| Previous changeset 11:9f5c0e23c205 (2018-09-03) Next changeset 13:c18040b6e8b9 (2019-10-24) |
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Commit message:
"planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694" |
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modified:
test-data/expected_dataMatrix.tsv test-data/rangefilter_dataMatrix.tsv test-data/rangefilter_sampleMetadata.tsv w4mclassfilter.xml w4mclassfilter_wrapper.R |
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| diff -r 9f5c0e23c205 -r 38f509903a0b test-data/expected_dataMatrix.tsv --- a/test-data/expected_dataMatrix.tsv Mon Sep 03 22:34:35 2018 -0400 +++ b/test-data/expected_dataMatrix.tsv Tue Oct 01 16:57:58 2019 -0400 |
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| @@ -3,7 +3,7 @@ HMDB00208 747080 595872 3143654 4059767 1433702 5593888 2477288 3346077 4230072 HMDB00251 368600 94936 293988 352855 767894 268331 310918 1248919 577184 HMDB00299 250551 456162 808657 614370 250403 768004 504108 1014041 1362408 -HMDB00512 0 280560 556003 590779 209285 342532 569970 525240 246282 +HMDB00512 525240 280560 556003 590779 209285 342532 569970 525240 246282 HMDB00518 0 85944 129886 175800 13154 230242 440223 315368 10657 HMDB00715 1252089 905408 5140022 2658555 814523 2558923 4184204 3865723 3236644 HMDB01032 2569205 1604999 26222916 257139 675754 59906109 31151730 18648127 14989438 |
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| diff -r 9f5c0e23c205 -r 38f509903a0b test-data/rangefilter_dataMatrix.tsv --- a/test-data/rangefilter_dataMatrix.tsv Mon Sep 03 22:34:35 2018 -0400 +++ b/test-data/rangefilter_dataMatrix.tsv Tue Oct 01 16:57:58 2019 -0400 |
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| @@ -1,6 +1,6 @@ - HU_017 HU_028 HU_034 HU_051 HU_060 HU_078 HU_091 HU_093 HU_099 HU_110 HU_130 HU_134 HU_138 HU_149 HU_152 HU_175 HU_178 HU_185 HU_208 -HMDB00191 19.0950724540801 19.5573683394871 19.1351832076319 18.581538968171 19.7610090032025 19.5831195045026 19.3006944055142 19.1741869272827 19.8736633887651 19.7958256457729 19.2864427002132 20.0597101691826 20.4262862563728 21.1281900906526 20.2494039981067 20.8917666482316 19.438513703552 19.5608253922588 19.2486364146654 -HMDB00208 19.5109032146715 23.6779611010349 19.1846429313023 20.1610039089984 22.7740711828923 21.5840110083096 21.9529654992985 20.451313755289 22.4154199380002 22.3652301844309 21.2403301698498 21.6740392144135 22.0122507889717 22.8615935600174 23.0952006159265 23.3011358356974 22.746605551146 20.5866803867983 21.2764220576728 -HMDB01032 21.2928905785523 24.6332887213057 20.6141409677961 18.7154961966847 22.9501240553341 24.6443247870262 17.9721889132336 19.3661386209868 25.8361997953493 18.0050049466979 24.8928089492302 24.1525273990616 23.8374429574498 20.5681658146509 24.2713659930314 22.4140893053724 19.7323297568288 13.958552715431 15.4342372710269 -HMDB01101.1 22.7134708439962 15.6722319530667 11.6247954558602 23.3631578345615 17.8085620299575 22.183613575742 21.8871689158671 19.8971659609365 19.6661147561338 19.214418735272 20.6142092807528 16.1361300108053 18.7553505325418 20.079142288524 20.4818181509538 14.9315685693242 21.3775881248719 16.1536311941017 14.9054340159519 -HMDB13189 21.3346290086766 19.4727602406215 20.6639784491577 19.2400016764968 17.0561931543153 21.3938481405109 19.1797706242895 19.6763582845664 21.7496566885488 20.9339312108399 20.6175661105571 21.7167470481744 20.8887603396637 16.7978767996065 21.5788388647145 21.4643567902489 20.9969706149343 19.9807336965562 19.6828797432404 + HU_017 HU_028 HU_034 HU_051 HU_060 HU_078 HU_091 HU_093 HU_099 HU_110 HU_130 HU_149 HU_152 HU_175 HU_178 HU_185 HU_208 +HMDB00191 19.0950724540801 19.5573683394871 19.1351832076319 18.581538968171 19.7610090032025 19.5831195045026 19.3006944055142 19.1741869272827 