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Merge pull request #517 from zargham-ahmad/issue507
Implemented dedicated require filters matchms tool
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,197 @@ | ||
| <tool id="matchms_remove_spectra" name="matchms remove spectra" version="@TOOL_VERSION@+galaxy0" profile="21.09"> | ||
| <description>Filters spectra based on metadata presence</description> | ||
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| <macros> | ||
| <import>macros.xml</import> | ||
| </macros> | ||
|
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| <expand macro="creator"/> | ||
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| <edam_operations> | ||
| <edam_operation>operation_3695</edam_operation> | ||
| </edam_operations> | ||
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| <expand macro="bio.tools"/> | ||
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| <requirements> | ||
| <requirement type="package" version="@TOOL_VERSION@">matchms</requirement> | ||
| </requirements> | ||
| <command detect_errors="exit_code"><![CDATA[ | ||
| python3 '${filter_spectra}' | ||
| ]]></command> | ||
|
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| <configfiles> | ||
| <configfile name="filter_spectra"> | ||
| from matchms.exporting import save_as_mgf, save_as_msp | ||
| from matchms.filtering.filter_utils.smile_inchi_inchikey_conversions import is_valid_inchi, is_valid_smiles, is_valid_inchikey | ||
| from matchms.filtering import require_compound_name, require_formula, require_precursor_mz, \ | ||
| require_retention_time, require_retention_index, require_valid_annotation | ||
| from matchms.importing import load_from_mgf, load_from_msp | ||
|
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| #set metadata_fields = str("', '").join([str($f) for $f in $metadata_fields]) | ||
| required_metadata = "$metadata_fields" | ||
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| if "$spectra.ext" == "msp": | ||
| spectra = list(load_from_msp("${spectra}")) | ||
| elif "$spectra.ext" == 'mgf': | ||
| spectra = list(load_from_mgf("${spectra}")) | ||
| else: | ||
| raise ValueError(f'File format {$spectra.ext} not supported for mass spectra file.') | ||
|
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| filtered_spectra = [] | ||
| removed_spectra = [] | ||
| keep = False | ||
|
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| for spectrum in spectra: | ||
| if 'smiles' in required_metadata: | ||
| keep = is_valid_smiles(spectrum.get('smiles')) | ||
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| if 'inchi' in required_metadata: | ||
| keep = is_valid_inchi(spectrum.get('inchi')) | ||
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| if 'inchikey' in required_metadata: | ||
| keep = is_valid_inchikey(spectrum.get('inchikey')) | ||
|
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| if 'precursor_mz' in required_metadata: | ||
| result = require_precursor_mz(spectrum) | ||
| if result is not None: | ||
| keep = True | ||
| else: | ||
| keep = False | ||
|
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| if 'valid_annotation' in required_metadata: | ||
| result = require_valid_annotation(spectrum) | ||
| if result is not None: | ||
| keep = True | ||
| else: | ||
| keep = False | ||
|
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| if 'formula' in required_metadata: | ||
| result = require_formula(spectrum) | ||
| if result is not None: | ||
| keep = True | ||
| else: | ||
| keep = False | ||
|
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| if 'compound_name' in required_metadata: | ||
| result = require_compound_name(spectrum) | ||
| if result is not None: | ||
| keep = True | ||
| else: | ||
| keep = False | ||
|
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| if 'retention_time' in required_metadata: | ||
| result = require_retention_time(spectrum) | ||
| if result is not None: | ||
| keep = True | ||
| else: | ||
| keep = False | ||
|
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| if 'retention_index' in required_metadata: | ||
| result = require_retention_index(spectrum) | ||
| if result is not None: | ||
| keep = True | ||
| else: | ||
| keep = False | ||
|
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| if keep: | ||
| filtered_spectra.append(spectrum) | ||
|
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| if "$spectra_removed" == "TRUE" and keep == False: | ||
| removed_spectra.append(spectrum) | ||
|
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| if "$spectra.ext" == "msp": | ||
| save_as_msp(filtered_spectra, "${output_filtered}") | ||
| save_as_msp(removed_spectra, "${output_removed}") | ||
| else: | ||
| save_as_mgf(filtered_spectra, "${output_filtered}") | ||
| save_as_mgf(removed_spectra, "${output_removed}") | ||
|
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| </configfile> | ||
