Mercurial > repos > recetox > recetox_aplcms_recover_weaker_signals
diff recetox_aplcms_recover_weaker_signals.xml @ 0:067a308223e3 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
author | recetox |
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date | Fri, 10 Jun 2022 10:18:24 +0000 |
parents | |
children | f9fb9d8fb710 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/recetox_aplcms_recover_weaker_signals.xml Fri Jun 10 10:18:24 2022 +0000 @@ -0,0 +1,131 @@ +<tool id="recetox_aplcms_recover_weaker_signals" name="RECETOX apLCMS - recover weaker signals" version="@TOOL_VERSION@+galaxy0"> + <description>recover weaker signals from LC/MS spectra</description> + <macros> + <import>macros.xml</import> + <import>macros_split.xml</import> + </macros> + <expand macro="creator"/> + + <expand macro="requirements"/> + <command detect_errors="aggressive"><![CDATA[ + sh ${symlink_inputs} && + Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${__tool_directory__}/main.R")' -e 'source("${run_script}")' + ]]></command> + <configfiles> + <configfile name="symlink_inputs"> + #for $infile in $ms_files + ln -s '${infile}' '${infile.element_identifier}' + #end for + #for $infile in $extracted_files + ln -s '${infile}' '${infile.element_identifier}' + #end for + #for $infile in $corrected_files + ln -s '${infile}' '${infile.element_identifier}' + #end for + </configfile> + <configfile name="run_script"><![CDATA[ + #set filenames = str("', '").join([str($f.element_identifier) for $f in $ms_files]) + filenames <- sort_samples_by_acquisition_number(c('$filenames')) + + #set extracted_files = str("', '").join([str($f.element_identifier) for $f in $extracted_files]) + extracted <- load_features(c('$extracted_files')) + + #set corrected_files = str("', '").join([str($f.element_identifier) for $f in $corrected_files]) + corrected <- load_features(c('$corrected_files')) + + aligned <- load_aligned_features('$rt_cross_table_file', '$int_cross_table_file', '$tolerances_file') + + cluster <- as.integer(Sys.getenv('GALAXY_SLOTS', unset = 1)) + + recovered <- recover_signals(cluster, + filenames, + extracted, + corrected, + aligned, + $mz_tol, + $weak_signal_recovery.recover_mz_range, + $weak_signal_recovery.recover_chr_range, + $weak_signal_recovery.use_observed_range, + $min_bandwidth, + $max_bandwidth, + $weak_signal_recovery.recover_min_count + ) + + aligned_feature_sample_table <- create_feature_sample_table(aligned) + recovered_feature_sample_table <- create_feature_sample_table(recovered) + + save_all_features(recovered, filenames) + save_all_feature_tables(aligned_feature_sample_table, recovered_feature_sample_table, + '${aligned_feature_sample_table}', '${recovered_feature_sample_table}', + '$output_format.out_format') + ]]></configfile> + </configfiles> + + <inputs> + <param name="ms_files" type="data" format="mzdata,mzml,mzxml,netcdf" multiple="true" min="2" label="Input data" + help="Mass spectrometry file for peak extraction." /> + <param name="extracted_files" type="data" format="parquet" multiple="true" min="2" label="Input extracted feature samples" + help="Mass spectrometry files containing feature samples." /> + <param name="corrected_files" type="data" format="parquet" multiple="true" min="2" label="Input corrected feature samples" + help="Mass spectrometry file containing corrected feature samples." /> + <param name="tolerances_file" type="data" format="parquet" label="Input tolerances" help="TBD"/> + <param name="rt_cross_table_file" type="data" format="parquet" label="Input rt cross table" help="TBD"/> + <param name="int_cross_table_file" type="data" format="parquet" label="Input int cross table" help="TBD"/> + <expand macro="mz_tol_macro"/> + <param name="min_bandwidth" type="float" optional="true" label="min_bandwidth (optional)" + help="The minimum bandwidth to use in the kernel smoother." /> + <param name="max_bandwidth" type="float" optional="true" label="max_bandwidth (optional)" + help="The maximum bandwidth to use in the kernel smoother." /> + <expand macro="weak_signal_recovery"/> + <expand macro="output_format"/> + </inputs> + + <outputs> + <expand macro="unsupervised_outputs"> + <collection name="extracted_features" type="list" label="${tool.name} extracted_features on ${on_string}"> + <discover_datasets pattern="__designation__" directory="extracted" format="parquet" /> + </collection > + <collection name="corrected_features" type="list" label="${tool.name} corrected_features on ${on_string}"> + <discover_datasets pattern="__designation__" directory="corrected" format="parquet" /> + </collection > + </expand> + </outputs> + + <tests> + <test> + <param name="ms_files" value="mbr_test2.mzml,mbr_test1.mzml,mbr_test0.mzml" ftype="mzml"/> + <param name="extracted_files" ftype="parquet" + value="extracted_expected/extracted_0.parquet,extracted_expected/extracted_1.parquet,extracted_expected/extracted_2.parquet"/> + <param name="corrected_files" ftype="parquet" + value="corrected_expected/corrected_0.parquet,corrected_expected/corrected_1.parquet,corrected_expected/corrected_2.parquet"/> + <param name="tolerances_file" value="tolerances.parquet" ftype="parquet"/> + <param name="rt_cross_table_file" value="rt_cross_table.parquet" ftype="parquet"/> + <param name="int_cross_table_file" value="int_cross_table.parquet" ftype="parquet"/> + + <output name="recovered_feature_sample_table" ftype="parquet" + file="unsupervised_output/unsupervised_recovered_feature_sample_table.parquet"/> + <output name="aligned_feature_sample_table" ftype="parquet" + file="unsupervised_output/unsupervised_aligned_feature_sample_table.parquet"/> + <output_collection name="corrected_features" type="list"> + <element name="mbr_test0.parquet" file="unsupervised_output/corrected_features_0.parquet" ftype="parquet"/> + <element name="mbr_test1.parquet" file="unsupervised_output/corrected_features_1.parquet" ftype="parquet"/> + <element name="mbr_test2.parquet" file="unsupervised_output/corrected_features_2.parquet" ftype="parquet"/> + </output_collection> + <output_collection name="extracted_features" type="list"> + <element name="mbr_test0.parquet" file="unsupervised_output/extracted_features_0.parquet" ftype="parquet"/> + <element name="mbr_test1.parquet" file="unsupervised_output/extracted_features_1.parquet" ftype="parquet"/> + <element name="mbr_test2.parquet" file="unsupervised_output/extracted_features_2.parquet" ftype="parquet"/> + </output_collection> + </test> + </tests> + + <help> + <![CDATA[ + This is a tool which runs apLCMS recovery of weaker signals. + + @GENERAL_HELP@ + ]]> + </help> + + <expand macro="citations"/> +</tool>