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comparison matchms_filtering.xml @ 20:86d265d2a334 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
author recetox
date Thu, 30 May 2024 18:08:27 +0000
parents da15e8ea3b28
children 00e66c401366
comparison
equal deleted inserted replaced
19:c5076cc15e8c 20:86d265d2a334
1 <tool id="matchms_filtering" name="matchms filtering" version="@TOOL_VERSION@+galaxy2" 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>
47 #if $mz_range.is_true == "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 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 $derive_precursor_mz_from_parent_mass.is_true == "TRUE" 52 #if $derive_precursor_mz_from_parent_mass.is_true == "TRUE"
59 -derive_precursor_mz_from_parent_mass \ 53 -derive_precursor_mz_from_parent_mass \
60 --estimate_from_adduct "${derive_precursor_mz_from_parent_mass.estimate_from_adduct}" \ 54 --estimate_from_adduct "${derive_precursor_mz_from_parent_mass.estimate_from_adduct}" \
61 #end if 55 #end if
62 #if $reduce_to_top_n_peaks.is_true == "TRUE" 56 #if $reduce_to_top_n_peaks.is_true == "TRUE"
99 <param label="Minimum m/z" name="from_mz" optional="true" type="float" help="Lower bound for m/z filter." /> 93 <param label="Minimum m/z" name="from_mz" optional="true" type="float" help="Lower bound for m/z filter." />
100 <param label="Maximum m/z" name="to_mz" optional="true" type="float" help="Upper bound for m/z filter." /> 94 <param label="Maximum m/z" name="to_mz" optional="true" type="float" help="Upper bound for m/z filter." />
101 </when> 95 </when>
102 <when value="FALSE"></when> 96 <when value="FALSE"></when>
103 </conditional> 97 </conditional>
104
105 <param name="require_smiles_is_true" label="Require SMILES" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
106 help="Remove spectra that does not contain SMILES." />
107
108 <param name="require_inchi_is_true" label="Require INCHI" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
109 help="Remove spectra that does not contain INCHI." />
110 98
111 <conditional name="derive_precursor_mz_from_parent_mass"> 99 <conditional name="derive_precursor_mz_from_parent_mass">
112 <param name="is_true" label="Derive precursor_mz from parent_mass" type="select" 100 <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."> 101 help="Derives the precursor_mz from the parent mass and adduct or charge.">
114 <option value="FALSE" selected="true">FALSE</option> 102 <option value="FALSE" selected="true">FALSE</option>
171 <param name="to_mz" value="800"/> 159 <param name="to_mz" value="800"/>
172 </section> 160 </section>
173 <output name="output" file="filtering/mz_range.msp" ftype="msp"/> 161 <output name="output" file="filtering/mz_range.msp" ftype="msp"/>
174 </test> 162 </test>
175 <test> 163 <test>
176 <param name="spectra" value="filtering/require_filter.msp" ftype="msp"/>
177 <param name="require_smiles_is_true" value="TRUE"/>
178 <output name="output" file="filtering/require_out.msp" ftype="msp"/>
179 </test>
180 <test>
181 <param name="spectra" value="filtering/require_filter.msp" ftype="msp"/>
182 <param name="require_inchi_is_true" value="TRUE"/>
183 <output name="output" file="filtering/require_out.msp" ftype="msp"/>
184 </test>
185 <test>
186 <param name="spectra" value="filtering/input.msp" ftype="msp"/> 164 <param name="spectra" value="filtering/input.msp" ftype="msp"/>
187 <section name="reduce_to_top_n_peaks"> 165 <section name="reduce_to_top_n_peaks">
188 <param name="is_true" value="TRUE"/> 166 <param name="is_true" value="TRUE"/>
189 <param name="n_max" value="5"/> 167 <param name="n_max" value="5"/>
190 </section> 168 </section>