Mercurial > repos > recetox > recetox_aplcms_hybrid
diff recetox_aplcms_hybrid.xml @ 4:c2213632ca71 draft
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
| author | recetox |
|---|---|
| date | Fri, 18 Jun 2021 13:54:00 +0000 |
| parents | |
| children | 3a8864093eac |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/recetox_aplcms_hybrid.xml Fri Jun 18 13:54:00 2021 +0000 @@ -0,0 +1,94 @@ +<tool id="recetox_aplcms_hybrid" name="apLCMS Hybrid" version="@TOOL_VERSION@+galaxy0"> + <description>generate a feature table from LC/MS spectra</description> + <macros> + <import>recetox_aplcms_macros.xml</import> + </macros> + + <expand macro="requirements" /> + + <command detect_errors="aggressive"><![CDATA[ + sh ${symlink_inputs} && + Rscript -e 'source("${__tool_directory__}/main.R")' -e 'source("${run_script}")' + ]]></command> + + <configfiles> + <configfile name="symlink_inputs"> + #for $infile in $files + ln -s '${infile}' '${infile.element_identifier}' + #end for + </configfile> + <configfile name="run_script"><![CDATA[ + #set filenames_str = str("', '").join([str($f.element_identifier) for $f in $files]) + + hybrid_main( + sample_files = c('$filenames_str'), + known_table_file = '${known_table}', + updated_known_table_file = '${updated_known_table}', + pairing_file = '${feature_known_table_pairing}', + aligned_file = '${aligned_feature_sample_table}', + recovered_file = '${recovered_feature_sample_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 = $weak_signal_recovery.recover_min_count, + cluster = as.integer(Sys.getenv('GALAXY_SLOTS', unset = 1)) + ) + ]]></configfile> + </configfiles> + + <expand macro="inputs"> + <expand macro="history_db" /> + <expand macro="noise_filtering" /> + <expand macro="feature_detection" /> + <expand macro="peak_alignment" /> + <expand macro="weak_signal_recovery" /> + </expand> + + <outputs> + <expand macro="unsupervised_outputs" /> + <data name="updated_known_table" format="parquet" label="${tool.name} updated_known_table on ${on_string}" /> + <data name="feature_known_table_pairing" format="tabular" label="${tool.name} feature_known_table_pairing on ${on_string}" hidden="true" /> + </outputs> + + <tests> + <test> + <param name="known_table" value="known_table.parquet" ftype="parquet" /> + <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml" /> + <output name="recovered_feature_sample_table" file="hybrid_recovered_feature_sample_table.parquet" ftype="parquet" compare="sim_size" delta="1000" /> + </test> + </tests> + + <help> + This is the Hybrid version of apLCMS which is incorporating the knowledge of known metabolites and historically + detected features on the same machinery to help detect and quantify lower-intensity peaks. + + CAUTION: To use such knowledge, especially historical data, you must keep using (1) the same chromatography + system (otherwise the retention time will not match), and (2) the same type of samples with similar extraction + technique, such as human serum. + + @GENERAL_HELP@ + </help> + + <expand macro="citations" /> +</tool>