Mercurial > repos > eschen42 > w4mclassfilter
changeset 8:d5cf23369d12 draft
planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
| author | eschen42 |
|---|---|
| date | Sat, 03 Mar 2018 22:58:14 -0500 |
| parents | 582a8a42a93b |
| children | 1ced8b5dfa3e |
| files | README test-data/rangefilter_dataMatrix.tsv w4mclassfilter.xml w4mclassfilter_wrapper.R |
| diffstat | 4 files changed, 293 insertions(+), 139 deletions(-) [+] |
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--- a/README Mon Jan 29 21:20:07 2018 -0500 +++ b/README Sat Mar 03 22:58:14 2018 -0500 @@ -1,7 +1,8 @@ Galaxy Wrapper for the w4mclassfilter R Package +<https://doi.org/10.5281/zenodo.1034793> -This is a planemo <http://planemo.readthedocs.io/en/latest/> -oriented galaxy-tool-wrapper <https://docs.galaxyproject.org/en/latest/dev/schema.htm> +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/> +flavor of Galaxy <https://galaxyproject.org/>. +The tool is built with Planemo <http://planemo.readthedocs.io/en/latest/>.
--- a/test-data/rangefilter_dataMatrix.tsv Mon Jan 29 21:20:07 2018 -0500 +++ b/test-data/rangefilter_dataMatrix.tsv Sat Mar 03 22:58:14 2018 -0500 @@ -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 560002 771533 575790 392284 888498 785428 645785 591569 960658 910201 639437 1092885 1409045 2292023 1246459 1945577 710519 773384 622898 -HMDB00208 747080 13420742 595872 1172376 7172632 3143654 4059767 1433702 5593888 5402629 2477288 3346077 4230072 7621236 8960828 10335722 7037373 1574738 2540044 -HMDB01032 2569205 26023086 1604999 430453 8103558 26222916 257139 675754 59906109 263055 31151730 18648127 14989438 1554658 20249262 5588731 871010 15920 44276 -HMDB01101.1 6877586 52217 3158 10789748 229568 4763576 3878773 976436 831937 608298 1605075 72021 442510 1107705 1464339 31250 2724553 72900 30689 -HMDB13189 2644620 727587 1661412 619181 136278 2755434 593863 837865 3526136 2003278 1608814 3446611 1941527 113937 3132404 2893445 2092753 1034666 841661 +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
--- a/w4mclassfilter.xml Mon Jan 29 21:20:07 2018 -0500 +++ b/w4mclassfilter.xml Sat Mar 03 22:58:14 2018 -0500 @@ -1,6 +1,7 @@ -<tool id="w4mclassfilter" name="Sample_Subset" version="0.98.7"> - <!-- this file is utf-8, not ASCII, because it contains the character é --> - <description>Filter W4M data by sample class</description> +<tool id="w4mclassfilter" name="W4m Data Subset" version="0.98.8"> + <description>Filter W4m data by values or metadata</description> + + <!-- Here is the hyphenation standard that I *try* to apply consistently in my documentation: http://www.sandranoonan.com/dont-let-hyphenation-drive-crazy/ --> <requirements> <!-- <requirement type="package" version="6.2">readline</requirement> --> @@ -23,8 +24,9 @@ inclusive '$inclusive' wildcards '$wildcards' classnameColumn '$classnameColumn' - samplenameColumn '$samplenameColumn' + samplenameColumn 'sampleMetadata' variable_range_filter '$variableRangeFilter' + transformation '$transformation' dataMatrix_out '$dataMatrix_out' sampleMetadata_out '$sampleMetadata_out' variableMetadata_out '$variableMetadata_out' @@ -34,12 +36,23 @@ <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, separator: tab" /> <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata columns, separator: tab" /> <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata columns, separator: tab" /> - <param name="samplenameColumn" label="Column that names the sample" type="text" value = "sampleMetadata" help="name of the column in the sample metadata file that has the name of the sample - defaults to 'sampleMetadata'" /> - <param name="classnameColumn" label="Column that names the sample-class" type="text" value = "class" help="name of the column in sample metadata that has the values to be tested against the 'classes' input parameter - defaults to 'class'" /> - <param name="sampleclassNames" label="Names of sample classes" type="text" value = "" help="comma-separated names (or comma-less regular expressions to match names) of sample-classes to filter in or out; defaults to no names"> + <param name="classnameColumn" label="Column that names the sample-class" type="text" value = "class" 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'"> <sanitizer> <valid initial="string.letters"> <add preset="string.digits"/> + <add value="-" /> <!