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author | galaxyp |
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date | Mon, 11 Jul 2022 19:22:25 +0000 |
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<tool id="mqppep_anova" name="MaxQuant Phosphopeptide ANOVA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05" > <description>Runs ANOVA and KSEA for phosphopeptides.</description> <macros> <import>macros.xml</import> </macros> <edam_topics> <edam_topic>topic_0121</edam_topic><!-- proteomics --> <edam_topic>topic_3520</edam_topic><!-- proteomics experiment--> </edam_topics> <edam_operations> <edam_operation>operation_0276</edam_operation><!-- Analyse a network of protein interactions. --> <edam_operation>operation_0531</edam_operation><!-- Heat map generation --> <edam_operation>operation_2938</edam_operation><!-- Dendrogram generation --> <edam_operation>operation_2938</edam_operation><!-- Imputation --> <edam_operation>operation_3435</edam_operation><!-- Standardisation and normalisation --> <edam_operation>operation_3501</edam_operation><!-- Enrichment analysis --> <edam_operation>operation_3658</edam_operation><!-- Statistical inference --> </edam_operations> <expand macro="requirements"/> <!-- The weird invocation used here is because knitr and install_tinytex both need access to a writeable directory, but most directories in a biocontainer are read-only, so this builds a pseudo-home under /tmp --> <command detect_errors="exit_code"><![CDATA[ cp '$__tool_directory__/mqppep_anova_script.Rmd' . && cp '$__tool_directory__/mqppep_anova.R' . && Rscript mqppep_anova.R --inputFile '$input_file' --alphaFile '$alpha_file' --preproc_sqlite '$preproc_sqlite' --firstDataColumn $intensity_column_regex_f --imputationMethod $imputation.imputation_method #if $imputation.imputation_method == "random" --meanPercentile '$imputation.meanPercentile' --sdPercentile '$imputation.sdPercentile' #end if --regexSampleNames $sample_names_regex_f --regexSampleGrouping $sample_grouping_regex_f --imputedDataFile $imputed_data_file --imputedQNLTDataFile '$imp_qn_lt_file' --ksea_sqlite '$ksea_sqlite' --ksea_cutoff_threshold '$ksea_cutoff_threshold' --ksea_cutoff_statistic 'FDR' --reportFile '$report_file' --anova_ksea_metadata '$anova_ksea_metadata' ]]></command> <configfiles> <configfile name="sample_names_regex_f"> $sample_names_regex </configfile> <configfile name="sample_grouping_regex_f"> $sample_grouping_regex </configfile> <configfile name="intensity_column_regex_f"> $intensity_column_regex </configfile> </configfiles> <inputs> <param name="input_file" type="data" format="tabular" label="Filtered Phosphopeptide Intensities" help="Phosphopeptide intensities filtered for minimal quality. First column label 'Phosphopeptide'; sample-intensities must begin in column 10 and must have column labels to match argument [sample_names_regex]" /> <param name="alpha_file" type="data" format="tabular" label="ANOVA alpha cutoff level" help="ANOVA alpha cutoff values for significance testing: tabular data having one column and no header" /> <param name="preproc_sqlite" type="data" format="sqlite" label="preproc_sqlite dataset from mqppep_preproc" help="'preproc_sqlite' dataset produced by 'MaxQuant Phosphopeptide Preprocessing' tool" /> <param name="intensity_column_regex" type="text" value="^Intensity[^_]" label="Intensity-column pattern" help="Pattern matching columns that have peptide intensity data (PERL-compatible regular expression matching column label)" /> <!-- imputation_method <- c("group-median","median","mean","random")[1] --> <conditional name="imputation"> <param name="imputation_method" type="select" label="Imputation method" help="Impute missing values by (1) using median for each sample-group; (2) using median across all samples; (3) using mean across all samples; or (4) using randomly generated values having same std. dev. as across all samples (with mean specified by [meanPercentile])" > <option value="random" selected="true">random</option> <option value="group-median">group-median</option> <option value="median">median</option> <option value="mean">mean</option> </param> <when value="group-median" /> <when value="median" /> <when value="mean" /> <when value="random"> <param name="meanPercentile" type="integer" value="1" min="1" max="99" label="Mean percentile for random values" help="Percentile center of random values; range [1,99]" /> <param name="sdPercentile" type="float" value="1.0" label="Percentile std. dev. for random values" help="Standard deviation adjustment-factor for random values; real number. (1.0 means SD equal to the SD for the entire data set.)" /> </when> </conditional> <param name="sample_names_regex" type="text" value="\.