Mercurial > repos > recetox > recetox_aplcms_align_features
diff recetox_aplcms_align_features.xml @ 2:abe783e0daca draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
| author | recetox |
|---|---|
| date | Mon, 13 Feb 2023 10:26:59 +0000 |
| parents | b07fd3d7ffd0 |
| children | 1e2a13bcb5a7 |
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--- a/recetox_aplcms_align_features.xml Thu Jun 16 10:26:58 2022 +0000 +++ b/recetox_aplcms_align_features.xml Mon Feb 13 10:26:59 2023 +0000 @@ -1,91 +1,63 @@ -<tool id="recetox_aplcms_align_features" name="RECETOX apLCMS - align features" version="@TOOL_VERSION@+galaxy1"> - <description>align features from LC/MS spectra across samples</description> +<tool id="recetox_aplcms_align_features" name="recetox-aplcms - align features" version="@TOOL_VERSION@+galaxy0"> + <description>align peaks across samples</description> <macros> <import>macros.xml</import> - <import>macros_split.xml</import> + <import>help.xml</import> </macros> <expand macro="creator"/> + <expand macro="requirements"/> - <expand macro="requirements"/> <command detect_errors="aggressive"><![CDATA[ - sh ${symlink_inputs} && Rscript -e 'source("${__tool_directory__}/utils.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 $corrected_files - ln -s '${infile}' '${infile.element_identifier}' - #end for - </configfile> <configfile name="run_script"><![CDATA[ - #set filenames_str = str("', '").join([str($f.element_identifier) for $f in $ms_files]) - files_list <- sort_samples_by_acquisition_number(c('$filenames_str')) - sample_names <- get_sample_name(files_list) + #set filenames = str("', '").join([str($f) for $f in $files]) + feature_tables <- load_parquet_collection(c('$filenames')) + sample_names <- unlist(lapply(feature_tables, load_sample_name)) + + validate_sample_names(sample_names) + + ordering <- order(sample_names) + feature_tables <- feature_tables[ordering] + sample_names <- sample_names[ordering] - #set corrected_files = str("', '").join([str($f.element_identifier) for $f in $corrected_files]) - corrected_features <- load_features(c('$corrected_files')) + tolerances <- load_data_from_parquet_file('$input_tolerances') - aligned <- align_features( - sample_names = sample_names, - features = corrected_features, - min.exp = $min_exp, - mz.tol = $peak_alignment.align_mz_tol, - chr.tol = $peak_alignment.align_chr_tol, - find.tol.max.d = 10 * $mz_tol, - max.align.mz.diff = $peak_alignment.max_align_mz_diff, - do.plot = FALSE - ) + aligned_features <- create_aligned_feature_table( + features_table = dplyr::bind_rows(feature_tables), + min_occurrence = $min_occurrence, + sample_names = sample_names, + mz_tol_relative = get_mz_tol(tolerances), + rt_tol_relative = get_rt_tol(tolerances) + ) - save_aligned_features(aligned, "$rt_cross_table", "$int_cross_table", "$tolerances") + save_aligned_features(aligned_features, '$metadata_file', '$rt_file', '$intensity_file') ]]></configfile> </configfiles> <inputs> - <param name="ms_files" type="data_collection" collection_type="list" format="mzdata,mzml,mzxml,netcdf" - label="Input data collection" help="Mass spectrometry file for peak extraction." /> - <param name="corrected_files" type="data_collection" collection_type="list" format="parquet" - label="Input corrected feature samples collection" - help="Mass spectrometry files containing corrected feature samples." /> - <expand macro="mz_tol_macro"/> - <param name="min_exp" type="integer" min="1" value="2" label="min_exp" - help="If a feature is to be included in the final feature table, it must be present in at least this number of spectra." /> - <expand macro="peak_alignment"/> + <param name="files" type="data_collection" collection_type="list" format="parquet" + label="Clustered features" help="List of tables containing clustered features." /> + <param label="Input tolerances values" name="input_tolerances" type="data" format="parquet" + help="Table containing tolerance values." /> + <param name="min_occurrence" type="integer" min="2" value="2" label="min_occurrence" + help="A feature has to show up in at least this number of profiles to be included in the final result." /> </inputs> <outputs> - <data name="tolerances" format="parquet" label="${tool.name} on ${on_string} (tolerances)" /> - <data name="rt_cross_table" format="parquet" label="${tool.name} on ${on_string} (rt cross table)" /> - <data name="int_cross_table" format="parquet" label="${tool.name} on ${on_string} (int cross table)" /> + <data name="metadata_file" format="parquet" label="${tool.name} on ${on_string} (metadata table)"/> + <data name="rt_file" format="parquet" label="${tool.name} on ${on_string} (rt table)"/> + <data name="intensity_file" format="parquet" label="${tool.name} on ${on_string} (intensity table)"/> </outputs> <tests> - <test> - <param name="ms_files"> - <collection type="list"> - <element name="mbr_test0.mzml" value="mbr_test0.mzml"/> - <element name="mbr_test1.mzml" value="mbr_test1.mzml"/> - <element name="mbr_test2.mzml" value="mbr_test2.mzml"/> - </collection> - </param> - <param name="corrected_files"> - <collection type="list"> - <element name="corrected_features_0.parquet" value="corrected_expected/corrected_0.parquet"/> - <element name="corrected_features_1.parquet" value="corrected_expected/corrected_1.parquet"/> - <element name="corrected_features_2.parquet" value="corrected_expected/corrected_2.parquet"/> - </collection> - </param> - <output name="tolerances" file="tolerances.parquet" ftype="parquet"/> - <output name="rt_cross_table" file="rt_cross_table.parquet" ftype="parquet"/> - <output name="int_cross_table" file="int_cross_table.parquet" ftype="parquet"/> - </test> + </tests> <help> <![CDATA[ - This is a tool which runs apLCMS alignment of features. + @ALIGN_FEATURES_HELP@ @GENERAL_HELP@ ]]>