Mercurial > repos > recetox > recetox_aplcms_unsupervised
diff aplcms_unsupervised.xml @ 1:52cec2e123fa draft
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
| author | recetox |
|---|---|
| date | Thu, 24 Sep 2020 00:15:56 +0000 |
| parents | bfe186af3dca |
| children | b0ba0287b76f |
line wrap: on
line diff
--- a/aplcms_unsupervised.xml Tue Aug 25 09:08:24 2020 +0000 +++ b/aplcms_unsupervised.xml Thu Sep 24 00:15:56 2020 +0000 @@ -1,70 +1,65 @@ -<tool id="recetox_aplcms_unsupervised" name="apLCMS - Unsupervised" version="@VERSION@"> - <macros> - <import>aplcms_macros.xml</import> - </macros> - - <expand macro="requirements" /> - - <command detect_errors="aggressive"><![CDATA[ - #set file_str = str('", "').join([str($f) for $f in $files]) - - Rscript - -e 'result <- apLCMS::unsupervised( - files = c("$file_str"), - min_exp = $noise_filtering.min_exp, - min_pres = $noise_filtering.min_pres, - min_run = $noise_filtering.min_run, - mz_tol = $noise_filtering.mz_tol, - baseline_correct = $noise_filtering.baseline_correct, - baseline_correct_noise_percentile = $noise_filtering.baseline_correct_noise_percentile, - intensity_weighted = $noise_filtering.intensity_weighted, - shape_model = "$feature_detection.shape_model", - BIC_factor = $feature_detection.BIC_factor, - peak_estim_method = "$feature_detection.peak_estim_method", - min_bandwidth = $feature_detection.min_bandwidth, - max_bandwidth = $feature_detection.max_bandwidth, - sd_cut = c($feature_detection.sd_cut_min, $feature_detection.sd_cut_max), - sigma_ratio_lim = c($feature_detection.sigma_ratio_lim_min, $feature_detection.sigma_ratio_lim_max), - component_eliminate = $feature_detection.component_eliminate, - moment_power = $feature_detection.moment_power, - align_chr_tol = $peak_alignment.align_chr_tol, - align_mz_tol = $peak_alignment.align_mz_tol, - max_align_mz_diff = $peak_alignment.max_align_mz_diff, - recover_mz_range = $weak_signal_recovery.recover_mz_range, - recover_chr_range = $weak_signal_recovery.recover_chr_range, - use_observed_range = $weak_signal_recovery.use_observed_range, - recover_min_count = $weak_signal_recovery.recover_min_count - )' - -e 'arrow::write_feather(result\$final_times, "$times")' - -e 'arrow::write_feather(result\$final_features, "$features")' - -e 'arrow::write_feather(result\$aligned_times, "$aligned_times")' - -e 'arrow::write_feather(result\$aligned_features, "$aligned_features")' - -e 'arrow::write_feather(result\$corrected_features, "$corrected_features")' - -e 'arrow::write_feather(result\$extracted_features, "$extracted_features")' - ]]></command> - - <expand macro="inputs"> - <expand macro="noise_filtering" /> - <expand macro="feature_detection" /> - <expand macro="peak_alignment" /> - <expand macro="weak_signal_recovery" /> - </expand> - - <outputs> - <data name="times" format="time_table.feather" /> - <data name="features" format="peak_table.feather" /> - <data name="aligned_times" format="time_table.feather" hidden="true" /> - <data name="aligned_features" format="peak_table.feather" hidden="true" /> - <data name="corrected_features" format="peak_table.feather" hidden="true" /> - <data name="extracted_features" format="peak_table.feather" hidden="true" /> - </outputs> - - <help> - This is the Unsupervised version of apLCMS which is not relying on any existing knowledge about metabolites or - any historically detected features. For such functionality please use the Hybrid version of apLCMS. - - @GENERAL_HELP@ - </help> - - <expand macro="citations" /> -</tool> \ No newline at end of file +<tool id="recetox_aplcms_unsupervised" name="apLCMS - Unsupervised" version="@TOOL_VERSION@+galaxy0"> + <macros> + <import>aplcms_macros.xml</import> + </macros> + + <expand macro="requirements" /> + + <command detect_errors="aggressive"><![CDATA[ + #set file_str = str('", "').join([str($f) for $f in $files]) + + Rscript + -e 'x <- apLCMS::unsupervised( + files = c("$file_str"), + min_exp = $noise_filtering.min_exp, + min_pres = $noise_filtering.min_pres, + min_run = $noise_filtering.min_run, + mz_tol = $noise_filtering.mz_tol, + baseline_correct = $noise_filtering.baseline_correct, + baseline_correct_noise_percentile = $noise_filtering.baseline_correct_noise_percentile, + intensity_weighted = $noise_filtering.intensity_weighted, + shape_model = "$feature_detection.shape_model", + BIC_factor = $feature_detection.BIC_factor, + peak_estim_method = "$feature_detection.peak_estim_method", + min_bandwidth = $feature_detection.min_bandwidth, + max_bandwidth = $feature_detection.max_bandwidth, + sd_cut = c($feature_detection.sd_cut_min, $feature_detection.sd_cut_max), + sigma_ratio_lim = c($feature_detection.sigma_ratio_lim_min, $feature_detection.sigma_ratio_lim_max), + component_eliminate = $feature_detection.component_eliminate, + moment_power = $feature_detection.moment_power, + align_chr_tol = $peak_alignment.align_chr_tol, + align_mz_tol = $peak_alignment.align_mz_tol, + max_align_mz_diff = $peak_alignment.max_align_mz_diff, + recover_mz_range = $weak_signal_recovery.recover_mz_range, + recover_chr_range = $weak_signal_recovery.recover_chr_range, + use_observed_range = $weak_signal_recovery.use_observed_range, + recover_min_count = $weak_signal_recovery.recover_min_count + )' + -e 'rhdf5::h5write(x\$final_peaks, "$peaks", "peaks")' + -e 'rhdf5::h5write(x\$aligned_peaks, "$peaks", "aligned_peaks")' + -e 'rhdf5::h5write(x\$corrected_features, "$peaks", "corrected_features")' + -e 'rhdf5::h5write(x\$extracted_features, "$peaks", "extracted_features")' + -e 'rhdf5::h5write(x\$aligned_mz_tolerance, "$peaks", "aligned_mz_tolerance")' + -e 'rhdf5::h5write(x\$aligned_rt_tolerance, "$peaks", "aligned_rt_tolerance")' + ]]></command> + + <expand macro="inputs"> + <expand macro="noise_filtering" /> + <expand macro="feature_detection" /> + <expand macro="peak_alignment" /> + <expand macro="weak_signal_recovery" /> + </expand> + + <outputs> + <data name="peaks" format="h5" /> + </outputs> + + <help> + This is the Unsupervised version of apLCMS which is not relying on any existing knowledge about metabolites or + any historically detected features. For such functionality please use the Hybrid version of apLCMS. + + @GENERAL_HELP@ + </help> + + <expand macro="citations" /> +</tool>