\d+[A-Z]$" help="Pattern extracting sample-names from names of columns that have peptide intensity data (PERL-compatible regular expression)" label="Sample-extraction pattern"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> </valid> </sanitizer> </param> <param name="sample_grouping_regex" type="text" value="\d+" help="Pattern extracting sample-group from the sample-names that are extracted by 'Sample-extraction pattern' (PERL-compatible regular expression)" label="Group-extraction pattern"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> </valid> </sanitizer> </param> <param name="ksea_cutoff_threshold" type="float" value="0.05" label="KSEA threshold level" help="Maximum FDR to be used to score a kinase enrichment as significant" /> </inputs> <outputs> <data name="imputed_data_file" format="tabular" label="${input_file.name}.${imputation.imputation_method}-imputed_intensities" ></data> <data name="imp_qn_lt_file" format="tabular" label="${input_file.name}.${imputation.imputation_method}-imputed_QN_LT_intensities" ></data> <data name="anova_ksea_metadata" format="tabular" label="${input_file.name}.${imputation.imputation_method}-anova_ksea_metadata" ></data> <!-- <data name="report_file" format="html" label="${input_file.name}.${imputation.imputation_method}-imputed_report (download/unzip to view)" ></data> --> <data name="report_file" format="pdf" label="${input_file.name}.${imputation.imputation_method}-imputed_report" ></data> <data name="ksea_sqlite" format="sqlite" label="${input_file.name}..${imputation.imputation_method}-imputed_ksea_sqlite"> </data> </outputs> <tests> <test> <param name="input_file" ftype="tabular" value="test_input_for_anova.tabular"/> <param name="preproc_sqlite" ftype="sqlite" value="test_input_for_anova.sqlite"/> <param name="alpha_file" ftype="tabular" value="alpha_levels.tabular"/> <param name="intensity_column_regex" value="^Intensity[^_]"/> <param name="imputation_method" value="median"/> <param name="sample_names_regex" value="\.\d+[A-Z]$"/> <param name="sample_grouping_regex" value="\d+"/> <output name="imputed_data_file"> <assert_contents> <has_text text="Phosphopeptide" /> <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" /> <!-- missing missing observd missing observd observd --> <has_text_matching expression="pSQKQEEENPAEETGEEK.*8765300.8765300.8765300.8765300.2355900.14706000" /> </assert_contents> </output> <output name="imp_qn_lt_file"> <assert_contents> <has_text text="Phosphopeptide" /> <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" /> <!-- missing missing observed missing observed observed --> <has_text_matching expression="pSQKQEEENPAEETGEEK.*6.962256.*6.908828.*6.814580.*6.865411.*6.908828.*7.088909" /> <has_text text="pSQKQEEENPAEETGEEK" /> </assert_contents> </output> </test> <test> <param name="input_file" ftype="tabular" value="test_input_for_anova.tabular"/> <param name="preproc_sqlite" ftype="sqlite" value="test_input_for_anova.sqlite"/> <param name="alpha_file" ftype="tabular" value="alpha_levels.tabular"/> <param name="intensity_column_regex" value="^Intensity[^_]"/> <param name="imputation_method" value="mean"/> <param name="sample_names_regex" value="\.\d+[A-Z]$"/> <param name="sample_grouping_regex" value="\d+"/> <output name="imputed_data_file"> <assert_contents> <has_text text="Phosphopeptide" /> <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" /> <!-- missing missing observd missing observd observd --> <has_text_matching expression="pSQKQEEENPAEETGEEK.*6721601.6721601.8765300.6721601.2355900.14706000" /> </assert_contents> </output> <output name="imp_qn_lt_file"> <assert_contents> <has_text text="Phosphopeptide" /> <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" /> <!-- missing missing observed missing observed observed --> <has_text_matching expression="pSQKQEEENPAEETGEEK.*6.839850.*6.797424.*6.797424.*6.797424.*6.896609.*7.092451" /> </assert_contents> </output> </test> <test> <param name="input_file" ftype="tabular" value="test_input_for_anova.tabular"/> <param name="preproc_sqlite" ftype="sqlite" value="test_input_for_anova.sqlite"/> <param name="alpha_file" ftype="tabular" value="alpha_levels.tabular"/> <param name="intensity_column_regex" value="^Intensity[^_]"/> <param name="imputation_method" value="group-median"/> <param name="sample_names_regex" value="\.\d+[A-Z]$"/> <param name="sample_grouping_regex" value="\d+"/> <output name="imputed_data_file"> <assert_contents> <has_text text="Phosphopeptide" /> <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" /> <!-- missing missing observd missing observd observd --> <has_text_matching expression="pSQKQEEENPAEETGEEK.*8765300.8765300.8765300.5886074.2355900.14706000" /> </assert_contents> </output> <output name="imp_qn_lt_file"> <assert_contents> <has_text text="Phosphopeptide" /> <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" /> <!-- missing missing observed missing observed observed --> <has_text_matching expression="pSQKQEEENPAEETGEEK.*6.946112.*6.888985.*6.792137.*6.792137.*6.888985.*7.089555" /> </assert_contents> </output> </test> <test> <param name="input_file" ftype="tabular" value="test_input_for_anova.tabular"/> <param name="preproc_sqlite" ftype="sqlite" value="test_input_for_anova.sqlite"/> <param name="alpha_file" ftype="tabular" value="alpha_levels.tabular"/> <param name="intensity_column_regex" value="^Intensity[^_]"/> <param name="imputation_method" value="random"/> <param name="meanPercentile" value="1" /> <param name="sdPercentile" value="1.0" /> <param name="sample_names_regex" value="\.