Mercurial > repos > recetox > recetox_aplcms_generate_feature_table
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/help.xml Mon Feb 13 10:26:41 2023 +0000 @@ -0,0 +1,255 @@ +<macros> + +<token name="@GENERAL_HELP@"> +General Information +=================== + +Overview +-------- + +recetox-aplcms is a software package for peak detection in high resolution mass spectrometry (HRMS) data. +It supports reading .mzml files in raw profile mode and uses a bi-Gaussian chromatographic peak shape for feature detection and quantification. + +recetox-aplcms is based on the apLCMS package developed by Tianwei Yu at Emory University - see the citations and the apLCMS section beneath. +This version includes various software updates and is actively developed and maintained on `GitHub`_. +Please submit eventual bug reports as `issues`_ on the repository. + +.. _GitHub: https://github.com/RECETOX/recetox-aplcms +.. _issues: https://github.com/RECETOX/recetox-aplcms/issues/new + + +Workflow +-------- + +.. image:: https://raw.githubusercontent.com/RECETOX/galaxytools/aee0dd6cf6c05936269efe4337c50e27cc68e86b/tools/recetox_aplcms/images/scheme.png + :width: 2560 + :height: 788 + :scale: 40 + :alt: A picture of a workflow diagram. + +The individual steps of the recetox-aplcms package can be combined in 2 separate workflows processing HRMS data in an unsupervised manner or by including a-priori knowledge. +The workflows consist of the following building blocks: + +(1) remove noise - denoise the raw data and extract the EIC +(2) generate feature table - group features in EIC into peaks using peak-shape model +(3) compute clusters - compute mz and rt clusters across samples +(4) compute template - find the template for rt correction +(5) correct time - correct the rt across samples using splines +(6) align features - align identical features across samples +(7) recover weaker signals - recover missed features in samples based on the aligned features +(8) merge known table - add known features to detected features table and vice versa + +For detailed documentation on the individual steps please see the individual tool wrappers. + + +apLCMS (Original Reference) +--------------------------- + +apLCMS is a software which generates a feature table from a batch of LC/MS spectra. The m/z and retention time +tolerance levels are estimated from the data. A run-filter is used to detect peaks and remove noise. +Non-parametric statistical methods are used to find-tune peak selection and grouping. After retention time +correction, a feature table is generated by aligning peaks across spectra. For further information on apLCMS +please refer to https://mypage.cuhk.edu.cn/academics/yutianwei/apLCMS/. +</token> + +<token name="@REMOVE_NOISE_HELP@"> +recetox-aplcms - remove noise +============================= + +This tool is the first step of recetox-aplcms. +It removes noise from the raw data and performs a first clustering step of points with close m/z values into the extracted ion chromatograms (EICs). +Only peaks with a minimum elution length of `min_run` seconds are kept. + +Example Output +-------------- +The raw data points contained in the scans of the `mzml` file are filtered for noise and grouped into clusters based on m/z values. +See an example output in the table below. The `group_number` column indicates the cluster index. + ++----------------------+-------------------+-----------------------+--------------------+ +| mz | rt | intensity | group_number | ++======================+===================+=======================+====================+ +| 70.01060119055192 | 350.58654 | 21178.330810546875 | 5 | ++----------------------+-------------------+-----------------------+--------------------+ +| 70.02334120404554 | 130.175262 | 287869.5478515625 | 10 | ++----------------------+-------------------+-----------------------+--------------------+ +| 70.0287408273165 | 134.801352 | 60883.15185546875 | 11 | ++----------------------+-------------------+-----------------------+--------------------+ +| 70.02872416715464 | 183.991896 | 9201.574584960938 | 11 | ++----------------------+-------------------+-----------------------+--------------------+ +| ... | ... | ... | ... | ++----------------------+-------------------+-----------------------+--------------------+ +</token> + +<token name="@GENERATE_FEATURE_TABLE_HELP@"> +recetox-aplcms - generate feature table +======================================= +The second step in the recetox-aplcms workflow performing peak shape parameter estimation. + +This tool takes the grouped features created with `recetox-aplcms-remove-noise` and computes the peak shape in `rt` domain and integrates the peak area. + + +Example Output +-------------- +The output contains the `mz` and `rt` of the peaks as well as the standard deviation in both direction of the peak for the bi-gaussian peak shape. + ++----------------------+-------------------+-----------------+-------------------+----------------------+ +| mz | rt | sd1 | sd2 | area | ++======================+===================+=================+===================+======================+ +| 70.02317542938793 | 142.36033 | 11.436659559 | 14.592754933 | 4159269.24595184 | ++----------------------+-------------------+-----------------+-------------------+----------------------+ +| 70.02869594233522 | 205.48765 | 0.263230763 | 0.285101428707 | 8849767.11861127 | ++----------------------+-------------------+-----------------+-------------------+----------------------+ +| 78.04643252598305 | 294.01713 | 0.51677558617 | 1.317028944141 | 1333044.50659719 | ++----------------------+-------------------+-----------------+-------------------+----------------------+ +| ... | ... | ... | ... | ... | ++----------------------+-------------------+-----------------+-------------------+----------------------+ +</token> + +<token name="@COMPUTE_CLUSTERS_HELP@"> +recetox-aplcms - compute clusters +================================= + +Group features with `mz` and `rt` using tolerances within the tolerance into clusters, creating larger features from raw data points. +Custom tolerances for `mz` and `rt` are computed based on the given parameters. +The tool takes a collection of all detected features and computes the clusters over a global feature table, adding the `sample_id` and `cluster` columns to the table. + +Example Output +-------------- + ++----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+ +| mz | rt | sd1 | sd2 | area | sample_id | cluster | ++======================+===================+=================+===================+======================+=====================+===============+ +| 70.02317542938793 | 142.36033 | 11.436659559 | 14.592754933 | 4159269.245951841 | 21_qc_no_dil_milliq | 7 | ++----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+ +| 70.02869594233522 | 205.48765 | 0.263230763 | 0.285101428707 | 8849767.11861127 | 21_qc_no_dil_milliq | 9 | ++----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+ +| 78.04643252598305 | 294.01713 | 0.51677558617 | 1.317028944141 | 1333044.506597194 | 21_qc_no_dil_milliq | 13 | ++----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+ +| ... | ... | ... | ... | ... | ... | ... | ++----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+ +</token> + +<token name="@CORRECT_TIME_HELP@"> +recetox-aplcms - correct time +============================= + +Apply spline-based retention time correction to a feature table given the template table and the computed `mz` and `rt` tolerances. + +Example Output +-------------- +The output has the same format as `compute clusters` but the retention time values are corrected based on the template table. + ++----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+ +| mz | rt | sd1 | sd2 | area | sample_id | cluster | ++======================+===================+=================+===================+======================+=====================+===============+ +| 70.02317542938793 | 142.36033 | 11.436659559 | 14.592754933 | 4159269.245951841 | 21_qc_no_dil_milliq | 7 | ++----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+ +| 70.02869594233522 | 205.48765 | 0.263230763 | 0.285101428707 | 8849767.11861127 | 21_qc_no_dil_milliq | 9 | ++----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+ +| 78.04643252598305 | 294.01713 | 0.51677558617 | 1.317028944141 | 1333044.506597194 | 21_qc_no_dil_milliq | 13 | ++----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+ +| ... | ... | ... | ... | ... | ... | ... | ++----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+ +</token> +<token name="@COMPUTE_TEMPLATE_HELP@"> +recetox-aplcms - compute template +================================= +Compute the template from a set of feature tables, choosing the