Mercurial > repos > eschen42 > w4mclassfilter
changeset 10:649cb1bafd3e draft
planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
| author | eschen42 |
|---|---|
| date | Thu, 09 Aug 2018 13:00:51 -0400 |
| parents | 1ced8b5dfa3e |
| children | 9f5c0e23c205 |
| files | w4mclassfilter.xml |
| diffstat | 1 files changed, 519 insertions(+), 607 deletions(-) [+] |
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--- a/w4mclassfilter.xml Wed Mar 28 12:04:22 2018 -0400 +++ b/w4mclassfilter.xml Thu Aug 09 13:00:51 2018 -0400 @@ -1,476 +1,478 @@ -<tool id="w4mclassfilter" name="W4m Data Subset" version="0.98.9"> - <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> --> - <requirement type="package" version="3.4.1">r-base</requirement> - <requirement type="package" version="1.1_4">r-batch</requirement> - <requirement type="package" version="0.98.7">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' - wildcards '$wildcards' - classnameColumn '$classnameColumn' - samplenameColumn 'sampleMetadata' - variable_range_filter '$variableRangeFilter' - transformation '$transformation' - dataMatrix_out '$dataMatrix_out' - sampleMetadata_out '$sampleMetadata_out' - variableMetadata_out '$variableMetadata_out' - ]]></command> - - <inputs> - <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, separator: tab" /> - <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata columns, separator: tab" /> - <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata columns, separator: tab" /> - <param name="classnameColumn" label="Column that names the sample-class" type="text" value = "class" help="name of the column in sample metadata that has the values to be tested against the 'Names of sample-classes' input parameter - defaults to 'class'"> - <sanitizer> - <valid initial="string.letters"> - <add preset="string.digits"/> - <add value="-" /> <!-- dash, hyphen --> - <add value="." /> <!-- dot, period --> - <add value="_" /> <!-- underscore --> - </valid> - </sanitizer> - </param> - <param name="sampleclassNames" label="Names of sample-classes" type="text" value = "" help="comma-separated names (or regular expressions to match names) of sample-classes to filter in or out; defaults to no names"> - <sanitizer> - <valid initial="string.letters"> - <add preset="string.digits"/> - <add value="{" /> <!-- l-cube, left-curly-bracket --> - <add value="|" /> <!-- pipe --> - <add value="}" /> <!-- r-cube, right-curly-bracket --> - <add value="$" /> <!-- dollar, dollar-sign --> - <add value="(" /> <!-- left-paren --> - <add value=")" /> <!-- right-paren --> - <add value="*" /> <!-- splat, asterisk --> - <add value="+" /> <!-- plus --> - <add value="-" /> <!-- dash, hyphen --> - <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="_" /> <!-- 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 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="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.)"> - <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="_" /> <!-- 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="${dataMatrix_in.name}.subset" format="tabular" ></data> - <data name="sampleMetadata_out" label="${sampleMetadata_in.name}.subset" format="tabular" ></data> - <data name="variableMetadata_out" label="${variableMetadata_in.name}.subset" format="tabular" ></data> - </outputs> - - <tests> - <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="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="sampleMetadata"/> - <!-- test that hyphens in regular expressions work --> - <param name="sampleclassNames" value="HU_[0-9][0-9][0-9]"/> - <param name="wildcards" value="FALSE"/> - <param name="inclusive" value="filter-in"/> - <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" /> - <has_text text="HU_051" /> - <has_text text="HU_060" /> - <has_text text="HU_110" /> - <has_text text="HU_149" /> - <has_text text="HU_152" /> - <has_text text="HU_175" /> - <has_text text="HU_178" /> - <has_text text="HU_185" /> - <not_has_text text="HU_204" /> - <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> - <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="gender"/> - <param name="sampleclassNames" value="M"/> - <param name="inclusive" value="filter-in"/> - <param name="transformation" value="none"/> - <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="*"/> - <param name="wildcards" value="TRUE"/> - <param name="inclusive" value="filter-in"/> - <output name="sampleMetadata_out"> - <assert_contents> - <not_has_text text="HU_204" /> - <has_text text="HU_028" /> - <has_text text="HU_051" /> - <has_text text="HU_060" /> - <has_text text="HU_110" /> - <has_text text="HU_149" /> - <has_text text="HU_152" /> - <has_text text="HU_175" /> - <has_text text="HU_178" /> - <has_text text="HU_185" /> - <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="wildcards" value="FALSE"/> - <param name="inclusive" value="filter-in"/> - <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="wildcards" value="FALSE"/> - <param name="inclusive" value="filter-in"/> - <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> - <test> - <param