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comparison matchms_filtering.xml @ 6:13de8005adba draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
author recetox
date Thu, 12 Oct 2023 13:24:59 +0000
parents a177ac3c752c
children 039e7ab31836
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5:a177ac3c752c 6:13de8005adba
1 <tool id="matchms_filtering" name="matchms filtering" version="@TOOL_VERSION@+galaxy0" profile="21.09"> 1 <tool id="matchms_filtering" name="matchms filtering" version="@TOOL_VERSION@+galaxy2" profile="21.09">
2 <description>filter and normalize mass spectrometry data</description> 2 <description>filter and normalize mass spectrometry data</description>
3 3
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 <import>help.xml</import> 6 <import>help.xml</import>
28 <configfiles> 28 <configfiles>
29 <configfile name="matchms_python_cli"> 29 <configfile name="matchms_python_cli">
30 python3 ${__tool_directory__}/matchms_filtering_wrapper.py \ 30 python3 ${__tool_directory__}/matchms_filtering_wrapper.py \
31 --spectra "$spectra" \ 31 --spectra "$spectra" \
32 --spectra_format "$spectra.ext" \ 32 --spectra_format "$spectra.ext" \
33 #if $normalise_intensities.is_true 33 #if $normalise_intensities_is_true == "TRUE"
34 -normalise_intensities \ 34 -normalise_intensities \
35 #end if 35 #end if
36 #if $default_filters.is_true 36 #if $default_filters_is_true == "TRUE"
37 -default_filters \ 37 -default_filters \
38 #end if 38 #end if
39 #if $clean_metadata.is_true 39 #if $clean_metadata_is_true == "TRUE"
40 -clean_metadata \ 40 -clean_metadata \
41 #end if 41 #end if
42 #if $relative_intensity.is_true 42 #if $relative_intensity.is_true == "TRUE"
43 -relative_intensity \ 43 -relative_intensity \
44 --from_intensity "$relative_intensity.from_intensity" \ 44 --from_intensity "$relative_intensity.from_intensity" \
45 --to_intensity "$relative_intensity.to_intensity" \ 45 --to_intensity "$relative_intensity.to_intensity" \
46 #end if 46 #end if
47 #if $mz_range.is_true 47 #if $mz_range.is_true == "TRUE"
48 -mz_range \ 48 -mz_range \
49 --from_mz "$mz_range.from_mz" \ 49 --from_mz "$mz_range.from_mz" \
50 --to_mz "$mz_range.to_mz" \ 50 --to_mz "$mz_range.to_mz" \
51 #end if
52 #if $require_smiles_is_true == "TRUE"
53 -require_smiles \
54 #end if
55 #if $require_inchi_is_true == "TRUE"
56 -require_inchi \
57 #end if
58 #if $reduce_to_top_n_peaks.is_true == "TRUE"
59 -reduce_to_top_n_peaks \
60 --n_max "$reduce_to_top_n_peaks.n_max" \
51 #end if 61 #end if
52 --output "$output" 62 --output "$output"
53 </configfile> 63 </configfile>
54 </configfiles> 64 </configfiles>
55 65
56 <inputs> 66 <inputs>
57 <param label="Spectra file" name="spectra" type="data" format="msp,mgf" help="Mass spectra file to be filtered." /> 67 <param label="Spectra file" name="spectra" type="data" format="msp,mgf" help="Mass spectra file to be filtered." />
58 68 <param name="normalise_intensities_is_true" label="Normalize intensities" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
59 <conditional name="normalise_intensities"> 69 help="Normalize intensities of peaks (and losses) to unit height."/>
60 <param name="is_true" label="Normalize intensities" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" 70 <param name="default_filters_is_true" label="Apply default filters" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
61 help="Normalize intensities of peaks (and losses) to unit height."/> 71 help="Collection of filters that are considered default and that do no require any (factory) arguments."/>
62 </conditional> 72 <param name="clean_metadata_is_true" label="Clean metadata" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
63 73 help="Apply all adding and cleaning filters if possible, so that the spectra have canonical metadata." />
64 <conditional name="default_filters">
65 <param name="is_true" label="Apply default filters" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
66 help="Collection of filters that are considered default and that do no require any (factory) arguments."/>
67 </conditional>
68
69 <conditional name="clean_metadata">
70 <param name="is_true" label="Clean metadata" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
71 help="Apply all adding and cleaning filters if possible, so that the spectra have canonical metadata." />
72 </conditional>
73 74
74 <conditional name="relative_intensity"> 75 <conditional name="relative_intensity">
75 <param name="is_true" label="Filter relative intensity" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" 76 <param name="is_true" label="Filter relative intensity" type="select"
76 help="Keep only peaks within set relative intensity range (keep if maximum >= intensity >= minimum)." /> 77 help="Keep only peaks within set relative intensity range (keep if maximum >= intensity >= minimum).">
78 <option value="FALSE" selected="true">FALSE</option>
79 <option value="TRUE">TRUE</option>
80 </param>
77 <when value="TRUE"> 81 <when value="TRUE">
78 <param label="Minimum intensity" name="from_intensity" value="0" type="float" help="Lower bound for intensity filter." /> 82 <param label="Minimum intensity" name="from_intensity" value="0" type="float" help="Lower bound for intensity filter." />
