# HG changeset patch # User eschen42 # Date 1497842758 14400 # Node ID caf0ce49b638372ccd3b334ccec26b5391854399 planemo upload for repository https://github.com/HegemanLab/w4mclstrpeakpics_galaxy_wrapper/tree/master commit 7ff527179eab946dd860be6b6a3e2c01b77d7dee diff -r 000000000000 -r caf0ce49b638 LICENSE --- /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. diff -r 000000000000 -r caf0ce49b638 README --- /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 diff -r 000000000000 -r caf0ce49b638 test-data/input_dataMatrix.tsv --- /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 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1970 +0000 +++ b/w4mclstrpeakpics.xml Sun Jun 18 23:25:58 2017 -0400 @@ -0,0 +1,283 @@ + + Visualize sample-cluster peaks + + + r-base + r-batch + r-reshape2 + r-sqldf + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + _figure + | (PDF) the output figure, described below. + | + +View Cluster_Peaks__table + | (tabular separated values) table of the values plotted in the upper-left graph in the output figure. + | + +View Cluster_Peaks__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 | ++------------------------------------+-----------------+ + + + + ]]> + + + 10.1021/ac051437y + 10.1093/bioinformatics/btu813 + + diff -r 000000000000 -r caf0ce49b638 w4mclstrpeakpics_0.98.1.tar.gz Binary file w4mclstrpeakpics_0.98.1.tar.gz has changed diff -r 000000000000 -r caf0ce49b638 w4mclstrpeakpics_wrapper.R --- /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)