name="dataMatrix_in" value="input_nofilter_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"/> - <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" /> - <not_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="[Mm],[fF]"/> - <param name="wildcards" value="FALSE"/> - <param name="inclusive" value="filter-in"/> - <output name="sampleMetadata_out"> - <assert_contents> - <has_text text="HU_028" /> - <has_text text="HU_051" /> - <has_text text="HU_060" /> - <has_text text="HU_110" /> - <has_text text="HU_149" /> - <has_text text="HU_152" /> - <has_text text="HU_175" /> - <has_text text="HU_178" /> - <has_text text="HU_185" /> - <not_has_text text="HU_204" /> - <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=""/> - <param name="sampleclassNames" value="M"/> - <param name="wildcards" value="FALSE"/> - <param name="inclusive" value="filter-in"/> - <output name="sampleMetadata_out"> - <assert_contents> - <has_text text="HU_028" /> - <has_text text="HU_051" /> - <has_text text="HU_060" /> - <has_text text="HU_110" /> - <has_text text="HU_149" /> - <has_text text="HU_152" /> - <has_text text="HU_175" /> - <has_text text="HU_178" /> - <has_text text="HU_185" /> - <not_has_text text="HU_204" /> - <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> - </tests> - - - - <help><![CDATA[ +<tool id="w4mclassfilter" name="W4m Data Subset" version="0.98.10"> + <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> --> + <requirement type="package" version="3.4.1">r-base</requirement> + <requirement type="package" version="1.1_4">r-batch</requirement> + <requirement type="package" version="0.98.7">w4mclassfilter</requirement> + </requirements> + <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' + wildcards '$wildcards' + classnameColumn '$classnameColumn' + samplenameColumn 'sampleMetadata' + variable_range_filter '$variableRangeFilter' + transformation '$transformation' + dataMatrix_out '$dataMatrix_out' + sampleMetadata_out '$sampleMetadata_out' + variableMetadata_out '$variableMetadata_out' + ]]></command> + <inputs> + <param name="dataMatrix_in" format="tabular" label="Data matrix file" type="data" + help="variables ✖ samples" /> + <param name="sampleMetadata_in" format="tabular" label="Sample metadata file" type="data" + help="sample metadata, one row per sample" /> + <param name="variableMetadata_in" format="tabular" label="Variable metadata file" type="data" + help="variable metadata, one row per variable" /> + <param name="classnameColumn" label="Column that names the sample-class" type="text" value = "class" + help="name of the column in sample metadata that has the values to be tested against the 'Names of sample-classes' input parameter - defaults to 'class'"> + <sanitizer> + <valid initial="string.letters"> + <add preset="string.digits"/> + <add value="-" /> <!-- dash, hyphen --> + <add value="." /> <!-- dot, period --> + <add value="_" /> <!-- underscore --> + </valid> + </sanitizer> + </param> + <param name="sampleclassNames" label="Names of sample-classes" type="text" value = "" + help="comma-separated names (or regular expressions to match names) of sample-classes to filter in or out; defaults to no names"> + <sanitizer> + <valid initial="string.letters"> + <add preset="string.digits"/> + <add value="{" /> <!-- l-cube, left-curly-bracket --> + <add value="|" /> <!-- pipe --> + <add value="}" /> <!-- r-cube, right-curly-bracket --> + <add value="$" /> <!-- dollar, dollar-sign --> + <add value="(" /> <!-- left-paren --> + <add value=")" /> <!-- right-paren --> + <add value="*" /> <!-- splat, asterisk --> + <add value="+" /> <!-- plus --> + <add value="-" /> <!-- dash, hyphen --> + <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="_" /> <!-- 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 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="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.)"> + <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="_" /> <!-- 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" format="tabular" label="${dataMatrix_in.name}.subset" ></data> + <data name="sampleMetadata_out" format="tabular" label="${sampleMetadata_in.name}.subset" ></data> + <data name="variableMetadata_out" format="tabular" label="${variableMetadata_in.name}.subset" ></data> + </outputs> + <tests> + <!-- test 1 --> + <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="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 2 --> + <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="sampleMetadata"/> + <!