| Previous changeset 13:c18040b6e8b9 (2019-10-24) Next changeset 15:f9cb2244fd01 (2021-03-11) |
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Commit message:
"planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc" |
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modified:
LICENSE README w4mclassfilter.xml w4mclassfilter_wrapper.R |
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| diff -r c18040b6e8b9 -r 87ec0d3c2266 LICENSE --- a/LICENSE Thu Oct 24 10:21:23 2019 -0400 +++ b/LICENSE Fri Jan 03 11:07:39 2020 -0500 |
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| @@ -1,6 +1,6 @@ MIT License -Copyright (c) 2017 Hegeman Lab +Copyright (c) 2017-2020 Adrian D. Hegeman's Laboratory Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal |
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| diff -r c18040b6e8b9 -r 87ec0d3c2266 README --- a/README Thu Oct 24 10:21:23 2019 -0400 +++ b/README Fri Jan 03 11:07:39 2020 -0500 |
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| @@ -1,8 +1,17 @@ Galaxy Wrapper for the w4mclassfilter R Package -<https://doi.org/10.5281/zenodo.1034793> +https://doi.org/10.5281/zenodo.1034793 + +This is a Galaxy tool-wrapper +https://docs.galaxyproject.org/en/latest/dev/schema.htm + +to wrap the w4mclassfilter R package +https://github.com/HegemanLab/w4mclassfilter -This is a Galaxy tool-wrapper <https://docs.galaxyproject.org/en/latest/dev/schema.htm> -to wrap the w4mclassfilter R package <https://github.com/HegemanLab/w4mclassfilter> -for use with the Workflow4Metabolomics <http://workflow4metabolomics.org/> -flavor of Galaxy <https://galaxyproject.org/>. -The tool is built with Planemo <http://planemo.readthedocs.io/en/latest/>. +for use with the Workflow4Metabolomics +https://workflow4metabolomics.org + +flavor of Galaxy +https://galaxyproject.org + +The tool is tested and deployed with Planemo +https://planemo.readthedocs.io/en/latest |
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| diff -r c18040b6e8b9 -r 87ec0d3c2266 w4mclassfilter.xml --- a/w4mclassfilter.xml Thu Oct 24 10:21:23 2019 -0400 +++ b/w4mclassfilter.xml Fri Jan 03 11:07:39 2020 -0500 |
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| b'@@ -1,40 +1,49 @@\n-<tool id="w4mclassfilter" name="W4m Data Subset" version="0.98.14">\n- <description>Filter W4m data by values or metadata</description>\n- <!-- Here is the hyphenation standard that I *try* to apply consistently in my documentation: http://www.sandranoonan.com/dont-let-hyphenation-drive-crazy/ -->\n+<tool id="w4mclassfilter" name="W4m Data Subset" version="0.98.18">\n+ <description>Filter W4M data by values or metadata</description>\n+ <!-- Here is the hyphenation standard that I *try* to apply consistently in my documentation: \n+ https://web.archive.org/web/20161014025757/http://www.sandranoonan.com/dont-let-hyphenation-drive-crazy/\n+ -->\n <requirements>\n- <requirement type="package" version="3.6.1">r-base</requirement>\n+ <requirement type="package" version="3.6.2">r-base</requirement>\n <requirement type="package" version="1.1_5">r-batch</requirement>\n- <requirement type="package" version="0.98.14">w4mclassfilter</requirement>\n+ <requirement type="package" version="0.98.18">w4mclassfilter</requirement>\n </requirements>\n <command detect_errors="aggressive"><![CDATA[\n unset R_HOME;\n- Rscript $__tool_directory__/w4mclassfilter_wrapper.R\n- dataMatrix_in \'$dataMatrix_in\'\n- sampleMetadata_in \'$sampleMetadata_in\'\n- variableMetadata_in \'$variableMetadata_in\'\n- sampleclassNames \'$sampleclassNames\'\n- inclusive \'$inclusive\'\n- wildcards \'$wildcards\'\n- classnameColumn \'$classnameColumn\'\n- samplenameColumn \'sampleMetadata\'\n- variable_range_filter \'$variableRangeFilter\'\n- transformation \'$transformation\'\n- imputation \'$imputation\'\n- dataMatrix_out \'$dataMatrix_out\'\n- sampleMetadata_out \'$sampleMetadata_out\'\n- variableMetadata_out \'$variableMetadata_out\'\n- order_vrbl \'$order_vrbl\'\n- order_smpl \'$order_smpl\'\n+ if [ \'$centering\' == \'medoid\' -a \'$imputation\' == \'none\' ]; then\n+ (echo \'medoid\' centering may not be chosen with imputation \'none\' 1>&2);\n+ [ ! 