Mercurial > repos > eschen42 > w4mclassfilter
changeset 6:f1eabb5973b1 draft
planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 08a878ac05ac0c05eafac27b9ebaadb88ae21eb7
| author | eschen42 |
|---|---|
| date | Thu, 11 Jan 2018 20:22:14 -0500 |
| parents | ae791fe4fbe9 |
| children | 8329f51e5e53 |
| files | w4mclassfilter.xml w4mclassfilter_wrapper.R |
| diffstat | 2 files changed, 85 insertions(+), 16 deletions(-) [+] |
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--- a/w4mclassfilter.xml Thu Sep 07 17:32:09 2017 -0400 +++ b/w4mclassfilter.xml Thu Jan 11 20:22:14 2018 -0500 @@ -1,10 +1,11 @@ -<tool id="w4mclassfilter" name="Sample_Subset" version="0.98.3"> +<tool id="w4mclassfilter" name="Sample_Subset" version="0.98.6"> <description>Filter W4M data by sample class</description> <requirements> - <requirement type="package" version="3.3.2">r-base</requirement> + <!-- <requirement type="package" version="6.2">readline</requirement> --> + <requirement type="package" version="3.4.1">r-base</requirement> <requirement type="package" version="1.1_4">r-batch</requirement> - <requirement type="package" version="0.98.3">w4mclassfilter</requirement> + <requirement type="package" version="0.98.6">w4mclassfilter</requirement> </requirements> <stdio> @@ -22,6 +23,7 @@ wildcards '$wildcards' classnameColumn '$classnameColumn' samplenameColumn '$samplenameColumn' + variable_range_filter '$variable_range_filter' dataMatrix_out '$dataMatrix_out' sampleMetadata_out '$sampleMetadata_out' variableMetadata_out '$variableMetadata_out' @@ -56,8 +58,8 @@ <add value="}" /> <!-- r-cube, right-curly-bracket --> </valid> </sanitizer> + </param> - </param> <param name="wildcards" label="Use wild-cards or regular-expressions" type="select" help="wild-cards (the default) - use '*' and '?' to match class names; regular-expressions - use comma-less regular expressions to match class names"> <option value="TRUE" selected="true">wild-cards</option> <option value="FALSE">regular-expressions</option> @@ -66,6 +68,32 @@ <option value="TRUE">filter-in</option> <option value="FALSE" selected="true">filter-out</option> </param> + + <param name="variable_range_filter" label="Variable range-filters" type="text" value = "" help="comma-separated filters specified as 'variableMetadataColumnName:min:max'; default is no filters. (See help below.)"> + <sanitizer> + <valid initial="string.letters"> + <add preset="string.digits"/> + <add value="$" /> <!-- dollar, dollar-sign --> + <add value="(" /> <!-- left-paren --> + <add value=")" /> <!-- right-paren --> + <add value="*" /> <!-- splat, asterisk --> + <add value="+" /> <!-- plus --> + <add value="," /> <!-- comma --> + <add value="." /> <!-- dot, period --> + <add value=":" /> <!-- colon --> + <add value=";" /> <!-- semi, semicolon --> + <add value="?" /> <!-- what, question mark --> + <add value="[" /> <!-- l-squib, left-squre-bracket --> + <add value="\" /> <!-- whack, backslash --> + <add value="]" /> <!-- r-squib, right-squre-bracket --> + <add value="^" /> <!-- hat, caret --> + <add value="{" /> <!-- l-cube, left-curly-bracket --> + <add value="|" /> <!-- pipe --> + <add value="}" /> <!-- r-cube, right-curly-bracket --> + </valid> + </sanitizer> + </param> + </inputs> <outputs> <data name="dataMatrix_out" label="${tool.name}_${dataMatrix_in.name}" format="tabular" ></data> @@ -436,6 +464,10 @@ | '``filter-out``' - exclude only the named sample classes | +Variable-range filters (default = no filters) + | comma-separated names of variable-range filters (see 'Variable-range filters' below) + | + ------------ @@ -512,6 +544,26 @@ - '``^[A-Z][A-Z]*[0-9][0-9]$``' - NO MATCH - the name does not end with the pattern '``[A-Z][0-9][0-9]$``', i.e., it ends with four digits, not two. - '``^[A-Z][0-9]*$``' - NO MATCH - the pattern specifies that second character and all those that