19.8736633887651 19.7958256457729 19.2864427002132 21.1281900906526 20.2494039981067 20.8917666482316 19.438513703552 19.5608253922588 19.2486364146654 +HMDB00208 19.5109032146715 23.6779611010349 19.1846429313023 20.1610039089984 22.7740711828923 21.5840110083096 21.9529654992985 20.451313755289 22.4154199380002 22.3652301844309 21.2403301698498 22.8615935600174 23.0952006159265 23.3011358356974 22.746605551146 20.5866803867983 21.2764220576728 +HMDB01032 21.2928905785523 24.6332887213057 20.6141409677961 18.7154961966847 22.9501240553341 24.6443247870262 17.9721889132336 19.3661386209868 25.8361997953493 18.0050049466979 24.8928089492302 20.5681658146509 24.2713659930314 22.4140893053724 19.7323297568288 13.958552715431 15.4342372710269 +HMDB01101.1 22.7134708439962 15.6722319530667 11.6247954558602 23.3631578345615 17.8085620299575 22.183613575742 21.8871689158671 19.8971659609365 19.6661147561338 19.214418735272 20.6142092807528 20.079142288524 20.4818181509538 14.9315685693242 21.3775881248719 16.1536311941017 14.9054340159519 +HMDB13189 21.3346290086766 19.4727602406215 20.6639784491577 19.2400016764968 17.0561931543153 21.3938481405109 19.1797706242895 19.6763582845664 21.7496566885488 20.9339312108399 20.6175661105571 16.7978767996065 21.5788388647145 21.4643567902489 20.9969706149343 19.9807336965562 19.6828797432404 |
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| diff -r 9f5c0e23c205 -r 38f509903a0b test-data/rangefilter_sampleMetadata.tsv --- a/test-data/rangefilter_sampleMetadata.tsv Mon Sep 03 22:34:35 2018 -0400 +++ b/test-data/rangefilter_sampleMetadata.tsv Tue Oct 01 16:57:58 2019 -0400 |
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| @@ -10,8 +10,6 @@ HU_099 46 pos 23 21.3 M HU_110 53 pos 50 20.9 F HU_130 63 pos 33 26.06 M -HU_134 67 pos 48 22.89 M -HU_138 68 pos 42 21.88 M HU_149 72 pos 35 19.49 F HU_152 75 pos 26 17.58 F HU_175 87 pos 35 21.26 F |
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| diff -r 9f5c0e23c205 -r 38f509903a0b w4mclassfilter.xml --- a/w4mclassfilter.xml Mon Sep 03 22:34:35 2018 -0400 +++ b/w4mclassfilter.xml Tue Oct 01 16:57:58 2019 -0400 |
| [ |
| b'@@ -1,27 +1,28 @@\n-<tool id="w4mclassfilter" name="W4m Data Subset" version="0.98.11">\n+<tool id="w4mclassfilter" name="W4m Data Subset" version="0.98.13">\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 <requirements>\n- <!-- <requirement type="package" version="6.2">readline</requirement> -->\n- <requirement type="package" version="3.4.1">r-base</requirement>\n- <requirement type="package" version="1.1_4">r-batch</requirement>\n- <requirement type="package" version="0.98.8">w4mclassfilter</requirement>\n+ <requirement type="package" version="3.6.1">r-base</requirement>\n+ <requirement type="package" version="1.1_5">r-batch</requirement>\n+ <requirement type="package" version="0.98.13">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+ 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 \'$transformation\'\n- dataMatrix_out \'$dataMatrix_out\'\n- sampleMetadata_out \'$sampleMetadata_out\'\n- variableMetadata_out \'$variableMetadata_out\'\n+ transformation \'$transformation\'\n+ imputation \'$imputation\'\n+ dataMatrix_out \'$dataMatrix_out\'\n+ sampleMetadata_out \'$sampleMetadata_out\'\n+ variableMetadata_out \'$variableMetadata_out\'\n ]]></command>\n <inputs>\n <param name="dataMatrix_in" format="tabular" label="Data matrix file" type="data"\n@@ -95,6 +96,12 @@\n <option value="log2">log2</option>\n <option value="log10">log10</option>\n </param>\n+ <param name="imputation" label="Imputation of missing values" type="select"\n+ help="\'zero\' (the default) - replace missing values with zero; \'center\' - replace missing values with feature-median; \'none\' - perform no imputation">\n+ <option