Mercurial > repos > recetox > matchms_filtering
diff matchms_filtering.xml @ 6:13de8005adba draft
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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--- a/matchms_filtering.xml Tue Jun 27 14:25:01 2023 +0000 +++ b/matchms_filtering.xml Thu Oct 12 13:24:59 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="matchms_filtering" name="matchms filtering" version="@TOOL_VERSION@+galaxy0" profile="21.09"> +<tool id="matchms_filtering" name="matchms filtering" version="@TOOL_VERSION@+galaxy2" profile="21.09"> <description>filter and normalize mass spectrometry data</description> <macros> @@ -30,63 +30,90 @@ python3 ${__tool_directory__}/matchms_filtering_wrapper.py \ --spectra "$spectra" \ --spectra_format "$spectra.ext" \ - #if $normalise_intensities.is_true + #if $normalise_intensities_is_true == "TRUE" -normalise_intensities \ #end if - #if $default_filters.is_true + #if $default_filters_is_true == "TRUE" -default_filters \ #end if - #if $clean_metadata.is_true + #if $clean_metadata_is_true == "TRUE" -clean_metadata \ #end if - #if $relative_intensity.is_true + #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 + #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." /> - - <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> + <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="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" - help="Keep only peaks within set relative intensity range (keep if maximum >= intensity >= minimum)." /> + <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="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" - help="Keep only peaks between set m/z range (keep if maximum >= m/z >= minimum)." /> + <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> @@ -98,23 +125,17 @@ <tests> <test> <param name="spectra" value="filtering/input.msp" ftype="msp"/> - <section name="normalise_intensities"> - <param name="is_true" value="TRUE"/> - </section> + <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"/> - <section name="default_filters"> - <param name="is_true" value="TRUE"/> - </section> + <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"/> - <section name="clean_metadata"> - <param name="is_true" value="TRUE"/> - </section> + <param name="clean_metadata_is_true" value="TRUE"/> <output name="output" file="filtering/clean_metadata.msp" ftype="msp"/> </test> <test> @@ -135,6 +156,24 @@ </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>