------+---------------+--------+-----------+
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138 | Name | Output File | Format | Parameter |
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139 +===========+===============+========+===========+
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140 | RAMClustR | Mass spectra | msp | references|
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141 +-----------+---------------+--------+-----------+
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142 | RAMClustR | Mass spectra | msp | queries |
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143 +-----------+---------------+--------+-----------+
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144
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145 Downstream Tools
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146 The output is an msp file after applying the specified filters.
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147 ]]></help>
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148
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149
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150 <citations>
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151 <citation type="doi">10.5281/zenodo.4589154</citation>
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152 <citation type="doi">10.21105/joss.02411</citation>
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153 </citations>
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154 </tool>