-- test that hyphens in regular expressions work --> + <param name="sampleclassNames" value="HU_[0-9][0-9][0-9]"/> + <param name="wildcards" value="FALSE"/> + <param name="inclusive" value="filter-in"/> + <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" /> + <has_text text="HU_051" /> + <has_text text="HU_060" /> + <has_text text="HU_110" /> + <has_text text="HU_149" /> + <has_text text="HU_152" /> + <has_text text="HU_175" /> + <has_text text="HU_178" /> + <has_text text="HU_185" /> + <not_has_text text="HU_204" /> + <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> + <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 3 --> + <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="inclusive" value="filter-in"/> + <param name="transformation" value="none"/> + <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 4 --> + <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="*"/> + <param name="wildcards" value="TRUE"/> + <param name="inclusive" value="filter-in"/> + <output name="sampleMetadata_out"> + <assert_contents> + <not_has_text text="HU_204" /> + <has_text text="HU_028" /> + <has_text text="HU_051" /> + <has_text text="HU_060" /> + <has_text text="HU_110" /> + <has_text text="HU_149" /> + <has_text text="HU_152" /> + <has_text text="HU_175" /> + <has_text text="HU_178" /> + <has_text text="HU_185" /> + <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 5 --> + <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="wildcards" value="FALSE"/> + <param name="inclusive" value="filter-in"/> + <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 6 --> + <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="wildcards" value="FALSE"/> + <param name="inclusive" value="filter-in"/> + <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> + <!-- test 7 --> + <test> + <param name="dataMatrix_in" value="input_nofilter_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"/> + <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" /> + <not_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 8 --> + <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="[Mm],[fF]"/> + <param name="wildcards" value="FALSE"/> + <param name="inclusive" value="filter-in"/> + <output name="sampleMetadata_out"> + <assert_contents> + <has_text text="HU_028" /> + <has_text text="HU_051" /> + <has_text text="HU_060" /> + <has_text text="HU_110" /> + <has_text text="HU_149" /> + <has_text text="HU_152" /> + <has_text text="HU_175" /> + <has_text text="HU_178" /> + <has_text text="HU_185" /> + <not_has_text text="HU_204" /> + <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 9 --> + <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=""/> + <param name="sampleclassNames" value="M"/> + <param name="wildcards" value="FALSE"/> + <param name="inclusive" value="filter-in"/> + <output name="sampleMetadata_out"> + <assert_contents> + <has_text text="HU_028" /> + <has_text text="HU_051" /> + <has_text text="HU_060" /> + <has_text text="HU_110" /> + <has_text text="HU_149" /> + <has_text text="HU_152" /> + <has_text text="HU_175" /> + <has_text text="HU_178" /> + <has_text text="HU_185" /> + <not_has_text text="HU_204" /> + <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> + </tests> + <help><![CDATA[ **Author** Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu) @@ -504,7 +506,7 @@ 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. +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. @@ -701,7 +703,7 @@ - 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: +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. @@ -720,15 +722,15 @@ Input Files ----------- -+------------------------------------------------------------------------------------------------------------------------+ -| Input File URL | -+========================================================================================================================+ -| https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/input_dataMatrix.tsv | -+------------------------------------------------------------------------------------------------------------------------+ -| https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/input_sampleMetadata.tsv | -+------------------------------------------------------------------------------------------------------------------------+ -| https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/input_variableMetadata.tsv | -+------------------------------------------------------------------------------------------------------------------------+ ++------------------------------------------------------------------------------------------------------------------------------------------------------+ +| Input File URL | ++======================================================================================================================================================+ +| https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/input_dataMatrix.tsv | ++------------------------------------------------------------------------------------------------------------------------------------------------------+ +| https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/input_sampleMetadata.tsv | ++------------------------------------------------------------------------------------------------------------------------------------------------------+ +| https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/input_variableMetadata.tsv | ++------------------------------------------------------------------------------------------------------------------------------------------------------+ .. class:: infomark @@ -756,15 +758,15 @@ **Expected outputs** -+-------------------+---------------------------------------------------------------------------------------------------------------------------+ -| Expected Output | Download from URL | -+===================+===========================================================================================================================+ -| Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/expected_dataMatrix.tsv | -+-------------------+---------------------------------------------------------------------------------------------------------------------------+ -| Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/expected_sampleMetadata.tsv | -+-------------------+---------------------------------------------------------------------------------------------------------------------------+ -| Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/expected_variableMetadata.tsv | -+-------------------+---------------------------------------------------------------------------------------------------------------------------+ ++-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+ +| Expected Output | Download from URL | ++===================+=================================================================================================================================================+ +| Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/expected_dataMatrix.tsv | ++-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+ +| Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/expected_sampleMetadata.tsv | ++-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+ +| Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/expected_variableMetadata.tsv | ++-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+ .. class:: infomark @@ -793,118 +795,28 @@ **Expected outputs** -+-------------------+------------------------------------------------------------------------------------------------------------------------------+ -| Expected Output | Download from URL | -+===================+==============================================================================================================================+ -| Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/rangefilter_dataMatrix.tsv | -+-------------------+------------------------------------------------------------------------------------------------------------------------------+ -| Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/rangefilter_sampleMetadata.tsv | -+-------------------+------------------------------------------------------------------------------------------------------------------------------+ -| Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/rangefilter_variableMetadata.tsv | -+-------------------+------------------------------------------------------------------------------------------------------------------------------+ - ------------------------------------------------------------------------------ - ----- -NEWS ----- - -Changes in version 0.98.9 -========================= - -New features - -- Fixed bug. - -Internal modifications - -- Added the hyphen to the characters permitted within regular expressions. - -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) now is always named "sampleMetadata". - -Internal modifications - -- Now uses w4mclassfilter R package v0.98.7. - -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 -========================= - -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. - -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. - -Internal modifications - -- 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. - -New features - -- 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 --> - <citation type="doi">10.1093/bioinformatics/btu813</citation> - <!-- 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> - <!-- Thevenot_2015 Urinary metabolome statistics --> - <citation type="doi">10.1021/acs.jproteome.5b00354</citation> - </citations> - <!-- - vim:noet:sw=2:ts=2 ++-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+ +| Expected Output | Download from URL | ++===================+===================================================================================================================================================+ +| Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/rangefilter_dataMatrix.tsv | ++-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+ +| Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/rangefilter_sampleMetadata.tsv | ++-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+ +| Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/rangefilter_variableMetadata.tsv | ++-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+ + ]]></help> + <citations> + <!-- Giacomoni_2014 W4m 2.5 --> + <citation type="doi">10.1093/bioinformatics/btu813</citation> + <!-- 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> + <!-- Thevenot_2015 Urinary metabolome statistics --> + <citation type="doi">10.1021/acs.jproteome.5b00354</citation> + </citations> + <!-- + vim:noet:sw=4:ts=4 --> </tool>