79 <param label="Maximum intensity" name="to_intensity" value="1" type="float" help="Upper bound for intensity filter." /> 83 <param label="Maximum intensity" name="to_intensity" value="1" type="float" help="Upper bound for intensity filter." />
80 </when> 84 </when>
85 <when value="FALSE"></when>
81 </conditional> 86 </conditional>
82 87
83 <conditional name="mz_range"> 88 <conditional name="mz_range">
84 <param name="is_true" label="Filter m/z range" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" 89 <param name="is_true" label="Filter m/z range" type="select"
85 help="Keep only peaks between set m/z range (keep if maximum >= m/z >= minimum)." /> 90 help="Keep only peaks between set m/z range (keep if maximum >= m/z >= minimum).">
91 <option value="FALSE" selected="true">FALSE</option>
92 <option value="TRUE">TRUE</option>
93 </param>
86 <when value="TRUE"> 94 <when value="TRUE">
87 <param label="Minimum m/z" name="from_mz" optional="true" type="float" help="Lower bound for m/z filter." /> 95 <param label="Minimum m/z" name="from_mz" optional="true" type="float" help="Lower bound for m/z filter." />
88 <param label="Maximum m/z" name="to_mz" optional="true" type="float" help="Upper bound for m/z filter." /> 96 <param label="Maximum m/z" name="to_mz" optional="true" type="float" help="Upper bound for m/z filter." />
89 </when> 97 </when>
98 <when value="FALSE"></when>
99 </conditional>
100
101 <param name="require_smiles_is_true" label="Require SMILES" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
102 help="Remove spectra that does not contain SMILES." />
103
104 <param name="require_inchi_is_true" label="Require INCHI" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
105 help="Remove spectra that does not contain INCHI." />
106
107 <conditional name="reduce_to_top_n_peaks">
108 <param name="is_true" label="Reduce to top n peaks" type="select"
109 help="Lowest intensity peaks will be removed when it has more peaks than desired.">
110 <option value="FALSE" selected="true">FALSE</option>
111 <option value="TRUE">TRUE</option>
112 </param>
113 <when value="TRUE">
114 <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." />
115 </when>
116 <when value="FALSE"></when>
90 </conditional> 117 </conditional>
91 118
92 </inputs> 119 </inputs>
93 120
94 <outputs> 121 <outputs>
96 </outputs> 123 </outputs>
97 124
98 <tests> 125 <tests>
99 <test> 126 <test>
100 <param name="spectra" value="filtering/input.msp" ftype="msp"/> 127 <param name="spectra" value="filtering/input.msp" ftype="msp"/>
101 <section name="normalise_intensities"> 128 <param name="normalise_intensities_is_true" value="TRUE"/>
102 <param name="is_true" value="TRUE"/>
103 </section>
104 <output name="output" file="filtering/normalise_intensities.msp" ftype="msp"/> 129 <output name="output" file="filtering/normalise_intensities.msp" ftype="msp"/>
105 </test> 130 </test>
106 <test> 131 <test>
107 <param name="spectra" value="filtering/input.msp" ftype="msp"/> 132 <param name="spectra" value="filtering/input.msp" ftype="msp"/>
108 <section name="default_filters"> 133 <param name="default_filters_is_true" value="TRUE"/>
109 <param name="is_true" value="TRUE"/>
110 </section>
111 <output name="output" file="filtering/default_filters.msp" ftype="msp"/> 134 <output name="output" file="filtering/default_filters.msp" ftype="msp"/>
112 </test> 135 </test>
113 <test> 136 <test>
114 <param name="spectra" value="filtering/input.msp" ftype="msp"/> 137 <param name="spectra" value="filtering/input.msp" ftype="msp"/>
115 <section name="clean_metadata"> 138 <param name="clean_metadata_is_true" value="TRUE"/>
116 <param name="is_true" value="TRUE"/>
117 </section>
118 <output name="output" file="filtering/clean_metadata.msp" ftype="msp"/> 139 <output name="output" file="filtering/clean_metadata.msp" ftype="msp"/>
119 </test> 140 </test>
120 <test> 141 <test>
121 <param name="spectra" value="filtering/input.msp" ftype="msp"/> 142 <param name="spectra" value="filtering/input.msp" ftype="msp"/>
122 <section name="relative_intensity"> 143 <section name="relative_intensity">
133 <param name="from_mz" value="300"/> 154 <param name="from_mz" value="300"/>
134 <param name="to_mz" value="800"/> 155 <param name="to_mz" value="800"/>
135 </section> 156 </section>
136 <output name="output" file="filtering/mz_range.msp" ftype="msp"/> 157 <output name="output" file="filtering/mz_range.msp" ftype="msp"/>
137 </test> 158 </test>
159 <test>
160 <param name="spectra" value="filtering/require_filter.msp" ftype="msp"/>
161 <param name="require_smiles_is_true" value="TRUE"/>
162 <output name="output" file="filtering/require_smiles_out.msp" ftype="msp"/>
163 </test>
164 <test>
165 <param name="spectra" value="filtering/require_filter.msp" ftype="msp"/>
166 <param name="require_inchi_is_true" value="TRUE"/>
167 <output name="output" file="filtering/require_inchi_out.msp" ftype="msp"/>
168 </test>
169 <test>
170 <param name="spectra" value="filtering/input.msp" ftype="msp"/>
171 <section name="reduce_to_top_n_peaks">
172 <param name="is_true" value="TRUE"/>
173 <param name="n_max" value="5"/>
174 </section>
175 <output name="output" file="filtering/reduce_to_top_n_peaks.msp" ftype="msp"/>
176 </test>
138 </tests> 177 </tests>
139 178
140 <help> 179 <help>
141 @HELP_matchms@ 180 @HELP_matchms@
142 </help> 181 </help>