Mercurial > repos > recetox > matchms_filtering

annotate matchms_filtering.xml @ 0:6303b43e29cb draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 46191b39a711f92418f1d412065bbb3648dbf42d"
author recetox
date Mon, 24 Jan 2022 11:15:00 +0000
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1 <tool id="matchms_filtering" name="matchMS filtering" version="0.11.0+galaxy0">
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2 <description>filter and normalize mass spectrometry data</description>
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3 <requirements>
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4 <requirement type="package" version="0.11.0">matchms</requirement>
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5 <requirement type="package" version="1.1.4">pandas</requirement>
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6 </requirements>
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8 <environment_variables>
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9 <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable>
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10 </environment_variables>
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11
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12 <command detect_errors="exit_code"><![CDATA[
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13 sh ${matchms_python_cli}
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14 ]]> </command>
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16 <configfiles>
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17 <configfile name="matchms_python_cli">
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18 python3 ${__tool_directory__}/matchms_filtering_wrapper.py \
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19 --spectra "$spectra" \
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20 --spectra_format "$spectra.ext" \
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21 #if $normalise_intensities.is_true
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22 -normalise_intensities \
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23 #end if
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24 #if $default_filters.is_true
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25 -default_filters \
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26 #end if
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27 #if $clean_metadata.is_true
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28 -clean_metadata \
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29 #end if
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30 #if $relative_intensity.is_true
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31 -relative_intensity \
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32 --from_intensity "$relative_intensity.from_intensity" \
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33 --to_intensity "$relative_intensity.to_intensity" \
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34 #end if
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35 #if $mz_range.is_true
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36 -mz_range \
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37 --from_mz "$mz_range.from_mz" \
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38 --to_mz "$mz_range.to_mz" \
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39 #end if
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40 --output "$output"
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41 </configfile>
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42 </configfiles>
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43
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44 <inputs>
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45 <param label="Spectra file" name="spectra" type="data" format="msp,mgf" help="Mass spectra file to be filtered." />
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46
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47 <conditional name="normalise_intensities">
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48 <param name="is_true" label="Normalize intensities" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
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49 help="Normalize intensities of peaks (and losses) to unit height."/>
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50 </conditional>
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51
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52 <conditional name="default_filters">
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53 <param name="is_true" label="Apply default filters" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
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54 help="Collection of filters that are considered default and that do no require any (factory) arguments."/>
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55 </conditional>
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56
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57 <conditional name="clean_metadata">
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58 <param name="is_true" label="Clean metadata" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
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59 help="Apply all adding and cleaning filters if possible, so that the spectra have canonical metadata." />
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60 </conditional>
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61
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62 <conditional name="relative_intensity">
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63 <param name="is_true" label="Filter relative intensity" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
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64 help="Keep only peaks within set relative intensity range (keep if maximum >= intensity >= minimum)." />
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65 <when value="TRUE">
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66 <param label="Minimum intensity" name="from_intensity" optional="true" type="float" help="Lower bound for intensity filter." />
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67 <param label="Maximum intensity" name="to_intensity" optional="true" type="float" help="Upper bound for intensity filter." />
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68 </when>
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69 </conditional>
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70
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71 <conditional name="mz_range">
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72 <param name="is_true" label="Filter m/z range" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
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73 help="Keep only peaks between set m/z range (keep if maximum >= m/z >= minimum)." />
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74 <when value="TRUE">
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75 <param label="Minimum m/z" name="from_mz" optional="true" type="float" help="Lower bound for m/z filter." />
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76 <param label="Maximum m/z" name="to_mz" optional="true" type="float" help="Upper bound for m/z filter." />
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77 </when>
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78 </conditional>
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79
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80 </inputs>
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81
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82 <outputs>
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83 <data label="${tool.name} on ${on_string}" name="output" format_source="spectra" />
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84 </outputs>
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85
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86 <tests>
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87 <test>
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88 <param name="spectra" value="filtering/input.msp" ftype="msp"/>
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89 <section name="normalise_intensities">
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90 <param name="is_true" value="TRUE"/>
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91 </section>
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92 <output name="output" file="filtering/normalise_intensities.msp" ftype="msp"/>
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93 </test>
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94 <test>
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95 <param name="spectra" value="filtering/input.msp" ftype="msp"/>
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96 <section name="default_filters">
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97 <param name="is_true" value="TRUE"/>
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98 </section>
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99 <output name="output" file="filtering/default_filters.msp" ftype="msp"/>
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100 </test>
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101 <test>
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102 <param name="spectra" value="filtering/input.msp" ftype="msp"/>
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103 <section name="clean_metadata">
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104 <param name="is_true" value="TRUE"/>
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105 </section>
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106 <output name="output" file="filtering/clean_metadata.msp" ftype="msp"/>
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107 </test>
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108 <test>
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109 <param name="spectra" value="filtering/input.msp" ftype="msp"/>
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110 <section name="normalise_intensities">
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111 <param name="is_true" value="TRUE"/>
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112 </section>
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113 <section name="relative_intensity">
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114 <param name="is_true" value="TRUE"/>
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115 <param name="from_intensity" value="0.3"/>
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116 <param name="to_intensity" value="0.9"/>
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117 </section>
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118 <output name="output" file="filtering/relative_intensity.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="mz_range">
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123 <param name="is_true" value="TRUE"/>
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124 <param name="from_mz" value="300"/>
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125 <param name="to_mz" value="800"/>
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126 </section>
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127 <output name="output" file="filtering/mz_range.msp" ftype="msp"/>
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128 </test>
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129 </tests>
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130
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131 <help><![CDATA[
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132 Documentation
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133 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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134
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135 Upstream Tools
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136 +-----------+---------------+--------+-----------+
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137 | Name | Output File | Format | Parameter |
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138 +===========+===============+========+===========+
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139 | RAMClustR | Mass spectra | msp | references|
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140 +-----------+---------------+--------+-----------+
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141 | RAMClustR | Mass spectra | msp | queries |
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142 +-----------+---------------+--------+-----------+
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143
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144 Downstream Tools
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145 The output is an msp file after applying the specified filters.
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146 ]]></help>
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147
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148
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149 <citations>
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150 <citation type="doi">10.5281/zenodo.4589154</citation>
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151 <citation type="doi">10.21105/joss.02411</citation>
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152 </citations>
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153 </tool>