Mercurial > repos > recetox > recetox_aplcms_two_step_hybrid
diff recetox_aplcms_two_step_hybrid.xml @ 0:c67f0eb6a909 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
author | recetox |
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date | Thu, 26 May 2022 16:47:09 +0000 |
parents | |
children | 87b669bdb51a |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/recetox_aplcms_two_step_hybrid.xml Thu May 26 16:47:09 2022 +0000 @@ -0,0 +1,111 @@ +<tool id="recetox_aplcms_two_step_hybrid" name="RECETOX apLCMS Two-Step Hybrid" version="@TOOL_VERSION@+galaxy0"> + <description>generate a feature table from LC/MS spectra of multi-batch experiments</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="creator"> + <person + givenName="Maksym" + familyName="Skoryk" + url="https://github.com/maximskorik" + identifier="0000-0003-2056-8018" /> + </expand> + + <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 $files]) + + two_step_hybrid_main( + sample_files = c('$filenames_str'), + known_table_file = '${known_table}', + updated_known_table_file = '${updated_known_table}', + recovered_file = '${recovered_feature_sample_table}', + aligned_file = '${aligned_feature_sample_table}', + out_format = '$output_format.out_format', + metadata = '${metadata}', + cluster = as.integer(Sys.getenv('GALAXY_SLOTS', unset = 1)), + min.within.batch.prop.detect = $multibatch_processing.min_within_batch_prop_detect, + min.within.batch.prop.report = $multibatch_processing.min_within_batch_prop_detect, + min.batch.prop = $multibatch_processing.min_batch_prop, + batch.align.mz.tol = $multibatch_processing.batch_align_mz_tol, + batch.align.chr.tol = $multibatch_processing.batch_align_chr_tol, + min.pres = $noise_filtering.min_pres, + min.run = $noise_filtering.min_run, + mz.tol = $noise_filtering.mz_tol, + baseline.correct.noise.percentile = $noise_filtering.baseline_correct_noise_percentile, + baseline.correct = $noise_filtering.baseline_correct, + intensity.weighted = $noise_filtering.intensity_weighted, + shape.model = '$feature_detection.shape_model', + peak.estim.method = '$feature_detection.peak_estim_method', + BIC.factor = $feature_detection.BIC_factor, + min.bw = $feature_detection.min_bandwidth, + max.bw = $feature_detection.max_bandwidth, + sd.cut = c($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.mz.tol = $peak_alignment.align_mz_tol, + align.chr.tol = $peak_alignment.align_chr_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, + match.tol.ppm = $history_db.match_tol_ppm, + new.feature.min.count = $history_db.new_feature_min_count + ) + ]]></configfile> + </configfiles> + + <expand macro="inputs"> + <param name="metadata" type="data" format="csv" label="metadata" help="A csv table with two columns, where the first column contains sample names and the second batch labels for each sample."/> + <expand macro="history_db"/> + <expand macro="noise_filtering" /> + <expand macro="feature_detection"/> + <expand macro="peak_alignment"/> + <expand macro="weak_signal_recovery"/> + <expand macro="multibatch_processing"/> + <expand macro="output_format"/> + </expand> + + <outputs> + <expand macro="unsupervised_outputs"/> + </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,mbr_test0_copy.mzml" ftype="mzml"/> + <param name="metadata" value="two_step_hybrid_info.csv" ftype="csv"/> + <param name="moment_power" value="2"/> + <param name="sd_cut_max" value="100"/> + <param name="sd_cut_min" value="0.1"/> + <param name="sigma_ratio_lim_max" value="20"/> + <param name="sigma_ratio_lim_min" value="0.05"/> + <section name="output_format"> + <param name="out_format" value="recetox"/> + </section> + <output name="recovered_feature_sample_table" file="two_step_hybrid.recetox.parquet" ftype="parquet"/> + </test> + </tests> + + <help> + <![CDATA[ + @HELP_two-step-hybrid@ + ]]> + </help> + + <expand macro="citations"> + <citation type="doi">10.1038/s41598-020-70850-0</citation> + </expand> +</tool>