Mercurial > repos > recetox > aplcms_hybrid
changeset 2:a1439454fe7f draft
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
| author | recetox |
|---|---|
| date | Mon, 19 Apr 2021 12:27:32 +0000 |
| parents | 87f5cf0baf34 |
| children | 2877bbac4c82 |
| files | aplcms_hybrid.xml aplcms_macros.xml |
| diffstat | 2 files changed, 43 insertions(+), 37 deletions(-) [+] |
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--- a/aplcms_hybrid.xml Tue Jan 26 17:11:11 2021 +0000 +++ b/aplcms_hybrid.xml Mon Apr 19 12:27:32 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="aplcms_hybrid" name="apLCMS - Hybrid" version="@TOOL_VERSION@+galaxy2"> +<tool id="aplcms_hybrid" name="apLCMS - Hybrid" version="@TOOL_VERSION@+galaxy3"> <macros> <import>aplcms_macros.xml</import> </macros> @@ -6,42 +6,48 @@ <expand macro="requirements" /> <command detect_errors="aggressive"><![CDATA[ - #set file_str = str("', '").join([str($f) for $f in $files]) + Rscript ${run_script} + ]]></command> + + <configfiles> + <configfile name="run_script"><![CDATA[ + #set file_str = str("', '").join([str($f) for $f in $files]) - Rscript - -e "x <- apLCMS::hybrid( - files = c('$file_str'), - known_table = apLCMS::load_known_table_from_hdf('$known_table'), - 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, - match_tol_ppm = $history_db.match_tol_ppm, - new_feature_min_count = $history_db.new_feature_min_count, - 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 = $weak_signal_recovery.recover_min_count, - cluster = as.integer(\${GALAXY_SLOTS:-1}) - )" - -e "apLCMS::save_peaks_to_hdf('$peaks', x)" - -e "apLCMS::save_known_table_to_hdf('$updated_known_table', x\\$updated_known_table)" ## NOTE the double \\ because we want cheetah and bash to ignore the $ character - ]]></command> + x <- apLCMS::hybrid( + files = c('$file_str'), + known_table = apLCMS::load_known_table_from_hdf('$known_table'), + 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, + match_tol_ppm = $history_db.match_tol_ppm, + new_feature_min_count = $history_db.new_feature_min_count, + 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 = $weak_signal_recovery.recover_min_count, + cluster = as.integer(Sys.getenv('GALAXY_SLOTS', unset = 1)) + ) + + apLCMS::save_peaks_to_hdf('$peaks', x) + apLCMS::save_known_table_to_hdf('$updated_known_table', x\$updated_known_table) ## NOTE the \ because we want cheetah to ignore the $ character + ]]></configfile> + </configfiles> <expand macro="inputs"> <expand macro="history_db" />
--- a/aplcms_macros.xml Tue Jan 26 17:11:11 2021 +0000 +++ b/aplcms_macros.xml Mon Apr 19 12:27:32 2021 +0000 @@ -131,7 +131,7 @@ tolerance levels are estimated from the data. A run-filter is used to detect peaks and remove noise. Non-parametric statistical methods are used to find-tune peak selection and grouping. After retention time correction, a feature table is generated by aligning peaks across spectra. For further information on apLCMS - please refer to http://web1.sph.emory.edu/apLCMS. + please refer to https://mypage.cuhk.edu.cn/academics/yutianwei/apLCMS/. </token> <xml name="citations">