-- dash, hyphen --> + <add value="." /> <!-- dot, period --> + <add value="_" /> <!-- underscore --> + </valid> + </sanitizer> + </param> + <param name="sampleclassNames" label="Names of sample-classes" type="text" value = "" help="comma-separated names (or regular expressions to match names) of sample-classes to filter in or out; defaults to no names"> + <sanitizer> + <valid initial="string.letters"> + <add preset="string.digits"/> + <add value="{" /> <!-- l-cube, left-curly-bracket --> + <add value="|" /> <!-- pipe --> + <add value="}" /> <!-- r-cube, right-curly-bracket --> <add value="$" /> <!-- dollar, dollar-sign --> <add value="(" /> <!-- left-paren --> <add value=")" /> <!-- right-paren --> @@ -54,38 +67,43 @@ <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 --> + <add value="_" /> <!-- underscore --> </valid> </sanitizer> </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"> + <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 regular expressions to match class names"> <option value="TRUE" selected="true">wild-cards</option> <option value="FALSE">regular-expressions</option> </param> - <param name="inclusive" label="Include named classes" type="select" help="filter-in - include only the named sample classes; filter-out (the default) - exclude only the named sample classes"> + <param name="inclusive" label="Exclude/include named classes" type="select" help="'filter-out' (the default) - exclude only the named sample-classes; 'filter-in' - include only the named sample-classes"> <option value="TRUE">filter-in</option> <option value="FALSE" selected="true">filter-out</option> </param> - <param name="variableRangeFilter" label="Variable range-filters" type="text" value = "" help="comma-separated filters, each specified as 'variableMetadataColumnName:min:max'; default is no filters. (See help below.)"> + <param name="variableRangeFilter" label="Variable-range filters" type="text" value = "" help="comma-separated filters, each specified as 'variableMetadataColumnName:min:max'; default is no filters. (See help below.)"> <sanitizer> <valid initial="string.letters"> <add preset="string.digits"/> <add value="," /> <!-- comma --> + <add value="-" /> <!-- dash, hyphen --> + <add value="." /> <!-- dot, period --> <add value=":" /> <!-- colon --> - <add value="." /> <!-- dot, period --> + <add value="_" /> <!-- underscore --> </valid> </sanitizer> </param> + <param name="transformation" label="Data-transformation" type="select" help="'none' (the default) - do not transform data; 'log2' - log base 2 of data; 'log10' - log base 10 of data; in all cases, negative and missing values are imputed to zero"> + <option value="none" selected="true">none</option> + <option value="log2">log2</option> + <option value="log10">log10</option> + </param> </inputs> <outputs> - <data name="dataMatrix_out" label="${tool.name}_${dataMatrix_in.name}" format="tabular" ></data> - <data name="sampleMetadata_out" label="${tool.name}_${sampleMetadata_in.name}" format="tabular" ></data> - <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data> + <data name="dataMatrix_out" label="${dataMatrix_in.name}.subset" format="tabular" ></data> + <data name="sampleMetadata_out" label="${sampleMetadata_in.name}.subset" format="tabular" ></data> + <data name="variableMetadata_out" label="${variableMetadata_in.name}.subset" format="tabular" ></data> </outputs> <tests> @@ -93,12 +111,76 @@ <param name="dataMatrix_in" value="input_dataMatrix.tsv"/> <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/> <param name="variableMetadata_in" value="input_variableMetadata.tsv"/> + <param name="classnameColumn" value="gender"/> + <param name="sampleclassNames" value="M"/> + <param name="wildcards" value="FALSE"/> + <param name="inclusive" value="filter-in"/> + <param name="variableRangeFilter" value="FEATMAX:6.30103:,mz:200:,rt::800"/> + <param name="transformation" value="log10"/> + <output name="dataMatrix_out"> + <assert_contents> + <has_text text="5.87336711011293" /> + </assert_contents> + </output> + <output name="sampleMetadata_out"> + <assert_contents> + <not_has_text text="HU_028" /> + <not_has_text text="HU_051" /> + <not_has_text text="HU_060" /> + <not_has_text text="HU_110" /> + <not_has_text text="HU_149" /> + <not_has_text text="HU_152" /> + <not_has_text text="HU_175" /> + <not_has_text text="HU_178" /> + <not_has_text