one with the most features as the template. +</token> + +<token name="@RECOVER_WEAKER_SIGNALS_HELP@"> +recetox-aplcms - recover weaker signals +======================================= +Second stage peak detection based on the aligned feature table from the `feature alignment` step. +If a feature is contained in the aligned feature table, this step revisits the raw data and searches +for this feature at the retention time obtained by mapping the corrected retention time back to the original sample. + +This recovers features which are present in a sample but might have been filtered out initially as noise due to low signal intensity. + +Example Output +-------------- +The table has the same format as the `compute clusters` output but might contain additional features which have been extracted based +on their presence in the aligned feature table. + ++----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+ +| mz | rt | sd1 | sd2 | area | sample_id | cluster | ++======================+===================+=================+===================+======================+=====================+===============+ +| 70.02317542938793 | 142.36033 | 11.436659559 | 14.592754933 | 4159269.245951841 | 21_qc_no_dil_milliq | 7 | ++----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+ +| 70.02869594233522 | 205.48765 | 0.263230763 | 0.285101428707 | 8849767.11861127 | 21_qc_no_dil_milliq | 9 | ++----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+ +| 78.04643252598305 | 294.01713 | 0.51677558617 | 1.317028944141 | 1333044.506597194 | 21_qc_no_dil_milliq | 13 | ++----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+ +| ... | ... | ... | ... | ... | ... | ... | ++----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+ +</token> + +<token name="@ALIGN_FEATURES_HELP@"> +recetox-aplcms - align features +=============================== +This step performs feature alignment after clustering and retention time correction. +The peaks clustered across samples are grouped based on the given tolerances to create an aligned feature table, connecting identical features across samples. +The parameter controls in how many samples a feature has to be detected at least in order to be included in the aligned feature table. + +Example Output +-------------- +The tool outputs 3 tables: the peak related `metadata`, the `retention times` and the `intensities` for all features across all samples. + +Metadata Table +~~~~~~~~~~~~~~ +The `npeaks` column denotes the number of peaks which have been grouped into this feature. The columns with the sample names indicate whether this feature is present in the sample. + ++-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+ +| id | mz | mzmin | mzmax | rt | rtmin | rtmax | npeaks | 21_qc_no_dil_milliq | 29_qc_no_dil_milliq | 8_qc_no_dil_milliq | ++=======+==============+==============+===============+================+===============+===============+===========+========================+========================+========================+ +| 1 | 70.03707021 | 70.037066 | 70.0370750 | 294.1038014 | 294.0634942 | 294.149985 | 3 | 1 | 1 | 1 | ++-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+ +| 2 | 70.06505677 | 70.065045 | 70.0650676 | 141.9560055 | 140.5762528 | 143.335758 | 2 | 1 | 0 | 1 | ++-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+ +| 57 | 78.04643252 | 78.046429 | 78.0464325 | 294.0063397 | 293.9406777 | 294.072001 | 2 | 1 | 1 | 0 | ++-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+ +| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ++-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+ + +Intensity Table +~~~~~~~~~~~~~~~ +This table contains the peak area for aligned features in all samples. + ++-------+------------------------+------------------------+------------------------+ +| id | 21_qc_no_dil_milliq | 29_qc_no_dil_milliq | 8_qc_no_dil_milliq | ++=======+========================+========================+========================+ +| 1 | 13187487.20482895 | 7957395.699119729 | 11700594.397257797 | ++-------+------------------------+------------------------+------------------------+ +| 2 | 2075168.6398983458 | 0 | 2574362.159289044 | ++-------+------------------------+------------------------+------------------------+ +| 57 | 2934524.4406785755 | 1333044.5065971944 | 0 | ++-------+------------------------+------------------------+------------------------+ +| ... | ... | ... | ... | ++-------+------------------------+------------------------+------------------------+ + +Retention Time Table +~~~~~~~~~~~~~~~~~~~~ +This table contains the retention times for all aligned features in all samples. + ++-------+------------------------+------------------------+------------------------+ +| id | 21_qc_no_dil_milliq | 29_qc_no_dil_milliq | 8_qc_no_dil_milliq | ++=======+========================+========================+========================+ +| 1 | 294.09792478513236 | 294.1499853056912 | 294.0634942428341 | ++-------+------------------------+------------------------+------------------------+ +| 2 | 140.57625284242982 | 0 | 143.33575827589172 | ++-------+------------------------+------------------------+------------------------+ +| 57 | 294.07200187644435 | 293.9406777222317 | 0 | ++-------+------------------------+------------------------+------------------------+ +| ... | ... | ... | ... | ++-------+------------------------+------------------------+------------------------+ +</token> + +<token name="@MERGE_KNOWN_TABLES_HELP@"> +recetox-aplcms - merge known table +================================== + +This tool allows merging the detected features back into the table of known features and vice versa. +It is used in the hybrid version of recetox-aplcms to augment the aligned feature table with the suspect peaks +and to augment this table with successfully detected features. +</token> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Feb 13 10:26:41 2023 +0000 @@ -0,0 +1,154 @@ +<macros> + <token name="@TOOL_VERSION@">0.10.1</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">r-recetox-aplcms</requirement> + <requirement type="package" version="2.5.2">pymzml</requirement> + </requirements> + </xml> + + <xml name="creator"> + <creator> + <person + givenName="Maksym" + familyName="Skoryk" + url="https://github.com/maximskorik" + identifier="0000-0003-2056-8018" /> + <person + givenName="Matej" + familyName="Troják" + url="https://github.com/xtrojak" + identifier="0000-0003-0841-2707" /> + <person + givenName="Martin" + familyName="Čech" + url="https://github.com/martenson" + identifier="0000-0002-9318-1781" /> + <person + givenName="Jiří" + familyName="Novotný" + url="https://github.com/xtracko" + identifier="0000-0001-5449-3523" /> + <person + givenName="Helge" + familyName="Hecht" + url="https://github.com/hechth" + identifier="0000-0001-6744-996X" /> + <organization + url="https://www.recetox.muni.cz/" + email="GalaxyToolsDevelopmentandDeployment@space.muni.cz" + name="RECETOX MUNI"/> + </creator> + </xml> + + <xml name="remove_noise_params"> + <param name="min_pres" type="float" value="0.5" label="min_pres" + help="The minimum proportion of presence in the time period for a series of signals grouped by m/z to be considered a peak." /> + <param name="min_run" type="float" value="12" label="min_run" + help="The minimum length of elution time for a series of signals grouped by m/z to be considered a peak." /> + <param name="mz_tol" type="float" value="1e-05" label="mz_tol" + help="The m/z tolerance level for the grouping of data points. This value is expressed as the fraction of the m/z value. This value, multiplied by the m/z value, becomes the cutoff level. The recommended value is the machine's nominal accuracy level. Divide the ppm value by 1e6. For FTMS, 1e-5 is recommended." /> + <param name="baseline_correct" type="float" value="0" label="baseline_correct" + help="After grouping the observations, the highest intensity in each group is found. If the highest is lower than this value, the entire group will be deleted. The default value is NA, in which case the program uses a percentile of the height of the noise groups. If given a value, the value will be used as the threshold, and baseline.correct.noise.percentile will be ignored." /> + <param name="intensity_weighted" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="intensity_weighted" + help="Whether to weight the local density by signal intensities in initial peak detection." /> + </xml> + + <xml name="generate_feature_table_params"> + <param name="sd_cut_min" type="float" value="0.01" label="sd_cut_min" + help="The minimum standard deviation of a feature to be not eliminated." /> + <param name="sd_cut_max" type="float" value="500" label="sd_cut_max" + help="The maximum standard deviation of a feature to be not eliminated." /> + <conditional name="shape"> + <param name="shape_model" type="select" display="radio" label="shape_model" + help="The mathematical model for the shape of a peak. There are two choices - bi-Gaussian and Gaussian. When the peaks are asymmetric, the bi-Gaussian is better."