Mercurial > repos > eschen42 > w4mclassfilter
diff w4mclassfilter.xml @ 0:bab3a658f74e draft
planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
| author | eschen42 |
|---|---|
| date | Tue, 09 May 2017 18:34:35 -0400 |
| parents | |
| children | 23c6d271def9 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/w4mclassfilter.xml Tue May 09 18:34:35 2017 -0400 @@ -0,0 +1,304 @@ +<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 : +-->