value="zero" selected="true">zero</option>\n+ <option value="center">center</option>\n+ <option value="none">none</option>\n+ </param>\n </inputs>\n <outputs>\n <data name="dataMatrix_out" format="tabular" label="${dataMatrix_in.name}.subset" ></data>\n@@ -110,16 +117,27 @@\n <param name="classnameColumn" value="gender"/>\n <param name="sampleclassNames" value="M"/>\n <param name="wildcards" value="FALSE"/>\n- <param name="inclusive" value="filter-in"/>\n- <param name="variableRangeFilter" value="FEATMAX:6.30103:,mz:200:,rt::800"/>\n- <param name="transformation" value="log10"/>\n+ <param name="inclusive" value="TRUE"/>\n+ <param name="variableRangeFilter" value="FEATMAX:2e6:,mz:200:,rt::800"/>\n+ <param name="transformation" value="none"/>\n <output name="dataMatrix_out">\n <assert_contents>\n- <has_text text="5.87336711011293" />\n+ <has_text text="747080" />\n+ <not_has_text text="13420742" />\n+ <not_has_text text="47259" />\n </assert_contents>\n </output>\n <output name="sampleMetadata_out">\n <assert_contents>\n+ <has_text text="'..b"------+\n+| Names of sample-classes | M |\n++---------------------------------------------+-------------------------------+\n+| Use 'wild-cards' or 'regular expressions' | wild-cards |\n++---------------------------------------------+-------------------------------+\n+| Exclude/include named classes | filter-in |\n++---------------------------------------------+-------------------------------+\n+| Variable range-filters | (Leave this field empty.) |\n++---------------------------------------------+-------------------------------+\n+| Data transforamtion | none |\n++---------------------------------------------+-------------------------------+\n+| Missing-value imputation | center |\n++---------------------------------------------+-------------------------------+\n \n **Expected outputs**\n \n@@ -766,8 +846,6 @@\n | Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/expected_variableMetadata.tsv |\n +-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+\n \n-.. class:: infomark\n-\n ----------------------------\n Running With Range-Filtering\n ----------------------------\n@@ -777,19 +855,23 @@\n \n **Input parameters**\n \n-+------------------------------------+------------------------------------+\n-| Input Parameter | Value |\n-+====================================+====================================+\n-| Names of sample-classes | (Leave this field empty.) |\n-+------------------------------------+------------------------------------+\n-| Include named classes | filter-out |\n-+------------------------------------+------------------------------------+\n-| Column that names the sample-class | gender |\n-+------------------------------------+------------------------------------+\n-| Variable range-filters | FEATMAX:20.93157:,mz:200:,rt::800 |\n-+------------------------------------+------------------------------------+\n-| Data transforamtion | log2 |\n-+------------------------------------+------------------------------------+\n++---------------------------------------------+-----------------------------------+\n+| Input Parameter | Value |\n++=============================================+===================================+\n+| Column that names the sample-class | sampleMetadata |\n++---------------------------------------------+-----------------------------------+\n+| Names of sample-classes | HU_13[48] |\n++---------------------------------------------+-----------------------------------+\n+| Use 'wild-cards' or 'regular expressions' | regular-expressions |\n++---------------------------------------------+-----------------------------------+\n+| Exclude/include named classes | filter-out |\n++---------------------------------------------+-----------------------------------+\n+| Variable range-filters | FEATMAX:20.93157:,mz:200:,rt::800 |\n++---------------------------------------------+-----------------------------------+\n+| Data transforamtion | log2 |\n++---------------------------------------------+-----------------------------------+\n+| Missing-value imputation | zero |\n++---------------------------------------------+-----------------------------------+\n \n **Expected outputs**\n \n" |
