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comparison spec2vec_training.xml @ 1:989d1e182576 draft default tip

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
author recetox
date Tue, 27 Jun 2023 14:23:47 +0000
parents 4e4d3c8efb22
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0:4e4d3c8efb22 1:989d1e182576
1 <tool id="spec2vec_training" name="Spec2Vec Model Training" version="@TOOL_VERSION@-@TOOL_DEV_VERSION@+galaxy0" python_template_version="3.5" profile="21.05"> 1 <tool id="spec2vec_training" name="spec2vec model training" version="@TOOL_VERSION@+galaxy0" profile="21.09">
2 <description>Train a Spec2Vec model for mass spectra similarity scoring</description> 2 <description>Train a Spec2Vec model for mass spectra similarity scoring</description>
3 3
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="creator"/> 7 <expand macro="creator"/>
8 <expand macro="edam" />
8 9
9 <requirements> 10 <requirements>
10 <container type="docker">recetox/spec2vec:@COMMIT_SHA@</container> 11 <requirement type="package" version="@TOOL_VERSION@">spec2vec</requirement>
11 </requirements> 12 </requirements>
12 13
13 <command detect_errors="exit_code"><![CDATA[ 14 <command detect_errors="exit_code"><![CDATA[
14 ln -fs '${weights_filename}' '${weights_filename}.npy' && 15 ln -fs '${weights_filename}' '${weights_filename}.npy' &&
15 sh ${spec2vec_python_cli} 16 sh ${spec2vec_python_cli}
243 </assert_contents> 244 </assert_contents>
244 </output> 245 </output>
245 </test> 246 </test>
246 </tests> 247 </tests>
247 248
248 <help><![CDATA[ 249 <help>
249 **Spec2vec** is a spectral similarity score inspired by a natural language processing algorithm – Word2Vec. 250 **Spec2vec** is a spectral similarity score inspired by a natural language processing algorithm – Word2Vec.
250 Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. 251 Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra.
251 The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data. 252 The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data.
252 ]]></help> 253 </help>
253 254
254 <citations> 255 <expand macro="citations"/>
255 <citation type="doi">10.1371/journal.pcbi.1008724</citation> 256
256 </citations>
257 </tool> 257 </tool>