Mercurial > repos > recetox > matchms_filtering
diff matchms_filtering.xml @ 20:86d265d2a334 draft
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 |
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--- a/matchms_filtering.xml Mon Apr 22 08:39:32 2024 +0000 +++ b/matchms_filtering.xml Thu May 30 18:08:27 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="matchms_filtering" name="matchms filtering" version="@TOOL_VERSION@+galaxy2" profile="21.09"> +<tool id="matchms_filtering" name="matchms filtering" version="@TOOL_VERSION@+galaxy1" profile="21.09"> <description>filter and normalize mass spectrometry data</description> <macros> @@ -49,12 +49,6 @@ --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 $derive_precursor_mz_from_parent_mass.is_true == "TRUE" -derive_precursor_mz_from_parent_mass \ --estimate_from_adduct "${derive_precursor_mz_from_parent_mass.estimate_from_adduct}" \ @@ -102,12 +96,6 @@ <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="derive_precursor_mz_from_parent_mass"> <param name="is_true" label="Derive precursor_mz from parent_mass" type="select" help="Derives the precursor_mz from the parent mass and adduct or charge."> @@ -173,16 +161,6 @@ <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_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_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"/>