text="HU_185" /> + <not_has_text text="HU_204" /> + <not_has_text text="HU_208" /> + <has_text text="HU_017" /> + <has_text text="HU_034" /> + <has_text text="HU_078" /> + <has_text text="HU_091" /> + <has_text text="HU_093" /> + <has_text text="HU_099" /> + <has_text text="HU_130" /> + <has_text text="HU_134" /> + <has_text text="HU_138" /> + </assert_contents> + </output> + <output name="variableMetadata_out"> + <assert_contents> + <not_has_text text="HMDB00191" /> + <has_text text="HMDB00208" /> + <not_has_text text="HMDB00251" /> + <not_has_text text="HMDB00299" /> + <not_has_text text="HMDB00512" /> + <not_has_text text="HMDB00518" /> + <not_has_text text="HMDB00715" /> + <not_has_text text="HMDB00822" /> + <has_text text="HMDB01032" /> + <has_text text="HMDB01101.1" /> + <not_has_text text="HMDB03193" /> + <not_has_text text="HMDB04824" /> + <not_has_text text="HMDB10348" /> + <has_text text="HMDB13189" /> + <not_has_text text="HMDB59717" /> + </assert_contents> + </output> + </test> + <test> + <param name="dataMatrix_in" value="input_dataMatrix.tsv"/> + <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/> + <param name="variableMetadata_in" value="input_variableMetadata.tsv"/> <param name="classnameColumn" value="class"/> <param name="sampleclassNames" value=""/> <param name="wildcards" value="FALSE"/> - <param name="samplenameColumn" value="sampleMetadata"/> <param name="inclusive" value="filter-out"/> - <param name="variableRangeFilter" value="FEATMAX:2e6:,mz:200:,rt::800"/> + <param name="variableRangeFilter" value="FEATMAX:20.93157:,mz:200:,rt::800"/> + <param name="transformation" value="log2"/> + <output name="dataMatrix_out"> + <assert_contents> + <has_text text="19.5109032146715" /> + </assert_contents> + </output> <output name="sampleMetadata_out"> <assert_contents> <has_text text="HU_028" /> @@ -149,8 +231,8 @@ <param name="variableMetadata_in" value="input_variableMetadata.tsv"/> <param name="classnameColumn" value="gender"/> <param name="sampleclassNames" value="M"/> - <param name="samplenameColumn" value="sampleMetadata"/> <param name="inclusive" value="filter-in"/> + <param name="transformation" value="none"/> <output name="dataMatrix_out"> <assert_contents> <not_has_text text="HU_028" /> @@ -199,7 +281,6 @@ <param name="classnameColumn" value="gender"/> <param name="sampleclassNames" value="*"/> <param name="wildcards" value="TRUE"/> - <param name="samplenameColumn" value="sampleMetadata"/> <param name="inclusive" value="filter-in"/> <output name="sampleMetadata_out"> <assert_contents> @@ -233,7 +314,6 @@ <param name="classnameColumn" value="gender"/> <param name="sampleclassNames" value="M"/> <param name="wildcards" value="FALSE"/> - <param name="samplenameColumn" value="sampleMetadata"/> <param name="inclusive" value="filter-in"/> <output name="sampleMetadata_out"> <assert_contents> @@ -267,7 +347,6 @@ <param name="classnameColumn" value="gender"/> <param name="sampleclassNames" value="M"/> <param name="wildcards" value="FALSE"/> - <param name="samplenameColumn" value="sampleMetadata"/> <param name="inclusive" value="filter-in"/> <output name="variableMetadata_out"> <assert_contents> @@ -297,7 +376,6 @@ <param name="classnameColumn" value="gender"/> <param name="sampleclassNames" value="M"/> <param name="wildcards" value="FALSE"/> - <param name="samplenameColumn" value="sampleMetadata"/> <param name="inclusive" value="filter-in"/> <output name="variableMetadata_out"> <assert_contents> @@ -327,7 +405,6 @@ <param name="classnameColumn" value="gender"/> <param name="sampleclassNames" value="[Mm],[fF]"/> <param name="wildcards" value="FALSE"/> - <param name="samplenameColumn" value="sampleMetadata"/> <param name="inclusive" value="filter-in"/> <output name="sampleMetadata_out"> <assert_contents> @@ -361,7 +438,6 @@ <param name="classnameColumn" value=""/> <param name="sampleclassNames" value="M"/> <param name="wildcards" value="FALSE"/> - <param name="samplenameColumn" value="sampleMetadata"/> <param name="inclusive" value="filter-in"/> <output name="sampleMetadata_out"> <assert_contents> @@ -402,7 +478,7 @@ **R package** -The *w4mclassfilter* package is available from the Hegeman lab github repository (https://github.com/HegemanLab/w4mclassfilter/releases). +The *w4mclassfilter* package (which is used by the W4m Data Subset tool) is available