> + <option value="Gaussian">Gaussian</option> + <option value="bi-Gaussian" selected="true">bi-Gaussian</option> + </param> + <when value="bi-Gaussian"> + <param name="sigma_ratio_lim_min" type="float" value="0.01" label="sigma_ratio_lim_min" + help="The lower limit of the believed ratio range between the left-standard deviation and the right-standard deviation of the bi-Gaussian function used to fit the data." /> + <param name="sigma_ratio_lim_max" type="float" value="100" label="sigma_ratio_lim_max" + help="The upper limit of the believed ratio range between the left-standard deviation and the right-standard deviation of the bi-Gaussian function used to fit the data." /> + </when> + </conditional> + <param name="peak_estim_method" type="select" display="radio" label="peak_estim_method" + help="The estimation method for the bi-Gaussian peak model. Two possible values: moment and EM."> + <option value="moment" selected="true">Moment</option> + <option value="EM">EM</option> + </param> + <param name="moment_power" type="float" value="1" label="moment_power" + help="The power parameter for data transformation when fitting the bi-Gaussian or Gaussian mixture model in an EIC." /> + <param name="component_eliminate" type="float" value="0.01" label="component_eliminate" + help="In fitting mixture of bi-Gaussian (or Gaussian) model of an EIC, when a component accounts for a proportion of intensities less than this value, the component will be ignored." /> + <param name="BIC_factor" type="float" value="2.0" label="BIC_factor" + help="A factor influencing Bayesian information criterion (BIC) in estimation of RT peak shape. If the value is larger than 1, models with more peaks are penalized more." /> + </xml> + + <xml name="compute_clusters_params"> + <conditional name="tolerances_input_method"> + <param name="input_method" type="select" display="radio" label="Tolerances input method" + help="Tolerances can be entered directly or loaded from a file."> + <option value="direct" selected="true">direct</option> + <option value="file">file</option> + </param> + <when value="direct"> + <param name="mz_tol_relative" type="float" optional="true" label="mz_tol_relative" + help="Relative m/z tolerance to use for grouping features." /> + <param name="rt_tol_relative" type="float" optional="true" label="rt_tol_relative" + help="Relative retention time tolerance to use for grouping features." /> + </when> + <when value="file"> + <param label="Input tolerances values" name="input_tolerances" type="data" format="parquet" + help="Table containing tolerance values." /> + </when> + </conditional> + <param name="mz_tol_absolute" type="float" label="mz_tol_absolute" value="1e-05" + help="Absolute m/z tolerance to use for grouping features." /> + <param name="mz_max_diff" type="float" label="mz_max_diff" value="0.01" + help="Maximum difference between feature m/z values to belong to the same cluster." /> + </xml> + + <xml name="recover_weaker_params"> + <param name="mz_tol" type="float" value="1e-05" label="mz_tol" + help="The m/z tolerance level for the grouping of data points. This value is expressed as the + fraction of the m/z value. This value, multiplied by the m/z value, becomes the cutoff level. + The recommended value is the machine's nominal accuracy level. Divide the ppm value by 1e6. + For FTMS, 1e-5 is recommended." /> + <param name="recover_mz_range" type="float" optional="true" label="recover_mz_range" + help="The m/z around the feature m/z to search for observations. The default value is NA, in which + case 1.5 times the m/z tolerance in the aligned object will be used." /> + <param name="recover_rt_range" type="float" optional="true" label="recover_rt_range" + help="The retention time around the feature retention time to search for observations. + The default value is NA, in which case 0.5 times the retention time tolerance in the aligned + object will be used." /> + <param name="use_observed_range" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" + label="use_observed_range" help="If