Mercurial > repos > recetox > matchms_filtering
view matchms_filtering.xml @ 8:11431418a707 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 13f4f7af12ec694a5f4ab7b3e52f46a4f67a245e
author | recetox |
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date | Sun, 19 Nov 2023 14:37:24 +0000 |
parents | 039e7ab31836 |
children | ca5a8db023e1 |
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<tool id="matchms_filtering" name="matchms filtering" version="@TOOL_VERSION@+galaxy0" profile="21.09"> <description>filter and normalize mass spectrometry data</description> <macros> <import>macros.xml</import> <import>help.xml</import> </macros> <expand macro="creator"/> <edam_operations> <edam_operation>operation_3695</edam_operation> </edam_operations> <expand macro="bio.tools"/> <requirements> <requirement type="package" version="@TOOL_VERSION@">matchms</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ sh ${matchms_python_cli} ]]> </command> <environment_variables> <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable> </environment_variables> <configfiles> <configfile name="matchms_python_cli"> python3 ${__tool_directory__}/matchms_filtering_wrapper.py \ --spectra "$spectra" \ --spectra_format "$spectra.ext" \ #if $normalise_intensities_is_true == "TRUE" -normalise_intensities \ #end if #if $default_filters_is_true == "TRUE" -default_filters \ #end if #if $clean_metadata_is_true == "TRUE" -clean_metadata \ #end if #if $relative_intensity.is_true == "TRUE" -relative_intensity \ --from_intensity "$relative_intensity.from_intensity" \ --to_intensity "$relative_intensity.to_intensity" \ #end if #if $mz_range.is_true == "TRUE" -mz_range \ --from_mz "$mz_range.from_mz" \ --to_mz "$mz_range.to_mz" \ #end if #if $require_smiles_is_true == "TRUE" -require_smiles \ #end if #if $require_inchi_is_true == "TRUE" -require_inchi \ #end if #if $reduce_to_top_n_peaks.is_true == "TRUE" -reduce_to_top_n_peaks \ --n_max "$reduce_to_top_n_peaks.n_max" \ #end if --output "$output" </configfile> </configfiles> <inputs> <param label="Spectra file" name="spectra" type="data" format="msp,mgf" help="Mass spectra file to be filtered." /> <param name="normalise_intensities_is_true" label="Normalize intensities" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" help="Normalize intensities of peaks (and losses) to unit height."/> <param name="default_filters_is_true" label="Apply default filters" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" help="Collection of filters that are considered default and that do no require any (factory) arguments."/> <param name="clean_metadata_is_true" label="Clean metadata" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" help="Apply all adding and cleaning filters if possible, so that the spectra have canonical metadata." /> <conditional name="relative_intensity"> <param name="is_true" label="Filter relative intensity" type="select" help="Keep only peaks within set relative intensity range (keep if maximum >= intensity >= minimum)."> <option value="FALSE" selected="true">FALSE</option> <option value="TRUE">TRUE</option> </param> <when value="TRUE"> <param label="Minimum intensity" name="from_intensity" value="0" type="float" help="Lower bound for intensity filter." /> <param label="Maximum intensity" name="to_intensity" value="1" type="float" help="Upper bound for intensity filter." /> </when> <when value="FALSE"></when> </conditional> <conditional name="mz_range"> <param name="is_true" label="Filter m/z range" type="select" help="Keep only peaks between set m/z range (keep if maximum >= m/z >= minimum)."> <option value="FALSE" selected="true">FALSE</option> <option value="TRUE">TRUE</option> </param> <when value="TRUE"> <param label="Minimum m/z" name="from_mz" optional="true" type="float" help="Lower bound for m/z filter." /> <param label="Maximum m/z" name="to_mz" optional="true" type="float" help="Upper bound for m/z filter." /> </when> <when value="FALSE"></when> </conditional> <param name="require_smiles_is_true" label="Require SMILES" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" help="Remove spectra that does not contain SMILES." /> <param name="require_inchi_is_true" label="Require INCHI" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" help="Remove spectra that does not contain INCHI." /> <conditional name="reduce_to_top_n_peaks"> <param name="is_true" label="Reduce to top n peaks" type="select" help="Lowest intensity peaks will be removed when it has more peaks than desired."> <option value="FALSE" selected="true">FALSE</option> <option value="TRUE">TRUE</option> </param> <when value="TRUE"> <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." /> </when> <when value="FALSE"></when> </conditional> </inputs> <outputs> <data label="${tool.name} on ${on_string}" name="output" format_source="spectra" /> </outputs> <tests> <test> <param name="spectra" value="filtering/input.msp" ftype="msp"/> <param name="normalise_intensities_is_true" value="TRUE"/> <output name="output" file="filtering/normalise_intensities.msp" ftype="msp"/> </test> <test> <param name="spectra" value="filtering/input.msp" ftype="msp"/> <param name="default_filters_is_true" value="TRUE"/> <output name="output" file="filtering/default_filters.msp" ftype="msp"/> </test> <test> <param name="spectra" value="filtering/input.msp" ftype="msp"/> <param name="clean_metadata_is_true" value="TRUE"/> <output name="output" file="filtering/clean_metadata.msp" ftype="msp"/> </test> <test> <param name="spectra" value="filtering/input.msp" ftype="msp"/> <section name="relative_intensity"> <param name="is_true" value="TRUE"/> <param name="from_intensity" value="0.3"/> <param name="to_intensity" value="0.9"/> </section> <output name="output" file="filtering/relative_intensity.msp" ftype="msp"/> </test> <test> <param name="spectra" value="filtering/input.msp" ftype="msp"/> <section name="mz_range"> <param name="is_true" value="TRUE"/> <param name="from_mz" value="300"/> <param name="to_mz" value="800"/> </section> <output name="output" file="filtering/mz_range.msp" ftype="msp"/> </test> <test> <param name="spectra" value="filtering/require_filter.msp" ftype="msp"/> <param name="require_smiles_is_true" value="TRUE"/> <output name="output" file="filtering/require_smiles_out.msp" ftype="msp"/> </test> <test> <param name="spectra" value="filtering/require_filter.msp" ftype="msp"/> <param name="require_inchi_is_true" value="TRUE"/> <output name="output" file="filtering/require_inchi_out.msp" ftype="msp"/> </test> <test> <param name="spectra" value="filtering/input.msp" ftype="msp"/> <section name="reduce_to_top_n_peaks"> <param name="is_true" value="TRUE"/> <param name="n_max" value="5"/> </section> <output name="output" file="filtering/reduce_to_top_n_peaks.msp" ftype="msp"/> </test> </tests> <help> @HELP_matchms@ </help> <expand macro="citations"/> </tool>