from the Hegeman lab github repository (https://github.com/HegemanLab/w4mclassfilter/releases). ----------------------------------------------------------------------------------------------------------------------------------------- @@ -413,44 +489,67 @@ --------------------------------------------------- -============================================== -Filter Workflow4Metabolomics data matrix files -============================================== +=========================================================== +"W4m Data Subset" - Filter Workflow4Metabolomics data files +=========================================================== + +---------- +Motivation +---------- + +GC-MS and LC-MS experiments seek to resolve as features chemicals that have distinct chromatographic retention-time ("rt") and (after ionization) mass-to-charge ratio ("m/z" or "mz"). +(If the MS protocol includes fragmentation, several features may result for each chemical.) +Data for a sample are collected as MS intensities, each of which is associated with a position on a 2D plane with dimensions of rt and m/z. +Ideally, features would be sufficiently reproducible among sample-runs to distinguish features that are commmon among samples from those that differ. + +The chromatographic retention-time for a chemical can vary from one chromatography run to the next. +Workflow4Metabolomics (W4m, [Giacomoni *et al.*, 2014, Guitton *et al.* 2017]) is a "flavor" of Galaxy that uses the XCMS preprocessing tools for "retention-time correction" to align features among samples. +Features may be better aligned if pooled samples and blanks are included. + +Multivariate statistical techniques may be used to discover clusters of similar samples (Th]]>é<![CDATA[venot *et al.*, 2015). +However, once retention-time alignment of features has been achieved among samples in GC-MS and LC-MS datasets: + +- The presence of pools and blanks may confound identification and separation of clusters. +- Multivariate statistical algorithms may be impacted by missing values or dimensions that have zero variance. ----------- Description ----------- -Filter a set of retention-corrected W4M files (dataMatrix, sampleMetadata, variableMetadata) by sample-class +The **W4m Data Subset** tool **selects subsets of samples, features, or data values** for further analysis. + +- The tool takes as input the data matrix, sample metadata, and variable metadata datasets produced by W4m's XCMS [Smith *et al.*, 2006] and CAMERA [Kuhl *et al.*, 2012] tools. +- The tool produces the same trio of output datasets, modified as follows. + +This tool can perform several operations to reduce the number samples or features to be analyzed (although **this should be done only in a statistically sound manner** consistent with the nature of the experiment): + +- Samples may be eliminated by filtering on a designated “sample class” column in sampleMetadata. +- Features may be eliminated by specifying minimum or maximum value (or both) allowable in columns of variableMetadata. +- Features may be eliminated by “range of row-maximum for each feature”, i.e., by specifying minimum or maximum intensity (or both) allowable in each row of the dataMatrix (i.e., for the feature across all samples). + +This tool also performs several operations to address several data issues that may impede downstream statistical analysis: + +- Missing values in dataMatrix are imputed to zero. +- The values in the dataMatrix may be log-transformed if desired. +- Samples that are missing from either sampleMetadata or dataMatrix are eliminated. +- Features that are missing from either variableMetadata or dataMatrix are eliminated. +- Features and samples that have zero variance are eliminated. +- Samples and features are sorted alphabetically in rows and columns of dataMatrix and in rows of variableMetadata and sampleMetadata. +- The names of the first columns of variableMetadata and sampleMetadata are set respectively to "variableMetadata" and "sampleMetadata". + +This tool may be applied several times sequentially, which may be useful for: + +- analyzing subsets of samples for progressively smaller sets of treatment-levels, or +- choosing subsets of samples based on criteria in several columns of the sampleMetadata table. ----------------- Workflow Position ----------------- -- Upstream tool category: Preprocessing -- Downstream tool categories: Normalisation, Statistical Analysis, Quality Control, Filter and Sort - ----------- -Motivation ----------- +This tool can be used at any point downstream of Preprocessing. -GC-MS1 and LC-MS1 experiments seek to resolve chemicals as features that have distinct chromatographic behavior and (after ionization) mass-to-charge ratio. -Data for a sample are collected as MS intensities, each of which is associated with a position on a 2D plane with dimensions of m/z ratio and chromatographic retention time. -Ideally, features would be sufficiently reproducible from sample-run to sample-run to identify features that are commmon among samples and those that differ. -However, the chromatographic retention time for a chemical can vary from one run to another. -In the Workflow4Metabolomics (W4M, [Giacomoni *et al.*, 2014, Guitton *et al.* 2017]) "flavor" of Galaxy, the XCMS [Smith *et al.*, 2006] preprocessing tools provide for "retention time correction" to align features among samples, but features may be better aligned if pooled samples and blanks are included. - -Multivariate statistical techniques may be used to discover clusters of similar samples, and sometimes it is desirable to apply clustering iteratively to smaller and smaller subsets of samples until observable separation of clusters is no longer significant. -Once feature-alignment has been achieved among samples in GC-MS and LC-MS datasets, however, the presence of pools and blanks may confound identification and separation of clusters. -Multivariate statistical algorithms also may be impacted by missing values or dimensions that have zero variance (Thévenot *et al.*, 2015). - -The w4mclassfilter tool provides a way to choose subsets of samples for further analysis. -The tool takes as input the data matrix, sample metadata, and variable metadata Galaxy datasets produced by W4M and produces the same trio of datasets with data only for the selected samples. -The tool uses a "sample-class" column in the sample metadata as the basis for including or eliminating samples for further analysis. -Class-values to be considered are provided by the user as a comma-separated list. -The user also provides an indication whether the list specifies classes to be included in further analysis ("filter-in") or rather to be excluded from it ("filter-out"). -Next, missing and negative intensites for features of the remaining samples are imputed to zero. -Finally, samples or features with zero variance are eliminated. +- Possible upstream tool categories: Preprocessing, Quality Control, Statistical Analysis, Filter and Sort +- Possible downstream tool categories: Normalisation, Statistical Analysis, Quality Control, Filter and Sort ----------- Input files @@ -472,7 +571,7 @@ ---------- Data matrix file - | 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 to the rownames of the sample and variable metadata, respectively (see below) + | 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 | Sample metadata file @@ -483,57 +582,58 @@ | variable x metadata **variableMetadata** (tabular separated values) file of the numeric and/or character variable metadata, with . as decimal and NA for missing values | -Column that names the sample (default = '``sampleMetadata``') - | name of the column in sample metadata that has the name of the sample +Column that names the sample-class (default = '``class``') + | name of the column in **sampleMetadata** that has the values to be tested against the '``Names of sample-classes``' input parameter | -Column that names the sample-class (default = '``class``') - | name of the column in sample metadata that has the values to be tested against the '``classes``' input parameter +Names of sample-classes (default = no names) + | comma-separated names (or regular expressions to match names) of sample-classes to include or exclude | -Names of sample classes (default = no names) - | comma-separated names of sample classes to include or exclude +'Wild cards' or 'regular expressions' (default = '``wild-cards``') + | '``wild-cards``' - use wild cards to match names of sample-classes (see the 'Wild card patterns to match class-names' section below) + | '``regular-expressions``' - use regular expressions to match the named sample-classes (see the 'Regular expression patterns to match