\d+[A-Z]$"/> <param name="sample_grouping_regex" value="\d+"/> <output name="imputed_data_file"> <assert_contents> <has_text text="Phosphopeptide" /> <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" /> <!-- observd observd observd --> <has_text_matching expression="pSQKQEEENPAEETGEEK.*8765300.*2355900.*4706000" /> </assert_contents> </output> <output name="imp_qn_lt_file"> <assert_contents> <has_text text="Phosphopeptide" /> <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" /> <has_text text="5.409549" /> <!-- log-transformed value for pTYVDPFTpYEDPNQAVR .1B --> <has_text text="6.464714" /> <!-- log-transformed value for pSQKQEEENPAEETGEEK .2A --> </assert_contents> </output> </test> </tests> <help><![CDATA[ ==================================================== Phopsphoproteomic Enrichment Pipeline ANOVA and KSEA ==================================================== **Input files** ``Filtered Phosphopeptide Intensities`` Phosphopeptides annotated with SwissProt and phosphosite metadata (in tabular format). This is the output from the "Phopsphoproteomic Enrichment Pipeline Merge and Filter" (``mqppep_mrgflt``) tool. ``ANOVA alpha cutoff level`` List of alpha cutoff values for significance testing; text file having one column and no header. For example: :: 0.2 0.1 0.05 **Input parameters** ``Intensity-column pattern`` First column of ``input_file`` having intensity values (integer or PERL-compatible regular expression matching column label). Default: **Intensity** ``Imputation method`` Impute missing values by: 1. ``group-median`` - use median for each sample-group; 2. ``mean`` - use mean across all samples; or 3. ``median`` - use median across all samples; 4. ``random`` - use randomly generated values where: - ``Mean percentile for random values`` specifies the percentile among non-missing values to be used as mean of random values, and - ``Percentile std. dev. for random values`` specifies the factor to be multiplied by the standard deviation among the non-missing values (across all samples) to determine the standard deviation of random values. ``Sample-extraction pattern`` PERL-compatible regular expression extracting the sample-name from the the name of a column of instensities (from ``input_file``) for one sample. - For example, ``"\.\d+[A-Z]$"`` applied to ``Intensity.splunge.10A`` would produce ``.10A`` - Note that *this is case sensitive* by default. ``Group-extraction pattern`` PERL-compatible regular expression extracting the sample-grouping from the sample-name that was extracted with ``sample_names_regex`` from a column of intensites (from ``input_file``). - For example, ``"\d+$"`` applied to ``.10A`` would produce ``10`` - Note that *this is case sensitive* by default. ``KSEA threshold level`` Specifies minimum FDR at which a kinase will be considered to be enriched; the default choice of 0.05 is arbitrary. **Outputs** ``imputed_intensities (input_file.imputation_method-imputed_intensities)`` Phosphopeptide MS intensities where missing values have been **imputed** by the chosen method, in tabular format. ``imputed_QN_LT_intensities (input_file.imputation_method-imputed_QN_LT_intensities)`` Phosphopeptide MS intensities where missing values have been **imputed** by the chosen method, quantile-normalized (**QN**), and log10-transformed (**LT**), in tabular format. ``report_file (input_file.imputation_method-imputed_report)`` Summary report for normalization, imputation, and **ANOVA**, in PDF format. ``anova_ksea_metadata (input_file.imputation_method-imputed_anova_ksea_metadata)`` Phosphopeptide metadata including ANOVA significance and KSEA enrichments. ``ksea_sqlite (input_file.imputation_method-imputed_ksea_sqlite)`` SQLite database for ad-hoc report creation. **Algorithm** The KSEA algorithm used here is as in the KSEAapp package as reported in [Wiredja 2017]. The code is adapted from "Danica D. Wiredja (2017). KSEAapp: Kinase-Substrate Enrichment Analysis. R package version 0.99.0." to work with output from the "MaxQuant Phosphopeptide Preprocessing" Galaxy tool. **Authors** ``Larry C. Cheng`` (`ORCiD 0000-0002-6922-6433 <https://orcid.org/0000-0002-6922-6433>`_) wrote the original script. ``Arthur C. Eschenlauer`` (`ORCiD 0000-0002-2882-0508 <https://orcid.org/0000-0002-2882-0508>`_) adapted the script to run in Galaxy. =================================== PERL-compatible regular expressions =================================== Note that the PERL-compatible regular expressions accepted by this tool are documented at http://rdrr.io/r/base/regex.html ]]></help> <citations> <!-- Cheng_2018 "Phosphopeptide Enrichment ..." PMID: 30124664 --> <citation type="doi">10.3791/57996</citation> <!-- Wiredja_2017 "The KSEA App ..." PMID: 28655153 --> <citation type="doi">10.1093/bioinformatics/btx415</citation> </citations> </tool>