1 ];\n+ else\n+ Rscript\n+ $__tool_directory__/w4mclassfilter_wrapper.R\n+ dataMatrix_in \'$dataMatrix_in\'\n+ sampleMetadata_in \'$sampleMetadata_in\'\n+ variableMetadata_in \'$variableMetadata_in\'\n+ sampleclassNames \'$sampleclassNames\'\n+ inclusive \'$inclusive\'\n+ wildcards \'$wildcards\'\n+ classnameColumn \'$classnameColumn\'\n+ samplenameColumn \'sampleMetadata\'\n+ variable_range_filter \'$variableRangeFilter\'\n+ transformation \'$transformation\'\n+ imputation \'$imputation\'\n+ dataMatrix_out \'$dataMatrix_out\'\n+ sampleMetadata_out \'$sampleMetadata_out\'\n+ variableMetadata_out \'$variableMetadata_out\'\n+ order_vrbl \'$order_vrbl\'\n+ order_smpl \'$order_smpl\'\n+ centering \'$centering\';\n+ fi\n ]]></command>\n <inputs>\n- <param name="dataMatrix_in" format="tabular" label="Data matrix file" type="data"\n- help="data matrix, with sample names in first row and feature names in first column" />\n- <param name="sampleMetadata_in" format="tabular" label="Sample metadata file" type="data"\n- help="sample metadata, with one row per sample" />\n- <param name="variableMetadata_in" format="tabular" label="Variable metadata file" type="data"\n- help="variable metadata, with one row per feature" />\n- <param name="classnameColumn" label="Column that names the sample-class" type="text" value = "class"\n- help="name of the column in sample metadata that has the values to be tested against the \'Names of sample-classes\' input parameter">\n+ <param name="dataMatrix_in" format="tabular" label="Data matrix" type="data"\n+ help="Choose data-matrix file (ta'..b'st-data/rangefilter_variableMetadata.tsv |\n +-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+\n+\n+--------------------------------\n+Example with Treatment-Centering\n+--------------------------------\n+\n+This example retains only the samples that are medoids for their gender.\n+\n+**Input parameters**\n+\n++---------------------------------------------+-----------------------------------+\n+| Input Parameter | Value |\n++=============================================+===================================+\n+| Column that names the sample class | gender |\n++---------------------------------------------+-----------------------------------+\n+| Sample-class names | (Leave this field empty.) |\n++---------------------------------------------+-----------------------------------+\n+| Exclude/include named classes | filter-out |\n++---------------------------------------------+-----------------------------------+\n+| Use \'wild-cards\' or \'regular expressions\' | wild-cards |\n++---------------------------------------------+-----------------------------------+\n+| Variable range-filters | (Leave this field empty.) |\n++---------------------------------------------+-----------------------------------+\n+| Data transformation | none |\n++---------------------------------------------+-----------------------------------+\n+| Missing-value imputation | zero |\n++---------------------------------------------+-----------------------------------+\n+| Sample-sort column | gender |\n++---------------------------------------------+-----------------------------------+\n+| Feature-sort column | rt |\n++---------------------------------------------+-----------------------------------+\n+| Compute centers for classes | medoid |\n++---------------------------------------------+-----------------------------------+\n+\n+**Expected outputs**\n+\n++-------------------+----------------------------------------------------------------------------------------------------------+\n+| Expected Output | Download from URL |\n++===================+==========================================================================================================+\n+| Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/exp_cent_medoid_dm.tsv |\n++-------------------+----------------------------------------------------------------------------------------------------------+\n+| Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/exp_cent_medoid_sm.tsv |\n++-------------------+----------------------------------------------------------------------------------------------------------+\n+| Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/exp_cent_medoid_vm.tsv |\n++-------------------+----------------------------------------------------------------------------------------------------------+\n ]]></help>\n <citations>\n- <!-- Giacomoni_2014 W4m 2.5 -->\n+ <!-- Giacomoni_2014 W4M 2.5 -->\n <citation type="doi">10.1093/bioinformatics/btu813</citation>\n- <!-- Guitton_2017 W4m 3.0 -->\n+ <!-- Guitton_2017 W4M 3.0 -->\n <citation type="doi">10.1016/j.biocel.2017.07.002</citation>\n <!-- Kuhl_2012 CAMERA -->\n <citation type="doi">10.1021/ac202450g</citation>\n' |
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| diff -r c18040b6e8b9 -r 87ec0d3c2266 w4mclassfilter_wrapper.R --- a/w4mclassfilter_wrapper.R Thu Oct 24 10:21:23 2019 -0400 +++ b/w4mclassfilter_wrapper.R Fri Jan 03 11:07:39 2020 -0500 |
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| @@ -23,8 +23,16 @@ suppressMessages(library(w4mclassfilter)) -if(packageVersion("w4mclassfilter") < "0.98.12") - stop("Please use 'w4mclassfilter' versions of 0.98.12 and above") +expected_version <- "0.98.18" +actual_version <- packageVersion("w4mclassfilter") +if(packageVersion("w4mclassfilter") < expected_version) { + stop( + sprintf( + "Unrecoverable error: Version %s of the 'w4mclassfilter' R package was loaded instead of expected version %s", + actual_version, expected_version + ) + ) +} ## constants ##---------- @@ -104,8 +112,14 @@ classnameColumn <- as.character(argVc["classnameColumn"]) samplenameColumn <- as.character(argVc["samplenameColumn"]) -order_smpl <- as.character(argVc["order_smpl"]) order_vrbl <- as.character(argVc["order_vrbl"]) +centering <- as.character(argVc["centering"]) +order_smpl <- + if (centering == 'centroid' || centering == 'median') { + "sampleMetadata" + } else { + as.character(argVc["order_smpl"]) + } variable_range_filter <- as.character(argVc["variable_range_filter"]) variable_range_filter <- strsplit(x = variable_range_filter, split = ",", fixed = TRUE)[[1]] @@ -115,6 +129,8 @@ ## ----------------------------- my_transformation_and_imputation <- if (transformation == "log10") { function(m) { + # convert negative intensities to missing values + m[m < 0] <- NA if (!is.matrix(m)) stop("Cannot transform and impute data - the supplied data is not in matrix form") if (nrow(m) == 0) @@ -130,6 +146,8 @@ } } else if (transformation == "log2") { function(m) { + # convert negative intensities to missing values + m[m < 0] <- NA if (!is.matrix(m)) stop("Cannot transform and impute data - the supplied data is not in matrix form") if (nrow(m) == 0) @@ -144,8 +162,21 @@ return ( my_imputation_function(m) ) } } else { - # use the method from the w4mclassfilter class - my_imputation_function + function(m) { + # convert negative intensities to missing values + m[m < 0] <- NA + if (!is.matrix(m)) + stop("Cannot transform and impute data - the supplied data is not in matrix form") + if (nrow(m) == 0) + stop("Cannot transform and impute data - data matrix has no rows") + if (ncol(m) == 0) + stop("Cannot transform and impute data - data matrix has no columns") + suppressWarnings({ + # suppress warnings here since non-positive values will produce NaN's that will be fixed in the next step + m[is.na(m)] <- NA + }) + return ( my_imputation_function(m) ) + } } ##------------------------------ @@ -165,6 +196,7 @@ , samplename_column = samplenameColumn , order_vrbl = order_vrbl , order_smpl = order_smpl +, centering = centering , variable_range_filter = variable_range_filter , failure_action = my_print , data_imputation = my_transformation_and_imputation |