Mercurial > repos > recetox > matchms_filtering

comparison matchms_filtering.xml @ 13:ca5a8db023e1 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0
author recetox
date Thu, 14 Dec 2023 13:45:58 +0000
parents 039e7ab31836
children da15e8ea3b28
comparison
equal deleted inserted replaced
12:a4661ff81aa4 13:ca5a8db023e1
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@+galaxy1" 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>
52 #if $require_smiles_is_true == "TRUE" 52 #if $require_smiles_is_true == "TRUE"
53 -require_smiles \ 53 -require_smiles \
54 #end if 54 #end if
55 #if $require_inchi_is_true == "TRUE" 55 #if $require_inchi_is_true == "TRUE"
56 -require_inchi \ 56 -require_inchi \
57 #end if
58 #if $derive_precursor_mz_from_parent_mass.is_true == "TRUE"
59 -derive_precursor_mz_from_parent_mass \
60 --estimate_from_adduct "${derive_precursor_mz_from_parent_mass.estimate_from_adduct}" \
57 #end if 61 #end if
58 #if $reduce_to_top_n_peaks.is_true == "TRUE" 62 #if $reduce_to_top_n_peaks.is_true == "TRUE"
59 -reduce_to_top_n_peaks \ 63 -reduce_to_top_n_peaks \
60 --n_max "$reduce_to_top_n_peaks.n_max" \ 64 --n_max "$reduce_to_top_n_peaks.n_max" \
61 #end if 65 #end if
102 help="Remove spectra that does not contain SMILES." /> 106 help="Remove spectra that does not contain SMILES." />
103 107
104 <param name="require_inchi_is_true" label="Require INCHI" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" 108 <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." /> 109 help="Remove spectra that does not contain INCHI." />
106 110
111 <conditional name="derive_precursor_mz_from_parent_mass">
112 <param name="is_true" label="Derive precursor_mz from parent_mass" type="select"
113 help="Derives the precursor_mz from the parent mass and adduct or charge.">
114 <option value="FALSE" selected="true">FALSE</option>
115 <option value="TRUE">TRUE</option>
116 </param>
117 <when value="TRUE">
118 <param label="Estimate from adduct" name="estimate_from_adduct" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" />
119 </when>
120 <when value="FALSE"></when>
121 </conditional>
122
107 <conditional name="reduce_to_top_n_peaks"> 123 <conditional name="reduce_to_top_n_peaks">
108 <param name="is_true" label="Reduce to top n peaks" type="select" 124 <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."> 125 help="Lowest intensity peaks will be removed when it has more peaks than desired.">
110 <option value="FALSE" selected="true">FALSE</option> 126 <option value="FALSE" selected="true">FALSE</option>
111 <option value="TRUE">TRUE</option> 127 <option value="TRUE">TRUE</option>
172 <param name="is_true" value="TRUE"/> 188 <param name="is_true" value="TRUE"/>
173 <param name="n_max" value="5"/> 189 <param name="n_max" value="5"/>
174 </section> 190 </section>
175 <output name="output" file="filtering/reduce_to_top_n_peaks.msp" ftype="msp"/> 191 <output name="output" file="filtering/reduce_to_top_n_peaks.msp" ftype="msp"/>
176 </test> 192 </test>
193 <test>
194 <param name="spectra" value="filtering/derive_precursor_mz.msp" ftype="msp"/>
195 <section name="derive_precursor_mz_from_parent_mass">
196 <param name="is_true" value="TRUE"/>
197 <param name="estimate_from_adduct" value="TRUE"/>
198 </section>
199 <output name="output" file="filtering/derive_precursor_mz_out.msp" ftype="msp"/>
200 </test>
177 </tests> 201 </tests>
178 202
179 <help> 203 <help>
180 @HELP_matchms@ 204 @HELP_matchms@
181 </help> 205 </help>