| </configfiles> | ||
|
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| <inputs> | ||
| <param name="spectra" type="data" format="msp,mgf" label="Input Spectra File" help="Input file containing mass spectra"/> | ||
| <param name="metadata_fields" type="select" multiple="true" label="Metadata Fields" help="Select metadata fields required in the spectra"> | ||
| <option value="smiles">SMILES</option> | ||
| <option value="inchi">InChI</option> | ||
| <option value="inchikey">InChIKey</option> | ||
| <option value="formula">Formula</option> | ||
| <option value="retention_time">Retention Time</option> | ||
| <option value="retention_index">Retention Index</option> | ||
| <option value="precursor_mz">Precursor MZ</option> | ||
| <option value="valid_annotation">Valid Annotation</option> | ||
| <option value="compound_name">Compound Name</option> | ||
| </param> | ||
| <param name="spectra_removed" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Output Removed Spectra" help="Output spectra that were removed due to missing metadata"/> | ||
| </inputs> | ||
|
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| <outputs> | ||
| <data name="output_filtered" format_source="spectra" label="${tool.name} on ${on_string}: Filtered Spectra"/> | ||
| <data name="output_removed" format_source="spectra" label="${tool.name} on ${on_string}: Removed Spectra"> | ||
| <filter>spectra_removed</filter> | ||
| </data> | ||
| </outputs> | ||
|
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| <tests> | ||
| <test expect_num_outputs="1"> | ||
| <param name="spectra" value="remove_spectra/require_filter.msp" ftype="msp"/> | ||
| <param name="metadata_fields" value="smiles"/> | ||
| <output name="output_filtered" file="remove_spectra/require_smiles.msp" ftype="msp"/> | ||
| </test> | ||
| <test expect_num_outputs="2"> | ||
| <param name="spectra" value="remove_spectra/require_filter.msp" ftype="msp"/> | ||
| <param name="metadata_fields" value="inchi"/> | ||
| <param name="spectra_removed" value="TRUE"/> | ||
| <output name="output_filtered" file="remove_spectra/require_inchi.msp" ftype="msp"/> | ||
| <output name="output_removed" file="remove_spectra/require_inchi_removed_spectra.msp" ftype="msp"/> | ||
| </test> | ||
| <test expect_num_outputs="1"> | ||
| <param name="spectra" value="remove_spectra/require_filter.msp" ftype="msp"/> | ||
| <param name="metadata_fields" value="inchikey"/> | ||
| <output name="output_filtered" file="remove_spectra/require_inchikey.msp" ftype="msp"/> | ||
| </test> | ||
| <test expect_num_outputs="1"> | ||
| <param name="spectra" value="remove_spectra/require_filter.msp" ftype="msp"/> | ||
| <param name="metadata_fields" value="formula"/> | ||
| <output name="output_filtered" file="remove_spectra/require_formula.msp" ftype="msp"/> | ||
| </test> | ||
| <test expect_num_outputs="1"> | ||
| <param name="spectra" value="remove_spectra/require_filter.msp" ftype="msp"/> | ||
| <param name="metadata_fields" value="retention_time"/> | ||
| <output name="output_filtered" file="remove_spectra/require_retention_time.msp" ftype="msp"/> | ||
| </test> | ||
| <test expect_num_outputs="1"> | ||
| <param name="spectra" value="remove_spectra/require_filter.msp" ftype="msp"/> | ||
| <param name="metadata_fields" value="retention_index"/> | ||
| <output name="output_filtered" file="remove_spectra/require_retention_index.msp" ftype="msp"/> | ||
| </test> | ||
| <test expect_num_outputs="1"> | ||
| <param name="spectra" value="remove_spectra/require_filter.msp" ftype="msp"/> | ||
| <param name="metadata_fields" value="precursor_mz"/> | ||
| <output name="output_filtered" file="remove_spectra/require_precursor_mz.msp" ftype="msp"/> | ||
| </test> | ||
| <test expect_num_outputs="1"> | ||
| <param name="spectra" value="remove_spectra/require_filter.msp" ftype="msp"/> | ||
| <param name="metadata_fields" value="compound_name"/> | ||
| <output name="output_filtered" file="remove_spectra/require_compound_name.msp" ftype="msp"/> | ||
| </test> | ||
| <test expect_num_outputs="1"> | ||
| <param name="spectra" value="remove_spectra/require_filter.msp" ftype="msp"/> | ||
| <param name="metadata_fields" value="valid_annotation"/> | ||
| <output name="output_filtered"> | ||
| <assert_contents> | ||
| <has_n_lines n="0"/> | ||
| </assert_contents> | ||
| </output> | ||
| </test> | ||
| </tests> | ||
|
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| <help><![CDATA[ | ||
| This tool filters input mass spectra based on the presence of specified metadata fields. Spectra missing any of the selected metadata fields are optionally logged and output separately. | ||
| Valid Annotation filter removes spectra that are not fully annotated (correct and matching, smiles, inchi and inchikey) | ||
| ]]></help> | ||
|
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| <expand macro="citations"/> | ||
| </tool> |
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