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| diff -r 9f5c0e23c205 -r 38f509903a0b w4mclassfilter_wrapper.R --- a/w4mclassfilter_wrapper.R Mon Sep 03 22:34:35 2018 -0400 +++ b/w4mclassfilter_wrapper.R Tue Oct 01 16:57:58 2019 -0400 |
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| @@ -23,8 +23,8 @@ suppressMessages(library(w4mclassfilter)) -if(packageVersion("w4mclassfilter") < "0.98.0") - stop("Please use 'w4mclassfilter' versions of 0.98.0 and above") +if(packageVersion("w4mclassfilter") < "0.98.12") + stop("Please use 'w4mclassfilter' versions of 0.98.12 and above") ## constants ##---------- @@ -83,6 +83,16 @@ # other parameters transformation <- as.character(argVc["transformation"]) +my_imputation_label <- as.character(argVc["imputation"]) +my_imputation_function <- if (my_imputation_label == "zero") { + w4m_filter_zero_imputation +} else if (my_imputation_label == "center") { + w4m_filter_median_imputation +} else if (my_imputation_label == "none") { + w4m_filter_no_imputation +} else { + stop(sprintf("Unknown value %s supplied for 'imputation' parameter. Expected one of {zero,center,none}.")) +} wildcards <- as.logical(argVc["wildcards"]) sampleclassNames <- as.character(argVc["sampleclassNames"]) sampleclassNames <- strsplit(x = sampleclassNames, split = ",", fixed = TRUE)[[1]] @@ -100,37 +110,39 @@ ## ----------------------------- ## Transformation and imputation ## ----------------------------- -my_w4m_filter_imputation <- if (transformation == "log10") { +my_transformation_and_imputation <- if (transformation == "log10") { function(m) { if (!is.matrix(m)) - stop("Cannot impute and transform data - the supplied data is not in matrix form") + stop("Cannot transform and impute data - the supplied data is not in matrix form") if (nrow(m) == 0) - stop("Cannot impute and transform data - data matrix has no rows") + stop("Cannot transform and impute data - data matrix has no rows") if (ncol(m) == 0) - stop("Cannot impute and transform data - data matrix has no columns") - suppressWarnings( + 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 <- log10(m) - ) - return ( w4m_filter_imputation(m) ) + m[is.na(m)] <- NA + }) + return ( my_imputation_function(m) ) } } else if (transformation == "log2") { function(m) { if (!is.matrix(m)) - stop("Cannot impute and transform data - the supplied data is not in matrix form") + stop("Cannot transform and impute data - the supplied data is not in matrix form") if (nrow(m) == 0) - stop("Cannot impute and transform data - data matrix has no rows") + stop("Cannot transform and impute data - data matrix has no rows") if (ncol(m) == 0) - stop("Cannot impute and transform data - data matrix has no columns") - suppressWarnings( + 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 <- log2(m) - ) - return ( w4m_filter_imputation(m) ) + m[is.na(m)] <- NA + }) + return ( my_imputation_function(m) ) } } else { # use the method from the w4mclassfilter class - w4m_filter_imputation + my_imputation_function } ##------------------------------ @@ -150,7 +162,7 @@ , samplename_column = samplenameColumn , variable_range_filter = variable_range_filter , failure_action = my_print -, data_imputation = my_w4m_filter_imputation +, data_imputation = my_transformation_and_imputation ) my_print("\nResult of '", modNamC, "' Galaxy module call to 'w4mclassfilter::w4m_filter_by_sample_class' R function: ", |