Mercurial > repos > recetox > matchms_filtering
view matchms_filtering.xml @ 4:357df6c47d92 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
author | recetox |
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date | Thu, 27 Apr 2023 12:01:48 +0000 |
parents | 1f2b13dbc0c8 |
children | a177ac3c752c |
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<tool id="matchms_filtering" name="matchMS filtering" version="@TOOL_VERSION@+galaxy0"> <description>filter and normalize mass spectrometry data</description> <macros> <import>macros.xml</import> </macros> <expand macro="creator"/> <requirements> <requirement type="package" version="@TOOL_VERSION@">matchms</requirement> <requirement type="package" version="1.1.4">pandas</requirement> </requirements> <environment_variables> <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable> </environment_variables> <command detect_errors="exit_code"><![CDATA[ sh ${matchms_python_cli} ]]> </command> <configfiles> <configfile name="matchms_python_cli"> python3 ${__tool_directory__}/matchms_filtering_wrapper.py \ --spectra "$spectra" \ --spectra_format "$spectra.ext" \ #if $normalise_intensities.is_true -normalise_intensities \ #end if #if $default_filters.is_true -default_filters \ #end if #if $clean_metadata.is_true -clean_metadata \ #end if #if $relative_intensity.is_true -relative_intensity \ --from_intensity "$relative_intensity.from_intensity" \ --to_intensity "$relative_intensity.to_intensity" \ #end if #if $mz_range.is_true -mz_range \ --from_mz "$mz_range.from_mz" \ --to_mz "$mz_range.to_mz" \ #end if --output "$output" </configfile> </configfiles> <inputs> <param label="Spectra file" name="spectra" type="data" format="msp,mgf" help="Mass spectra file to be filtered." /> <conditional name="normalise_intensities"> <param name="is_true" label="Normalize intensities" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" help="Normalize intensities of peaks (and losses) to unit height."/> </conditional> <conditional name="default_filters"> <param name="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."/> </conditional> <conditional name="clean_metadata"> <param name="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> <conditional name="relative_intensity"> <param name="is_true" label="Filter relative intensity" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" help="Keep only peaks within set relative intensity range (keep if maximum >= intensity >= minimum)." /> <when value="TRUE"> <param label="Minimum intensity" name="from_intensity" optional="true" type="float" help="Lower bound for intensity filter." /> <param label="Maximum intensity" name="to_intensity" optional="true" type="float" help="Upper bound for intensity filter." /> </when> </conditional> <conditional name="mz_range"> <param name="is_true" label="Filter m/z range" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" help="Keep only peaks between set m/z range (keep if maximum >= m/z >= minimum)." /> <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> </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"/> <section name="normalise_intensities"> <param name="is_true" value="TRUE"/> </section> <output name="output" file="filtering/normalise_intensities.msp" ftype="msp"/> </test> <test> <param name="spectra" value="filtering/input.msp" ftype="msp"/> <section name="default_filters"> <param name="is_true" value="TRUE"/> </section> <output name="output" file="filtering/default_filters.msp" ftype="msp"/> </test> <test> <param name="spectra" value="filtering/input.msp" ftype="msp"/> <section name="clean_metadata"> <param name="is_true" value="TRUE"/> </section> <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> </tests> <help><![CDATA[ Documentation For documentation on the tool see https://github.com/matchms/matchms/blob/master/README.rst and https://matchms.readthedocs.io/en/latest/. Upstream Tools +-----------+---------------+--------+-----------+ | Name | Output File | Format | Parameter | +===========+===============+========+===========+ | RAMClustR | Mass spectra | msp | references| +-----------+---------------+--------+-----------+ | RAMClustR | Mass spectra | msp | queries | +-----------+---------------+--------+-----------+ Downstream Tools The output is an msp file after applying the specified filters. ]]></help> <expand macro="citations"/> </tool>