Mercurial > repos > eschen42 > w4mclassfilter
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author | eschen42 |
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date | Tue, 09 May 2017 18:37:51 -0400 |
parents | bab3a658f74e |
children | 23c6d271def9 |
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<tool id="W4MClassFilter" name="W4MClassFilter" version="0.98.1"> <description>Filter W4M data by sample class</description> <requirements> <requirement type="package" version="3.3.1">r-base</requirement> <requirement type="package" version="1.1_4">r-batch</requirement> <requirement type="package" version="0.98.1">w4mclassfilter</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" /> </stdio> <command detect_errors="aggressive"><![CDATA[ Rscript $__tool_directory__/w4mclassfilter_wrapper.R dataMatrix_in "$dataMatrix_in" sampleMetadata_in "$sampleMetadata_in" variableMetadata_in "$variableMetadata_in" sampleclassNames "$sampleclassNames" inclusive "$inclusive" classnameColumn "$classnameColumn" samplenameColumn "$samplenameColumn" dataMatrix_out "$dataMatrix_out" sampleMetadata_out "$sampleMetadata_out" variableMetadata_out "$variableMetadata_out" information "$information" ]]></command> <inputs> <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, sep: tabular" /> <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata, decimal: '.', missing: NA, mode: character and numerical, sep: tabular" /> <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata, decimal: '.', missing: NA, mode: character and numerical, sep: tabular" /> <param name="sampleclassNames" label="Names of sample classes" type="text" value = "" help="comma-separated names of sample classes to filter in or out; defaults to no names" /> <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"> <option value="TRUE">filter-in</option> <option value="FALSE" selected="true">filter-out</option> </param> <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="samplenameColumn" label="Column that names the sample" type="text" value = "sampleMetadata" help="name of the column in sample metadata that has the name of the sample - defaults to 'sampleMetadata'" /> </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="information" label="${tool.name}__information.txt" format="txt"/> </outputs> <tests> <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="gender"/> <param name="sampleclassNames" value="M"/> <param name="samplenameColumn" value="sampleMetadata"/> <param name="inclusive" value="filter-in"/> <param name="information" value="test-information.txt"/> <output name="dataMatrix_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" /> <has_text text="HMDB03193" /> <not_has_text text="HMDB00822" /> <has_text text="HMDB01101" /> <has_text text="HMDB01101.1" /> <has_text text="HMDB10348" /> <has_text text="HMDB59717" /> <has_text text="HMDB13189" /> <has_text text="HMDB00299" /> <has_text text="HMDB00191" /> <has_text text="HMDB00518" /> <has_text text="HMDB00715" /> <has_text text="HMDB01032" /> <has_text text="HMDB00208" /> <has_text text="HMDB04824" /> <has_text text="HMDB00512" /> <has_text text="HMDB00251" /> </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="gender"/> <param name="sampleclassNames" value="M"/> <param name="samplenameColumn" value="sampleMetadata"/> <param name="inclusive" value="filter-in"/> <param name="information" value="test-information.txt"/> <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> </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="gender"/> <param name="sampleclassNames" value="M"/> <param name="samplenameColumn" value="sampleMetadata"/> <param name="inclusive" value="filter-in"/> <param name="information" value="test-information.txt"/> <output name="variableMetadata_out"> <assert_contents> <has_text text="HMDB03193" /> <not_has_text text="HMDB00822" /> <has_text text="HMDB01101" /> <has_text text="HMDB01101.1" /> <has_text text="HMDB10348" /> <has_text text="HMDB59717" /> <has_text text="HMDB13189" /> <has_text text="HMDB00299" /> <has_text text="HMDB00191" /> <has_text text="HMDB00518" /> <has_text text="HMDB00715" /> <has_text text="HMDB01032" /> <has_text text="HMDB00208" /> <has_text text="HMDB04824" /> <has_text text="HMDB00512" /> <has_text text="HMDB00251" /> </assert_contents> </output> </test> </tests> <help> .. class:: infomark **Author** Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu) -------------------------------------------------------------------------- .. class:: infomark **R package** The *w4mclassfilter* package is available from the Hegeman lab github repository (https://github.com/HegemanLab/w4mclassfilter/releases). ----------------------------------------------------------------------------------------------------------------------------------------- .. class:: infomark **Tool updates** See the **NEWS** section at the bottom of this page --------------------------------------------------- ============================================== Filter Workflow4Metabolomics data matrix files ============================================== ----------- Description ----------- Filter set of retention-corrected W4M files (dataMatrix, sampleMetadata, variableMetadata) by sample class -------- Comments -------- The *inclusive* parameter indicates: - when 'filter-in', that only the sample-classes named should be included - when 'filter-out', that all sample-classes should be included excepting the sample-classes named ----------- Input files ----------- +---------------------------+------------+ | File | Format | +===========================+============+ | 1) Data matrix | tabular | +---------------------------+------------+ | 2) Sample metadata | tabular | +---------------------------+------------+ | 3) Variable metadata | tabular | +---------------------------+------------+ ---------- Parameters ---------- Data matrix file | variable x sample **dataMatrix** tabular separated 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) | Sample metadata file | sample x metadata **sampleMetadata** tabular separated file of the numeric and/or character sample metadata, with . as decimal and NA for missing values | Variable metadata file | variable x metadata **variableMetadata** tabular separated file of the numeric and/or character variable metadata, with . as decimal and NA for missing values | Names of sample classes (default = no names) | comma-separated names of sample classes to include or exclude | Include named classes (default = filter-out) | *filter-in* - include only the named sample classes | *filter-out* - exclude only the named sample classes | 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 | Column that names the sample (default = 'sampleMetadata') | name of the column in sample metadata that has the name of the sample | ------------ Output files ------------ sampleMetadata_out.tabular | **sampleMetadata** tabular separated file identical to the file given as argument, excepting lacking rows for samples that have been filtered out | variableMetadata_out.tabular | **variableMetadata** tabular separated file identical to the file given as argument, excepting lacking rows for variables (xC-MS features) that have been filtered out (because of zero variance) | dataMatrix_out.tabular | **dataMatrix** tabular separated file identical to the file given as argument, excepting lacking columns for samples that have been filtered out (because of the sample-classes specified in the input parameters) and rows for variables (xC-MS features) that have been filtered out (because of zero variance) | information.txt | Text file with all messages and warnings generated during the computation | ----------------------------------------------------------------------------- ---- NEWS ---- CHANGES IN VERSION 0.98.1 ========================= NEW FEATURES First release - R package that implements filtering of W4M data matrix, variable metadata, and sample metadata by class of sample. *dataMatrix* *is* modified by the tool, so it *does* appear as an output file INTERNAL MODIFICATIONS none </help> <citations> </citations> </tool> <!-- vim: et sw=2 ts=2 : -->