the value is true, the actual range of the observed locations of + the feature in all the spectra will be used." /> + <param name="recover_min_count" type="integer" value="3" label="recover_min_count" + help="The minimum number of raw data points to be considered as a true feature." /> + <param name="intensity_weighted" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" + label="intensity_weighted" help="Whether to weight the local density by signal intensities in initial peak detection." /> + </xml> + + <xml name="bandwidth_params"> + <param name="bandwidth" type="float" value="0.5" label="bandwidth" + help="A value between zero and one. Multiplying this value to the length of the signal along + the time axis helps determine the bandwidth in the kernel smoother used for peak identification." /> + <param name="min_bandwidth" type="float" optional="true" label="min_bandwidth" + help="The minimum bandwidth to use in the kernel smoother." /> + <param name="max_bandwidth" type="float" optional="true" label="max_bandwidth" + help="The maximum bandwidth to use in the kernel smoother." /> + </xml> + + <xml name="citations"> + <citations> + <citation type="doi">10.1093/bioinformatics/btp291</citation> + <citation type="doi">10.1186/1471-2105-11-559</citation> + <citation type="doi">10.1021/pr301053d</citation> + <citation type="doi">10.1093/bioinformatics/btu430</citation> + <citation type="doi">10.1038/s41598-020-70850-0</citation> + <yield /> + </citations> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mzml_id_getter.py Mon Feb 13 10:26:41 2023 +0000 @@ -0,0 +1,23 @@ +#!/usr/bin/env python + +import argparse +import sys + +from pymzml.run import Reader + + +def main(argv): + parser = argparse.ArgumentParser(description='Get run ID from an mzML file.') + parser.add_argument('mzml_file', help='Path to an mzML file to get run ID from.') + args = parser.parse_args() + + mzml = Reader(args.mzml_file) + id = mzml.info['run_id'] + + if id is not None: + with open("sample_name.txt", mode='x') as f: + f.write(id) + + +if __name__ == '__main__': + main(sys.argv[1:])
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/recetox_aplcms_generate_feature_table.xml Mon Feb 13 10:26:41 2023 +0000 @@ -0,0 +1,78 @@ +<tool id="recetox_aplcms_generate_feature_table" name="recetox-aplcms - generate feature table" version="@TOOL_VERSION@+galaxy0"> + <description>generate feature table from noise-removed HRMS profile data</description> + <macros> + <import>macros.xml</import> + <import>help.xml</import> + </macros> + <expand macro="creator"/> + <expand macro="requirements"/> + + <command detect_errors="aggressive"><![CDATA[ + Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")' + ]]></command> + <configfiles> + <configfile name="run_script"><![CDATA[ + profile <- load_data_from_parquet_file('$profile') + sample_name <- load_sample_name(profile) + + if(is.na(sample_name)) { + message("The file does not contain sample name.") + } + + feature_table <- prof.to.features( + profile = profile, + bandwidth = $bandwidth, + #if $min_bandwidth: + min_bandwidth = $min_bandwidth, + #else: + min_bandwidth = NA, + #end if + #if $max_bandwidth: + max_bandwidth = $max_bandwidth, + #else: + max_bandwidth = NA, + #end if + sd_cut = c($sd_cut_min, $sd_cut_max), + #if $shape.shape_model == "bi-Gaussian": + sigma_ratio_lim = c($shape.sigma_ratio_lim_min, $shape.sigma_ratio_lim_max), + #else: + sigma_ratio_lim = NA, + #end if + shape_model = "$shape.shape_model", + peak_estim_method = "$peak_estim_method", + component_eliminate = $component_eliminate, + moment_power = $moment_power, + BIC_factor = $BIC_factor, + do.plot = FALSE + ) + + feature_table <- save_sample_name(feature_table, sample_name) + save_data_as_parquet_file(feature_table, '$output_file') + ]]></configfile> + </configfiles> + + <inputs> + <param label="Input profile data" name="profile" type="data" format="parquet" + help="Mass spectrometry profile data." /> + <expand macro="bandwidth_params"/> + <expand macro="generate_feature_table_params"/> + </inputs> + + <outputs> + <data label="${tool.name} on ${on_string}" name="output_file" format="parquet" /> + </outputs> + + <tests> + + </tests> + + <help> + <![CDATA[ + @GENERATE_FEATURE_TABLE_HELP@ + + @GENERAL_HELP@ + ]]> + </help> + + <expand macro="citations"/> +</tool>
