Mercurial > repos > eschen42 > w4mclstrpeakpics
changeset 0:caf0ce49b638 draft
planemo upload for repository https://github.com/HegemanLab/w4mclstrpeakpics_galaxy_wrapper/tree/master commit 7ff527179eab946dd860be6b6a3e2c01b77d7dee
author | eschen42 |
---|---|
date | Sun, 18 Jun 2017 23:25:58 -0400 |
parents | |
children | 17356c5fe43e |
files | LICENSE README test-data/input_dataMatrix.tsv test-data/input_sampleMetadata.tsv test-data/input_variableMetadata.tsv w4mclstrpeakpics.xml w4mclstrpeakpics_0.98.1.tar.gz w4mclstrpeakpics_wrapper.R |
diffstat | 8 files changed, 1329 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LICENSE Sun Jun 18 23:25:58 2017 -0400 @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) 2017 Hegeman Lab + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Sun Jun 18 23:25:58 2017 -0400 @@ -0,0 +1,2 @@ +# w4mclstrpeakpics_galaxy_wrapper +Planemo-based galaxy-tool-wrapper to wrap the w4mclstrpeakpics R package
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_dataMatrix.tsv Sun Jun 18 23:25:58 2017 -0400 @@ -0,0 +1,439 @@ + pool_RA3_01_211 pool_RA3_01_224 pool_RA3_01_237 pool_RA3_01_250 pool_RA3_01_263 pool_RA3_01_276 pool_RA3_01_289 pool_RA3_01_301 pool_RA3_01_303 pool_RA3_01_310 +M118T229 151737.251080355 198532.775418514 202853.239189335 315974.30584947 0 0 332058.387104673 256944.106907267 140973.935493046 135527.855932342 +M143.875T249 0 412526.569433742 285569.830287109 236342.179019013 431259.353940135 0 317192.069862169 320298.566354543 242481.566316342 247947.832383392 +M145.875T229 408250.603370209 468408.379888979 454438.683290455 513173.587949441 595715.750463455 0 663947.001934605 604712.142600508 369013.604852545 365567.431257037 +M156.875T518 861416.399762545 0 432356.201900483 585535.546437633 566219.852942064 419167.738152617 0 929341.651231975 871390.665554843 0 +M161.875T214 0 0 219224.982843631 0 0 126700.188444678 103625.914985189 0 0 133006.78886257 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_sampleMetadata.tsv Sun Jun 18 23:25:58 2017 -0400 @@ -0,0 +1,11 @@ +sampleMetadata class polarity sampleType injectionOrder batch +pool_RA3_01_211 pool unknown pool 211 1 +pool_RA3_01_224 pool unknown pool 224 1 +pool_RA3_01_237 pool unknown pool 237 1 +pool_RA3_01_250 pool unknown pool 250 1 +pool_RA3_01_263 pool unknown pool 263 1 +pool_RA3_01_276 pool unknown pool 276 1 +pool_RA3_01_289 pool unknown pool 289 1 +pool_RA3_01_301 pool unknown pool 301 1 +pool_RA3_01_303 pool unknown pool 303 1 +pool_RA3_01_310 pool unknown pool 310 1
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/w4mclstrpeakpics.xml Sun Jun 18 23:25:58 2017 -0400 @@ -0,0 +1,283 @@ +<tool id="w4mclstrpeakpics" name="View Cluster_Peaks" version="0.98.1"> + <description>Visualize sample-cluster peaks</description> + + <requirements> + <requirement type="package" version="3.3.1">r-base</requirement> + <requirement type="package" version="1.1_4">r-batch</requirement> + <requirement type="package" version="1.4.2">r-reshape2</requirement> + <requirement type="package" version="0.4_10">r-sqldf</requirement> + </requirements> + + <stdio> + <exit_code range="1:" level="fatal" /> + </stdio> + + + <command detect_errors="exit_code"><![CDATA[ + Rscript $__tool_directory__/w4mclstrpeakpics_wrapper.R + data_matrix_path '$dataMatrix_in' + variable_metadata_path '$variableMetadata_in' + sample_metadata_path '$sampleMetadata_in' + sample_selector_column_name '$sampleSelectorColumnName' + sample_selector_value '$sampleSelectorValue' + output_pdf '$outputFigure' + output_tsv '$outputTable' + output_rdata '$outputRdata' + r_package_archive $__tool_directory__/w4mclstrpeakpics_0.98.1.tar.gz + ; echo exit code $? + ]]></command> + + <inputs> + <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, separator: tab" /> + <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata columns, separator: tab" /> + <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata columns, separator: tab" /> + <param name="sampleSelectorColumnName" label="Selector-column name" type="text" value = "sampleType" help="Name of column containing selector values." /> + <param name="sampleSelectorValue" label="Selector value" type="text" value = "pool" help="Value to match in sample-selector column." /> + </inputs> + <outputs> + <data name="outputTable" label="${tool.name}_${sampleSelectorValue}_table" format="tabular" ></data> + <data name="outputFigure" label="${tool.name}_${sampleSelectorValue}_figure" format="pdf" ></data> + <data name="outputRdata" label="${tool.name}_${sampleSelectorValue}_RData" format="rdata" ></data> + </outputs> + + <tests> + <test> + <param