Mercurial > repos > recetox > recetox_aplcms_unsupervised
comparison aplcms_unsupervised.xml @ 0:bfe186af3dca draft
"planemo upload commit 40818fd30d8cf43485c215e7ce10c16757024957-dirty"
| author | recetox |
|---|---|
| date | Tue, 25 Aug 2020 09:08:24 +0000 |
| parents | |
| children | 52cec2e123fa |
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| -1:000000000000 | 0:bfe186af3dca |
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| 1 <tool id="recetox_aplcms_unsupervised" name="apLCMS - Unsupervised" version="@VERSION@"> | |
| 2 <macros> | |
| 3 <import>aplcms_macros.xml</import> | |
| 4 </macros> | |
| 5 | |
| 6 <expand macro="requirements" /> | |
| 7 | |
| 8 <command detect_errors="aggressive"><![CDATA[ | |
| 9 #set file_str = str('", "').join([str($f) for $f in $files]) | |
| 10 | |
| 11 Rscript | |
| 12 -e 'result <- apLCMS::unsupervised( | |
| 13 files = c("$file_str"), | |
| 14 min_exp = $noise_filtering.min_exp, | |
| 15 min_pres = $noise_filtering.min_pres, | |
| 16 min_run = $noise_filtering.min_run, | |
| 17 mz_tol = $noise_filtering.mz_tol, | |
| 18 baseline_correct = $noise_filtering.baseline_correct, | |
| 19 baseline_correct_noise_percentile = $noise_filtering.baseline_correct_noise_percentile, | |
| 20 intensity_weighted = $noise_filtering.intensity_weighted, | |
| 21 shape_model = "$feature_detection.shape_model", | |
| 22 BIC_factor = $feature_detection.BIC_factor, | |
| 23 peak_estim_method = "$feature_detection.peak_estim_method", | |
| 24 min_bandwidth = $feature_detection.min_bandwidth, | |
| 25 max_bandwidth = $feature_detection.max_bandwidth, | |
| 26 sd_cut = c($feature_detection.sd_cut_min, $feature_detection.sd_cut_max), | |
| 27 sigma_ratio_lim = c($feature_detection.sigma_ratio_lim_min, $feature_detection.sigma_ratio_lim_max), | |
| 28 component_eliminate = $feature_detection.component_eliminate, | |
| 29 moment_power = $feature_detection.moment_power, | |
| 30 align_chr_tol = $peak_alignment.align_chr_tol, | |
| 31 align_mz_tol = $peak_alignment.align_mz_tol, | |
| 32 max_align_mz_diff = $peak_alignment.max_align_mz_diff, | |
| 33 recover_mz_range = $weak_signal_recovery.recover_mz_range, | |
| 34 recover_chr_range = $weak_signal_recovery.recover_chr_range, | |
| 35 use_observed_range = $weak_signal_recovery.use_observed_range, | |
| 36 recover_min_count = $weak_signal_recovery.recover_min_count | |
| 37 )' | |
| 38 -e 'arrow::write_feather(result\$final_times, "$times")' | |
| 39 -e 'arrow::write_feather(result\$final_features, "$features")' | |
| 40 -e 'arrow::write_feather(result\$aligned_times, "$aligned_times")' | |
| 41 -e 'arrow::write_feather(result\$aligned_features, "$aligned_features")' | |
| 42 -e 'arrow::write_feather(result\$corrected_features, "$corrected_features")' | |
| 43 -e 'arrow::write_feather(result\$extracted_features, "$extracted_features")' | |
| 44 ]]></command> | |
| 45 | |
| 46 <expand macro="inputs"> | |
| 47 <expand macro="noise_filtering" /> | |
| 48 <expand macro="feature_detection" /> | |
| 49 <expand macro="peak_alignment" /> | |
| 50 <expand macro="weak_signal_recovery" /> | |
| 51 </expand> | |
| 52 | |
| 53 <outputs> | |
| 54 <data name="times" format="time_table.feather" /> | |
| 55 <data name="features" format="peak_table.feather" /> | |
| 56 <data name="aligned_times" format="time_table.feather" hidden="true" /> | |
| 57 <data name="aligned_features" format="peak_table.feather" hidden="true" /> | |
| 58 <data name="corrected_features" format="peak_table.feather" hidden="true" /> | |
| 59 <data name="extracted_features" format="peak_table.feather" hidden="true" /> | |
| 60 </outputs> | |
| 61 | |
| 62 <help> | |
| 63 This is the Unsupervised version of apLCMS which is not relying on any existing knowledge about metabolites or | |
| 64 any historically detected features. For such functionality please use the Hybrid version of apLCMS. | |
| 65 | |
| 66 @GENERAL_HELP@ | |
| 67 </help> | |
| 68 | |
| 69 <expand macro="citations" /> | |
| 70 </tool> |