Mercurial > repos > recetox > recetox_aplcms_unsupervised

comparison recetox_aplcms_unsupervised.xml @ 10:6057540f65a9 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 46f606d8d234807e603b55eb2791f76663b551ee"
author recetox
date Thu, 21 Oct 2021 15:03:18 +0000
parents b18c2d014b28
children e0f77e03599e
comparison
equal deleted inserted replaced
9:b18c2d014b28 10:6057540f65a9
1 <tool id="recetox_aplcms_unsupervised" name="RECETOX apLCMS Unsupervised" version="@TOOL_VERSION@+galaxy1"> 1 <tool id="recetox_aplcms_unsupervised" name="RECETOX apLCMS Unsupervised" version="@TOOL_VERSION@+galaxy2">
2 <description>generate a feature table from LC/MS spectra</description> 2 <description>generate a feature table from LC/MS spectra</description>
3 <macros> 3 <macros>
4 <import>recetox_aplcms_macros.xml</import> 4 <import>recetox_aplcms_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
20 20
21 unsupervised_main( 21 unsupervised_main(
22 sample_files = c('$filenames_str'), 22 sample_files = c('$filenames_str'),
23 aligned_file = '${aligned_feature_sample_table}', 23 aligned_file = '${aligned_feature_sample_table}',
24 recovered_file = '${recovered_feature_sample_table}', 24 recovered_file = '${recovered_feature_sample_table}',
25 out_format = '$output_format.out_format',
25 min_exp = $noise_filtering.min_exp, 26 min_exp = $noise_filtering.min_exp,
26 min_pres = $noise_filtering.min_pres, 27 min_pres = $noise_filtering.min_pres,
27 min_run = $noise_filtering.min_run, 28 min_run = $noise_filtering.min_run,
28 mz_tol = $noise_filtering.mz_tol, 29 mz_tol = $noise_filtering.mz_tol,
29 baseline_correct = $noise_filtering.baseline_correct, 30 baseline_correct = $noise_filtering.baseline_correct,
53 <expand macro="inputs"> 54 <expand macro="inputs">
54 <expand macro="noise_filtering" /> 55 <expand macro="noise_filtering" />
55 <expand macro="feature_detection" /> 56 <expand macro="feature_detection" />
56 <expand macro="peak_alignment" /> 57 <expand macro="peak_alignment" />
57 <expand macro="weak_signal_recovery" /> 58 <expand macro="weak_signal_recovery" />
59 <expand macro="output_format" />
58 </expand> 60 </expand>
59 61
60 <outputs> 62 <outputs>
61 <expand macro="unsupervised_outputs" /> 63 <expand macro="unsupervised_outputs" />
62 </outputs> 64 </outputs>
63 65
64 <tests> 66 <tests>
65 <test> 67 <test>
66 <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml" /> 68 <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml" />
67 <output name="recovered_feature_sample_table" file="unsupervised_recovered_feature_sample_table.parquet" ftype="parquet"/> 69 <output name="recovered_feature_sample_table" file="unsupervised_recovered_feature_sample_table.parquet" ftype="parquet"/>
70 </test>
71 <test>
72 <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml" />
73 <section name="output_format">
74 <param name="out_format" value="recetox" />
75 </section>
76 <output name="recovered_feature_sample_table" file="unsupervised.recetox.parquet" ftype="parquet"/>
68 </test> 77 </test>
69 </tests> 78 </tests>
70 79
71 <help> 80 <help>
72 This is the Unsupervised version of apLCMS which is not relying on any existing knowledge about metabolites or 81 This is the Unsupervised version of apLCMS which is not relying on any existing knowledge about metabolites or