name="dataMatrix_in" value="input_dataMatrix.tsv"/> + <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/> + <param name="variableMetadata_in" value="input_variableMetadata.tsv"/> + <param name="sampleSelectorColumnName" value="sampleType"/> + <param name="sampleSelectorValue" value="pool"/> + <output name="outputTable"> + <assert_contents> + <has_text text="0.464572" /> + <has_text text="0.114304" /> + <has_text text="0.131016" /> + <has_text text="0.0701871" /> + <has_text text="0.0661764" /> + <has_text text="0.0384358" /> + <has_text text="0.0614973" /> + <has_text text="0.0260695" /> + <has_text text="0.0193850" /> + <has_text text="0.00835561" /> + </assert_contents> + </output> + </test> + </tests> + + + + <help> + <![CDATA[ + +**Author** Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu) + +-------------------------------------------------------------------------- + + +**R package** + +The *w4mclstrpeakpics* package is available from the Hegeman lab github repository (https://github.com/HegemanLab/w4mclstrpeakpics/releases). + +----------------------------------------------------------------------------------------------------------------------------------------- + + +**Tool updates** + +See the **NEWS** section at the bottom of this page + +--------------------------------------------------- + +================================== +Visualize W4M sample-cluster peaks +================================== + +----------- +Description +----------- + +Produce a figure to assess the similarities and differences among peaks in a cluster of samples using XCMS-preprocessed data files as input. + +----------------- +Workflow Position +----------------- + + - Upstream tool category: Preprocessing + - Downstream tool categories: (Not applicable.) + +---------- +Motivation +---------- + +GC-MS1 and LC-MS1 experiments seek to resolve chemicals as features that have distinct chromatographic behavior and (after ionization) mass-to-charge ratio. +Data for a sample are collected as MS intensities, each of which is associated with a position on a 2D plane with dimensions of m/z ratio and chromatographic retention time. +Ideally, features would be sufficiently reproducible from sample-run to sample-run to identify features that are commmon among samples and those that differ. +However, the chromatographic retention time for a chemical can vary from one run to another. +In the Workflow4Metabolomics (W4M, [Giacomoni *et al.*, 2014]) "flavor" of Galaxy, the XCMS [Smith *et al.*, 2006] preprocessing tools provide for "retention time correction" to align features among samples. + +In a typical GC-MS or LC-MS experiment, a pooled sample is repeatedly injected for quality control. +Since this is the same mixture for each injection, the identified peaks would be expected to be identical for all injections. +However, the parameters for peak-picking can exacerbate injection-to-injection variation in performance of the experimental apparatus. +This tool exists to assess the variation in the peaks picked among pooled samples, replicates, or indeed any cluster of samples. + +----------- +Input files +----------- + ++---------------------------+------------+ +| File | Format | ++===========================+============+ +| Data matrix | tabular | ++---------------------------+------------+ +| Sample metadata | tabular | ++---------------------------+------------+ +| Variable metadata | tabular | ++---------------------------+------------+ + + +---------- +Parameters +---------- + +Data matrix file + | variable x sample **dataMatrix** (tabular separated values) file of the numeric data matrix, with . as decimal, and NA for missing values; the table must not contain metadata apart from row and column names; the row and column names must be identical to the rownames of the sample and variable metadata, respectively (see below) + | + +Sample metadata file + | sample x metadata **sampleMetadata** (tabular separated values) file of the numeric and/or character sample metadata, with . as decimal and NA for missing values + | + +Variable metadata file + | variable x metadata **variableMetadata** (tabular separated values) file of the numeric and/or character variable metadata, with . as decimal and NA for missing values + | + +Selector-column name (default = "sampleType") + | column of W4M/XCMS sampleMetadata holding selector string values. + | + +Selector value (default = "pool") + | value within selector column to identify samples for assessment. + | + +Include named classes (default = filter-out) + | *filter-in* - include only the named sample classes + | *filter-out* - exclude only the named sample classes + | + + +Column that names the sample-class (default = 'class') + | name of the column in sample metadata that has the values to be tested against the 'classes' input parameter + | + +Column that names the sample (default = 'sampleMetadata') + | name of the column in sample metadata that has the name of the sample + | + + +------------ +Output files +------------ + + +View Cluster_Peaks_<SelectorName>_figure + | (PDF) the output figure, described below. + | + +View Cluster_Peaks_<SelectorName>_table + | (tabular separated values) table of the values plotted in the upper-left graph in the output figure. + | + +View Cluster_Peaks_<SelectorName>_rdata + | (R data) RData containing all processing and plotting intermediates.. + | + + +------ +Graphs +------ + + +**The "Feature Number and Likelihood" graph** + +The upper left graph in the output figure shows the following: + +* The X axis reflects the number of samples in which a given feature is present (“the prevalance of a feature among the samples”). +* For open circles, the Y axis reflects the number of features having the number of samples reflected on the X axis. +* For solid triangles, the Y axis reflects the relative likelihood of features having the number of samples reflected on the X axis, calculated as + + .. math:: \frac{(number\hspace{1 mm}of\hspace{1 mm}features) (number\hspace{1 mm}of\hspace{1 mm}samples\hspace{1 mm}per\hspace{1 mm}feature)}{maximum(number\hspace{1 mm}of\hspace{1 mm}samples\hspace{1 mm}per\hspace{1 mm}feature)} + +Ideally, there would be an upward trend from left to right; if not, XCMS peak-picking parameters may need to be adjusted to suppress low-intensity “noise” peaks or to address peak-splitting. + + +**The "Peak Intensity" graph** + +The lower left graph in the output figure presents the data in the upper figure without summarization, so that “the eye” can do the interpretation. It shows the following: + +* The X axis reflects the number of samples in which a given feature is present (“the prevalance of a feature among the samples”). +* The Y axis reflects the intensity each sample for each feature having the number of samples reflected on the X axis. + +Ideally, there would be an upward trend from left to right, with more points on the right; if not, XCMS peak-picking parameters may need to be adjusted to suppress low-intensity “noise” peaks or to address peak-splitting. + + +**The "Symbol area/intensity reflect ion intensity" graph** + +The upper right graph in the output figure shows the following: + +* The X axis reflects the corrected retention time for each feature shown. +* The Y axis reflects the m/z for each feature shown. +* Symbol area reflects intensity for a feature for one sample. +* Overlapping symbols make the overlapping area darker, so the area and darkness reflect the aggregated intensity of a feature. (It is doubtful that a densitometer would be able to recover aggregate intensities accurately from this graph, but philosophically that is how this graph is designed.) +* The graph is not designed to communicate prevalence of a feature among the samples, but the hue of the symbol reflects the prevalance, albeit subtly. + +Consequently, if the graph has a lot of large, dark, blueish symbols for repeated runs of a pooled sample, there is strong evidence that the XCMS peak-picking parameters need adjustment to make peak-picking more consistent. + + +**The "Symbol size/shape reflects prevalence" graph** + +By contrast with the area/intensity graph, lower right graph’s primary purpose is to communicate prevalence of a feature among the samples. It`shows the following: + +* The X axis reflects the corrected retention time for each feature shown. +* The Y axis reflects the m/z for each feature shown. +* Symbol size and shape reflect the prevalence of a feature among the samples. +* “Vividness” of color reflects the aggregate intensity across all samples for a feature, in an attempt to draw attention to the more intense features. + +Consequently, if the graph has a lot of small, vivid symbols for repeated runs of a pooled sample, there is strong evidence that the XCMS peak-picking parameters need adjustment to make peak-picking more consistent. + + +--------------- +Working example +--------------- + +**Input files** + ++-------------------+----------------------------------------------------------------------------------------------------------------+ +| Input File | Download from URL | ++===================+================================================================================================================+ +| Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mclstrpeakpics/master/tests/testthat/input_dataMatrix.tsv | ++-------------------+----------------------------------------------------------------------------------------------------------------+ +| Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mclstrpeakpics/master/tests/testthat/input_sampleMetadata.tsv | ++-------------------+----------------------------------------------------------------------------------------------------------------+ +| Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclstrpeakpics/master/tests/testthat/input_variableMetadata.tsv | ++-------------------+----------------------------------------------------------------------------------------------------------------+ + +**Other input parameters** + ++------------------------------------+-----------------+ +| Input Parameter | Value | ++====================================+=================+ +| Selector-column name | sampleType | ++------------------------------------+-----------------+ +| Selector value | pool | ++------------------------------------+-----------------+ + + + + ]]> + </help> + <citations> + <citation type="doi">10.1021/ac051437y</citation> + <citation type="doi">10.1093/bioinformatics/btu813</citation> + </citations> + <!-- + vim:noet:sw=4:ts=4 +--> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/w4mclstrpeakpics_wrapper.R Sun Jun 18 23:25:58 2017 -0400 @@ -0,0 +1,134 @@ +#!/usr/bin/env Rscript + +library(batch) ## parseCommandArgs + +######## +# MAIN # +######## + +argVc <- unlist(parseCommandArgs(evaluate=FALSE)) + +##------------------------------ +## Initializing +##------------------------------ + +## options +##-------- + +strAsFacL <- options()$stringsAsFactors +options(stringsAsFactors = FALSE) + +## libraries +##---------- + +# begin HACK - suppress " Can't find a usable init.tcl ... probably means that Tcl wasn't installed properly" issue +library("gsubfn") +options(gsubfn.engine = "R") +# end HACK + +r_package_archive <- as.character(argVc["r_package_archive"]) +install.packages(r_package_archive, repos = NULL, type = "source") +suppressMessages( library("w4mclstrpeakpics") ) + +## constants +##---------- + +modNamC <- "w4mclsltrpeakpics" ## module name + +topEnvC <- environment() +flgC <- "\n" + +## functions +##---------- + + +## log file +##--------- + +my_print <- function(x, ...) { cat(c(x, ...))} + +my_print("\nStart of the '", modNamC, "' Galaxy module call: ", + format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="") + +## arguments +##---------- + +# files + +output_pdf <- as.character(argVc["output_pdf"]) +output_tsv <- as.character(argVc["output_tsv"]) +output_rdata <- as.character(argVc["output_rdata"]) +data_matrix_path <- as.character(argVc["data_matrix_path"]) +variable_metadata_path <- as.character(argVc["variable_metadata_path"]) +sample_metadata_path <- as.character(argVc["sample_metadata_path"]) + +# other parameters + +sample_selector_column_name <- as.character(argVc["sample_selector_column_name"]) +sample_selector_value <- as.character(argVc["sample_selector_value"]) + +##------------------------------ +## Computation +##------------------------------ + +# from 'demo(error.catching)' +tryCatch.W.E <- function(expr) { + W <- NULL + w.handler <- function(w){ + # warning handler + W <<- w + invokeRestart("muffleWarning") + } + list( + value = withCallingHandlers( + tryCatch(expr, error = function(e) e) + , warning = w.handler + ) + , warning = W + ) +} + +result <- cluster_peak_assessment( + sample_selector_column_name = sample_selector_column_name +, sample_selector_value = sample_selector_value +, sample_metadata_path = sample_metadata_path +, variable_metadata_path = variable_metadata_path +, data_matrix_path = data_matrix_path +, output_pdf = output_pdf +, output_tsv = output_tsv +, output_rdata = output_rdata +, failure_action = my_print +) + + +my_print("\nResult of '", modNamC, "' Galaxy module call to 'w4mclassfilter::w4m_filter_by_sample_class' R function: ", + as.character(result), "\n", sep = "") + +##-------- +## Closing +##-------- + +my_print("\nEnd of '", modNamC, "' Galaxy module call: ", + as.character(Sys.time()), "\n", sep = "") + +#sink() + +if (!file.exists(output_pdf)) { + print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, output_pdf)) +} + +if (!file.exists(output_tsv)) { + print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, output_tsv)) +} + +if (!file.exists(output_rdata)) { + print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, output_rdata)) +} + +# 'stop' causes Rscript to return a non-zero exit code +if( !result ) { + stop(sprintf("ERROR %s::w4m_filter_by_sample_class - method failed", modNamC)) +} + +# exit with status code zero +q(save = "no", status = 0, runLast = FALSE)