follow, if present, must be digits. +---------------------- +Variable-range filters +---------------------- + +An array of range-specification strings may be supplied in the `variable_range_filter` +argument. If supplied, only features having numerical values in the specified column +of `variableMetadata` that fall within the specified ranges will be retained +in the output. Each range is a string of three colon-separated values (e.g., "mz:200:800") in the +following order: + +- the **name of a column of `variableMetadata`** which must have numerical data (e.g., "mz"); +- the **minimum allowed value** in that column for the feature to be retained (e.g., 200); +- the **maximum allowed value** (e.g., 800). + +Note for the range specification strings: + +- **If the "maximum" is less than the "minimum", then the range is exclusive** (e.g., "mz:800:200" means retain only features whose mz is NOT in the range 200-800) +- **If the name supplied in the first field is 'FEATMAX',** then the string is defining the minimum (and possibly, though less useful, maximum) intensity for each feature in the dataMatrix. For example, "FEATMAX:1e6:" would specify that any feature would be excluded if no sample had an intensity for that feature greater than 1000000. + + - Note, however, that when the "maximum" is greater than the "minimum" for the FEATMAX range specification, then the specification is ignored. --------------- Working example @@ -568,6 +620,19 @@ NEWS ---- +CHANGES IN VERSION 0.98.6 +========================= + +NEW FEATURES + +* Added support for filtering out features whose attributes fall outside specified ranges. + For more detail, see "Variable-range filters" above. + +INTERNAL MODIFICATIONS + +* Now uses w4mclassfilter R package v0.98.6. +* Now sorts sample names and feature names in output files because some statistical tools expect the same order in `dataMatrix` row and column names as in the corresponding metadata files. + CHANGES IN VERSION 0.98.3 =========================
--- a/w4mclassfilter_wrapper.R Thu Sep 07 17:32:09 2017 -0400 +++ b/w4mclassfilter_wrapper.R Thu Jan 11 20:22:14 2018 -0500 @@ -82,8 +82,8 @@ # other parameters +wildcards <- as.logical(argVc["wildcards"]) sampleclassNames <- as.character(argVc["sampleclassNames"]) -wildcards <- as.logical(argVc["wildcards"]) sampleclassNames <- strsplit(x = sampleclassNames, split = ",", fixed = TRUE)[[1]] if (wildcards) { sampleclassNames <- gsub("[.]", "[.]", sampleclassNames) @@ -93,22 +93,26 @@ classnameColumn <- as.character(argVc["classnameColumn"]) samplenameColumn <- as.character(argVc["samplenameColumn"]) +variable_range_filter <- as.character(argVc["variable_range_filter"]) +variable_range_filter <- strsplit(x = variable_range_filter, split = ",", fixed = TRUE)[[1]] + ##------------------------------ ## Computation ##------------------------------ result <- w4m_filter_by_sample_class( - dataMatrix_in = dataMatrix_in -, sampleMetadata_in = sampleMetadata_in -, variableMetadata_in = variableMetadata_in -, dataMatrix_out = dataMatrix_out -, sampleMetadata_out = sampleMetadata_out -, variableMetadata_out = variableMetadata_out -, classes = sampleclassNames -, include = inclusive -, class_column = classnameColumn -, samplename_column = samplenameColumn -, failure_action = my_print + dataMatrix_in = dataMatrix_in +, sampleMetadata_in = sampleMetadata_in +, variableMetadata_in = variableMetadata_in +, dataMatrix_out = dataMatrix_out +, sampleMetadata_out = sampleMetadata_out +, variableMetadata_out = variableMetadata_out +, classes = sampleclassNames +, include = inclusive +, class_column = classnameColumn +, samplename_column = samplenameColumn +, variable_range_filter = variable_range_filter +, failure_action = my_print ) my_print("\nResult of '", modNamC, "' Galaxy module call to 'w4mclassfilter::w4m_filter_by_sample_class' R function: ",