Mercurial > repos > recetox > recetox_aplcms_hybrid

comparison recetox_aplcms_hybrid.xml @ 10:27853894eeac 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 15:03:51 +0000
parents d62f052efae6
children ab2b7948bdb7
comparison
equal deleted inserted replaced
9:d62f052efae6 10:27853894eeac
1 <tool id="recetox_aplcms_hybrid" name="RECETOX apLCMS Hybrid" version="@TOOL_VERSION@+galaxy1"> 1 <tool id="recetox_aplcms_hybrid" name="RECETOX apLCMS Hybrid" 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" />
23 known_table_file = '${known_table}', 23 known_table_file = '${known_table}',
24 updated_known_table_file = '${updated_known_table}', 24 updated_known_table_file = '${updated_known_table}',
25 pairing_file = '${feature_known_table_pairing}', 25 pairing_file = '${feature_known_table_pairing}',
26 aligned_file = '${aligned_feature_sample_table}', 26 aligned_file = '${aligned_feature_sample_table}',
27 recovered_file = '${recovered_feature_sample_table}', 27 recovered_file = '${recovered_feature_sample_table}',
28 out_format = '$output_format.out_format',
28 min_exp = $noise_filtering.min_exp, 29 min_exp = $noise_filtering.min_exp,
29 min_pres = $noise_filtering.min_pres, 30 min_pres = $noise_filtering.min_pres,
30 min_run = $noise_filtering.min_run, 31 min_run = $noise_filtering.min_run,
31 mz_tol = $noise_filtering.mz_tol, 32 mz_tol = $noise_filtering.mz_tol,
32 baseline_correct = $noise_filtering.baseline_correct, 33 baseline_correct = $noise_filtering.baseline_correct,
59 <expand macro="history_db" /> 60 <expand macro="history_db" />
60 <expand macro="noise_filtering" /> 61 <expand macro="noise_filtering" />
61 <expand macro="feature_detection" /> 62 <expand macro="feature_detection" />
62 <expand macro="peak_alignment" /> 63 <expand macro="peak_alignment" />
63 <expand macro="weak_signal_recovery" /> 64 <expand macro="weak_signal_recovery" />
65 <expand macro="output_format" />
64 </expand> 66 </expand>
65 67
66 <outputs> 68 <outputs>
67 <expand macro="unsupervised_outputs" /> 69 <expand macro="unsupervised_outputs" />
68 <data name="updated_known_table" format="parquet" label="${tool.name} updated_known_table on ${on_string}" /> 70 <data name="updated_known_table" format="parquet" label="${tool.name} updated_known_table on ${on_string}" />
72 <tests> 74 <tests>
73 <test> 75 <test>
74 <param name="known_table" value="known_table.parquet" ftype="parquet" /> 76 <param name="known_table" value="known_table.parquet" ftype="parquet" />
75 <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml" /> 77 <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml" />
76 <output name="recovered_feature_sample_table" file="hybrid_recovered_feature_sample_table.parquet" ftype="parquet" /> 78 <output name="recovered_feature_sample_table" file="hybrid_recovered_feature_sample_table.parquet" ftype="parquet" />
79 </test>
80 <test>
81 <param name="known_table" value="known_table.parquet" ftype="parquet" />
82 <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml" />
83 <section name="output_format">
84 <param name="out_format" value="recetox" />
85 </section>
86 <output name="recovered_feature_sample_table" file="hybrid.recetox.parquet" ftype="parquet" />
77 </test> 87 </test>
78 </tests> 88 </tests>
79 89
80 <help> 90 <help>
81 This is the Hybrid version of apLCMS which is incorporating the knowledge of known metabolites and historically 91 This is the Hybrid version of apLCMS which is incorporating the knowledge of known metabolites and historically