| Previous changeset 12:38f509903a0b (2019-10-01) Next changeset 14:87ec0d3c2266 (2020-01-03) |
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Commit message:
"planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 1a5dd14c3697516bc55950bd6e46c978af7c19cf" |
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modified:
w4mclassfilter.xml w4mclassfilter_wrapper.R |
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| diff -r 38f509903a0b -r c18040b6e8b9 w4mclassfilter.xml --- a/w4mclassfilter.xml Tue Oct 01 16:57:58 2019 -0400 +++ b/w4mclassfilter.xml Thu Oct 24 10:21:23 2019 -0400 |
| [ |
| b'@@ -1,10 +1,10 @@\n-<tool id="w4mclassfilter" name="W4m Data Subset" version="0.98.13">\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 <requirements>\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+ <requirement type="package" version="0.98.14">w4mclassfilter</requirement>\n </requirements>\n <command detect_errors="aggressive"><![CDATA[\n unset R_HOME;\n@@ -23,16 +23,18 @@\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 ]]></command>\n <inputs>\n <param name="dataMatrix_in" format="tabular" label="Data matrix file" type="data"\n- help="variables ✖ samples" />\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, one row per sample" />\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, one row per variable" />\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 - defaults to \'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 <sanitizer>\n <valid initial="string.letters">\n <add preset="string.digits"/>\n@@ -42,7 +44,7 @@\n </sanitizer>\n </param>\n <param name="sampleclassNames" label="Names of sample-classes" type="text" value = ""\n- help="comma-separated names (or regular expressions to match names) of sample-classes to filter in or out; defaults to no names">\n+ help="comma-separated names (or regular expressions to match names) of sample-classes to filter in or out (Leave empty to match no names.)">\n <sanitizer>\n <valid initial="string.letters">\n <add preset="string.digits"/>\n@@ -69,17 +71,17 @@\n </sanitizer>\n </param>\n <param name="wildcards" label="Use \'wild cards\' or \'regular expressions\'" type="select"\n- help="\'wild-cards\' (the default) - use \'*\' and \'?\' to match class names; \'regular-expressions\' - use regular expressions to match class names">\n+ help="\'wild-cards\' - use \'*\' and \'?\' to match class names;    \'regular-expressions\' - use regular expressions to match class names">\n <option value="TRUE" selected="true">wild-cards</option>\n <option value="FALSE">regular-expressions</option>\n </param>\n <param name="inclusive" label="Exclude/include named classes" type="select"\n- help="\'filter-out\' (the default) - exclude only the named sample-classes; \'filter-in\' - include only the named sample-classes">\n+ help="\'filter-out\' - exclude only the named sample-classes;    \'filter-in\' - include only the named sample-classes">\n <option value="TRUE">filter-in</option>\n <option value='..b'\n+ </sanitizer>\n+ </param>\n </inputs>\n <outputs>\n <data name="dataMatrix_out" format="tabular" label="${dataMatrix_in.name}.subset" ></data>\n@@ -552,7 +574,7 @@\n \n **Tool updates**\n \n-See the **NEWS** section at the bottom of this page\n+See https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper#news\n \n ---------------------------------------------------\n \n@@ -599,7 +621,8 @@\n - Samples that are missing from either sampleMetadata or dataMatrix are eliminated.\n - Features that are missing from either variableMetadata or dataMatrix are eliminated.\n - Features and samples that have zero variance are eliminated.\n-- Samples and features are sorted alphabetically in rows and columns of dataMatrix and in rows of variableMetadata and sampleMetadata.\n+- Samples and features have consistent order in `variableMetadata`, `sampleMetadata`, and `dataMatrix`.\n+ (The column for sorting `variableMetadata` or `sampleMetadata` may be specified.)\n - The names of the first columns of variableMetadata and sampleMetadata are set respectively to "variableMetadata" and "sampleMetadata".\n - If desired, the values in the dataMatrix may be log-transformed.\n - If desired, each missing value in dataMatrix is replaced with zero or the median value observed for the corresponding feature.\n@@ -638,7 +661,7 @@\n ----------\n \n Data matrix file\n-\t| 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, respectively, to the rownames of the sample metadata file and variable metadata file\n+\t| feature x sample **dataMatrix** (tabular separated values) file of the numeric data matrix, with period-character (\'.\') as decimal, and \'NA\' for missing values; the table must not contain metadata apart from the required row and column names; the row and column names must be identical (with regard to both content or order) to the respective rownames of the sample metadata file and variable metadata file\n \t|\n \n Sample metadata file\n@@ -683,6 +706,13 @@\n \t| \'``center``\' - For each feature, negative and missing values are imputed to the median of other values.\n \t|\n \n+Column that specifies order for samples (default = \'sampleMetadata\')\n+\t| name of the column in **sampleMetadata** that is used to sort samples; only letters, digits, periods, and underscores are permitted.\n+\t|\n+\n+Column that specifies order for features (default = \'variableMetadata\')\n+\t| name of the column in **variableMetadata** that is used to sort features; only letters, digits, periods, and underscores are permitted.\n+\t|\n \n ------------\n Output files\n@@ -833,6 +863,10 @@\n +---------------------------------------------+-------------------------------+\n | Missing-value imputation | center |\n +---------------------------------------------+-------------------------------+\n+| Sample-sort column | sampleMetadata |\n++---------------------------------------------+-------------------------------+\n+| Feature-sort column | variableMetadata |\n++---------------------------------------------+-------------------------------+\n \n **Expected outputs**\n \n@@ -872,6 +906,10 @@\n +---------------------------------------------+-----------------------------------+\n | Missing-value imputation | zero |\n +---------------------------------------------+-----------------------------------+\n+| Sample-sort column | sampleMetadata |\n++---------------------------------------------+-----------------------------------+\n+| Feature-sort column | variableMetadata |\n++---------------------------------------------+-----------------------------------+\n \n **Expected outputs**\n \n' |
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| diff -r 38f509903a0b -r c18040b6e8b9 w4mclassfilter_wrapper.R --- a/w4mclassfilter_wrapper.R Tue Oct 01 16:57:58 2019 -0400 +++ b/w4mclassfilter_wrapper.R Thu Oct 24 10:21:23 2019 -0400 |
| [ |
| @@ -104,6 +104,9 @@ classnameColumn <- as.character(argVc["classnameColumn"]) samplenameColumn <- as.character(argVc["samplenameColumn"]) +order_smpl <- as.character(argVc["order_smpl"]) +order_vrbl <- as.character(argVc["order_vrbl"]) + variable_range_filter <- as.character(argVc["variable_range_filter"]) variable_range_filter <- strsplit(x = variable_range_filter, split = ",", fixed = TRUE)[[1]] @@ -160,6 +163,8 @@ , include = inclusive , class_column = classnameColumn , samplename_column = samplenameColumn +, order_vrbl = order_vrbl +, order_smpl = order_smpl , variable_range_filter = variable_range_filter , failure_action = my_print , data_imputation = my_transformation_and_imputation |