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<fileChecksum>23b8703ddaf744e69e1ba72be2584fd3df6f2dc4</fileChecksum> +</indexedmzML>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two_step_hybrid_info.csv Mon Feb 13 10:26:41 2023 +0000 @@ -0,0 +1,5 @@ +sample_name, batch +mbr_test0, 1 +mbr_test1, 1 +mbr_test2, 2 +mbr_test0_copy, 2
Binary file test-data/unsupervised_output/unsupervised_aligned_feature_sample_table.parquet has changed
Binary file test-data/unsupervised_output/unsupervised_recovered_feature_sample_table.parquet has changed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/utils.R Mon Feb 13 10:26:41 2023 +0000 @@ -0,0 +1,125 @@ +library(recetox.aplcms) + +get_env_sample_name <- function() { + sample_name <- Sys.getenv("SAMPLE_NAME", unset = NA) + if (nchar(sample_name) == 0) { + sample_name <- NA + } + if (is.na(sample_name)) { + message("The mzML file does not contain run ID.") + } + return(sample_name) +} + +save_sample_name <- function(df, sample_name) { + attr(df, "sample_name") <- sample_name + return(df) +} + +load_sample_name <- function(df) { + sample_name <- attr(df, "sample_name") + if (is.null(sample_name)) { + return(NA) + } else { + return(sample_name) + } +} + +save_data_as_parquet_file <- function(data, filename) { + arrow::write_parquet(data, filename) +} + +load_data_from_parquet_file <- function(filename) { + return(arrow::read_parquet(filename)) +} + +load_parquet_collection <- function(files) { + features <- lapply(files, arrow::read_parquet) + features <- lapply(features, tibble::as_tibble) + return(features) +} + +save_parquet_collection <- function(table, sample_names, subdir) { + dir.create(subdir) + for (i in seq_len(length(table$feature_tables))) { + filename <- file.path(subdir, paste0(subdir, "_", sample_names[i], ".parquet")) + feature_table <- as.data.frame(table$feature_tables[[i]]) + feature_table <- save_sample_name(feature_table, sample_names[i]) + arrow::write_parquet(feature_table, filename) + } +} + +sort_by_sample_name <- function(tables, sample_names) { + return(tables[order(sample_names)]) +} + +save_tolerances <- function(table, tol_file) { + mz_tolerance <- c(table$mz_tol_relative) + rt_tolerance <- c(table$rt_tol_relative) + arrow::write_parquet(data.frame(mz_tolerance, rt_tolerance), tol_file) +} + +get_mz_tol <- function(tolerances) { + return(tolerances$mz_tolerance) +} + +get_rt_tol <- function(tolerances) { + return(tolerances$rt_tolerance) +} + +save_aligned_features <- function(aligned_features, metadata_file, rt_file, intensity_file) { + save_data_as_parquet_file(aligned_features$metadata, metadata_file) + save_data_as_parquet_file(aligned_features$rt, rt_file) + save_data_as_parquet_file(aligned_features$intensity, intensity_file) +} + +select_table_with_sample_name <- function(tables, sample_name) { + sample_names <- lapply(tables, load_sample_name) + index <- which(sample_names == sample_name) + if (length(index) > 0) { + return(tables[[index]]) + } else { + stop(sprintf("Mismatch - sample name '%s' not present in %s", + sample_name, paste(sample_names, collapse = ", "))) + } +} + +select_adjusted <- function(recovered_features) { + return(recovered_features$adjusted_features) +} + +known_table_columns <- function() { + c("chemical_formula", "HMDB_ID", "KEGG_compound_ID", "mass", "ion.type", + "m.z", "Number_profiles_processed", "Percent_found", "mz_min", "mz_max", + "RT_mean", "RT_sd", "RT_min", "RT_max", "int_mean(log)", "int_sd(log)", + "int_min(log)", "int_max(log)") +} + +save_known_table <- function(table, filename) { + columns <- known_table_columns() + arrow::write_parquet(table$known_table[columns], filename) +} + +read_known_table <- function(filename) { + arrow::read_parquet(filename, col_select = known_table_columns()) +} + +save_pairing <- function(table, filename) { + df <- table$pairing %>% as_tibble() %>% setNames(c("new", "old")) + arrow::write_parquet(df, filename) +} + +join_tables_to_list <- function(metadata, rt_table, intensity_table) { + features <- new("list") + features$metadata <- metadata + features$intensity <- intensity_table + features$rt <- rt_table + return(features) +} + +validate_sample_names <- function(sample_names) { + if ((any(is.na(sample_names))) || (length(unique(sample_names)) != length(sample_names))) { + stop(sprintf("Sample names absent or not unique - provided sample names: %s", + paste(sample_names, collapse = ", "))) + } +}