Mercurial > repos > recetox > recetox_aplcms_align_features
view recetox_aplcms_align_features.xml @ 1:b07fd3d7ffd0 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 699355cdf45b2157e9eea3962a01950d469fb0ba
author | recetox |
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date | Thu, 16 Jun 2022 10:26:58 +0000 |
parents | 57c644d3f24c |
children | abe783e0daca |
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<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> <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("${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 corrected_files = str("', '").join([str($f.element_identifier) for $f in $corrected_files]) corrected_features <- load_features(c('$corrected_files')) 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 = $peak_alignment.max_align_mz_diff, do.plot = FALSE ) save_aligned_features(aligned, "$rt_cross_table", "$int_cross_table", "$tolerances") ]]></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"/> </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)" /> </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. @GENERAL_HELP@ ]]> </help> <expand macro="citations"/> </tool>