class-names' section below) | -Wild-cards (default = '``wild-cards``') - | '``wild-cards``' - use wild-cards to match names of sample classes (see 'Wild card patterns to match class-names' below) - | '``regular-expressions``' - exclude only the named sample classes (see 'Regular expression patterns to match class-names' below) - | - -Include named classes (default = '``filter-out``') - | '``filter-in``' - include only the named sample classes - | '``filter-out``' - exclude only the named sample classes +Exclude/include named classes (default = '``filter-out``') + | '``filter-in``' - include only the named sample-classes + | '``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) + | comma-separated names of variable-range filters (see the 'Variable-range filters' section below) | +Data-transformation (default = '``none``') + | '``none``' - do not transform data matrix values + | '``log2``' - take the log base 2 of the values in the data matrix + | '``log10``' - take the log base 10 of the values in the data matrix + | In both cases, negative and missing values are imputed to zero. + | ------------ Output files ------------ - sampleMetadata - | (tabular separated values) file identical to the **sampleMetadata** file given as an input argument, excepting lacking rows for samples (xC-MS features) that have been filtered out (by the sample-class filter or because of zero variance) + | (tabular separated values) file identical to the **sampleMetadata** file given as an input argument, excepting lacking rows for samples that have been filtered out (by the sample-class filter, or because of zero variance, or because they were missing in the input data matrix) | variableMetadata - | (tabular separated values) file identical to the **variableMetadata** file given as an input argument, excepting lacking rows for variables (xC-MS features) that have been filtered out (because of zero variance) + | (tabular separated values) file identical to the **variableMetadata** file given as an input argument, excepting lacking rows for variables (xC-MS features) that have been filtered out (by the variable-range filter, or because of zero variance, or because they were missing in the input data matrix) | dataMatrix - | (tabular separated values) file identical to the **dataMatrix** file given as an input argument, excepting lacking rows for variables (xC-MS features) that have been filtered out (because of zero variance) and columns that have been filtered out (by the sample-class filter or because of zero variance) + | (tabular separated values) file identical to the **dataMatrix** file given as an input argument, excepting lacking rows and columns for variables and samples that have been filtered out, respectively | ---------------------------------------- -Wild card patterns to match class-names ---------------------------------------- +----------------------------------------- +'Wild card' patterns to match class-names +----------------------------------------- -Beginning with v0.98.2, w4mclassfilter supports use of R "wild card" patterns to select class-names. +W4m Data Subset supports use of R "wild card" patterns to select class-names. - use '``?``' to match a single character - use '``*``' to match zero or more characters @@ -545,11 +645,11 @@ - '``*.sample``' matches '``my.sample``' and '``my.own.sample``' - '``*.sampl``' matches neither '``my.sample``' nor '``my.own.sample``' ------------------------------------------------- -Regular expression patterns to match class-names ------------------------------------------------- +-------------------------------------------------- +'Regular expression' patterns to match class-names +-------------------------------------------------- -Beginning with v0.98.2, w4mclassfilter supports use of R "regular expression" patterns to select class-names. +W4m Data Subset supports use of R "regular expression" patterns to select class-names. R uses POSIX 1003.2 standard regular expressions, which allow precise pattern-matching and are exhaustively defined at: http://pubs.opengroup.org/onlinepubs/9699919799/basedefs/V1_chap09.html @@ -638,17 +738,19 @@ **Input parameters** -+------------------------------------+-----------------+ -| Input Parameter | Value | -+====================================+=================+ -| Names of sample classes | M | -+------------------------------------+-----------------+ -| Include named classes | filter-in | -+------------------------------------+-----------------+ -| Column that names the sample-class | gender | -+------------------------------------+-----------------+ -| Column that names the sample | sampleMetadata | -+------------------------------------+-----------------+ ++------------------------------------+-------------------------------+ +| Input Parameter | Value | ++====================================+===============================+ +| Names of sample-classes | M | ++------------------------------------+-------------------------------+ +| Include named classes | filter-in | ++------------------------------------+-------------------------------+ +| Column that names the sample-class | gender | ++------------------------------------+-------------------------------+ +| Variable range-filters | (Leave this field empty.) | ++------------------------------------+-------------------------------+ +| Data transforamtion | none | ++------------------------------------+-------------------------------+ **Expected outputs** @@ -673,19 +775,19 @@ **Input parameters** -+------------------------------------+-------------------------------+ -| Input Parameter | Value | -+====================================+===============================+ -| Names of sample classes | (Leave this field empty.) | -+------------------------------------+-------------------------------+ -| Include named classes | filter-out | -+------------------------------------+-------------------------------+ -| Column that names the sample-class | class | -+------------------------------------+-------------------------------+ -| Column that names the sample | sampleMetadata | -+------------------------------------+-------------------------------+ -| Variable range-filters | FEATMAX:2e6:,mz:200:,rt::800 | -+------------------------------------+-------------------------------+ ++------------------------------------+------------------------------------+ +| Input Parameter | Value | ++====================================+====================================+ +| Names of sample-classes | (Leave this field empty.) | ++------------------------------------+------------------------------------+ +| Include named classes | filter-out | ++------------------------------------+------------------------------------+ +| Column that names the sample-class | gender | ++------------------------------------+------------------------------------+ +| Variable range-filters | FEATMAX:20.93157:,mz:200:,rt::800 | ++------------------------------------+------------------------------------+ +| Data transforamtion | log2 | ++------------------------------------+------------------------------------+ **Expected outputs** @@ -705,76 +807,89 @@ NEWS ---- -CHANGES IN VERSION 0.98.7 +Changes in version 0.98.8 +========================= + +New features + +- The tool now appears in Galaxy with a new, more representative name: "W4m Data Subset". (Earlier versions of this tool appeared in Galaxy with the name "Sample Subset".) +- Option was added to log-transform data matrix values. +- Output datasets are named in conformance with the W4m convention of appending the name of each preprocessing tool to the input dataset name. +- Superflous "Column that names the sample" input parameter was eliminated. +- Some documentation was updated or clarified. + +Internal modifications + +- None + +Changes in version 0.98.7 ========================= New features -* First column of output variableMetadata (that has feature names) now is always named "variableMetadata". -* First column of output sampleMetadata now (that has sample names) is always named "sampleMetadata". +- First column of output variableMetadata (that has feature names) now is always named "variableMetadata". +- First column of output sampleMetadata now (that has sample names) now is always named "sampleMetadata". Internal modifications -* Now uses w4mclassfilter R package v0.98.7. +- Now uses w4mclassfilter R package v0.98.7. -CHANGES IN VERSION 0.98.6 +Changes in version 0.98.6 ========================= New features -* Added support for filtering out features whose attributes fall outside specified ranges. +- 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. +- 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 ========================= Internal modifications -* Improved input handling. -* Now uses w4mclassfilter R package v0.98.3, although that version has no functional implications for this tool. -* Improved reference-list. +- Improved input handling. +- Now uses w4mclassfilter R package v0.98.3, although that version has no functional implications for this tool. +- Improved reference-list. Changes in version 0.98.2 ========================= New features -* Added support for R-flavored regular expression pattern-matching when selecting names of sample-classes. -* Empty classes argument or zero-length class_column result in no samples filtered out. +- Added support for R-flavored regular expression pattern-matching when selecting names of sample-classes. +- Empty classes argument or zero-length class_column result in no samples filtered out. Internal modifications -* Support and tests for new features. +- Support and tests for new features. Changes in version 0.98.1 ========================= -First release - Wrap the w4mclassfilter R package that implements filtering of W4M data matrix, variable metadata, and sample metadata by class of sample. +First release - Wrap the w4mclassfilter R package that implements filtering of W4m data matrix, variable metadata, and sample metadata by class of sample. New features -* *dataMatrix* *is* modified by the tool, so it *does* appear as an output file -* *sampleMetadata* *is* modified by the tool, so it *does* appear as an output file -* *variableMetadata* *is* modified by the tool, so it *does* appear as an output file - -Internal modifications - -* N/A +- Output *dataMatrix* is input dataMatrix as modified by the tool +- Output *sampleMetadata* is input sampleMetadata as modified by the tool +- Output *variableMetadata* is input variableMetadata as modified by the tool ]]></help> <citations> - <!-- Giacomoni_2014 W4M 2.5 --> + <!-- Giacomoni_2014 W4m 2.5 --> <citation type="doi">10.1093/bioinformatics/btu813</citation> - <!-- Guitton_2017 W4M 3.0 --> + <!-- Guitton_2017 W4m 3.0 --> <citation type="doi">10.1016/j.biocel.2017.07.002</citation> + <!-- Kuhl_2012 CAMERA --> + <citation type="doi">10.1021/ac202450g</citation> <!-- Smith_2006 XCMS --> <citation type="doi">10.1021/ac051437y</citation> - <!-- Th_venot_2015 Urinary metabolome statistics --> + <!-- Thevenot_2015 Urinary metabolome statistics --> <citation type="doi">10.1021/acs.jproteome.5b00354</citation> </citations> <!--
--- a/w4mclassfilter_wrapper.R Mon Jan 29 21:20:07 2018 -0500 +++ b/w4mclassfilter_wrapper.R Sat Mar 03 22:58:14 2018 -0500 @@ -82,6 +82,7 @@ # other parameters +transformation <- as.character(argVc["transformation"]) wildcards <- as.logical(argVc["wildcards"]) sampleclassNames <- as.character(argVc["sampleclassNames"]) sampleclassNames <- strsplit(x = sampleclassNames, split = ",", fixed = TRUE)[[1]] @@ -96,6 +97,42 @@ variable_range_filter <- as.character(argVc["variable_range_filter"]) variable_range_filter <- strsplit(x = variable_range_filter, split = ",", fixed = TRUE)[[1]] +## ----------------------------- +## Transformation and imputation +## ----------------------------- +my_w4m_filter_imputation <- if (transformation == "log10") { + function(m) { + if (!is.matrix(m)) + stop("Cannot impute and transform data - the supplied data is not in matrix form") + if (nrow(m) == 0) + stop("Cannot impute and transform data - data matrix has no rows") + if (ncol(m) == 0) + stop("Cannot impute and transform 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) ) + } +} else if (transformation == "log2") { + function(m) { + if (!is.matrix(m)) + stop("Cannot impute and transform data - the supplied data is not in matrix form") + if (nrow(m) == 0) + stop("Cannot impute and transform data - data matrix has no rows") + if (ncol(m) == 0) + stop("Cannot impute and transform 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) ) + } +} else { + # use the method from the w4mclassfilter class + w4m_filter_imputation +} + ##------------------------------ ## Computation ##------------------------------ @@ -113,6 +150,7 @@ , samplename_column = samplenameColumn , variable_range_filter = variable_range_filter , failure_action = my_print +, data_imputation = my_w4m_filter_imputation ) my_print("\nResult of '", modNamC, "' Galaxy module call to 'w4mclassfilter::w4m_filter_by_sample_class' R function: ",