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Commit message:
planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c |
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modified:
w4mclassfilter.xml |
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| diff -r 1ced8b5dfa3e -r 649cb1bafd3e w4mclassfilter.xml --- a/w4mclassfilter.xml Wed Mar 28 12:04:22 2018 -0400 +++ b/w4mclassfilter.xml Thu Aug 09 13:00:51 2018 -0400 |
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| b'@@ -1,476 +1,478 @@\n-<tool id="w4mclassfilter" name="W4m Data Subset" version="0.98.9">\n- <description>Filter W4m data by values or metadata</description>\n-\n- <!-- Here is the hyphenation standard that I *try* to apply consistently in my documentation: http://www.sandranoonan.com/dont-let-hyphenation-drive-crazy/ -->\n-\n- <requirements>\n- <!-- <requirement type="package" version="6.2">readline</requirement> -->\n- <requirement type="package" version="3.4.1">r-base</requirement>\n- <requirement type="package" version="1.1_4">r-batch</requirement>\n- <requirement type="package" version="0.98.7">w4mclassfilter</requirement>\n- </requirements>\n-\n- <stdio>\n- <exit_code range="1:" level="fatal" />\n- </stdio>\n-\n-\n- <command detect_errors="aggressive"><![CDATA[\n- Rscript $__tool_directory__/w4mclassfilter_wrapper.R\n- dataMatrix_in \'$dataMatrix_in\'\n- sampleMetadata_in \'$sampleMetadata_in\'\n- variableMetadata_in \'$variableMetadata_in\'\n- sampleclassNames \'$sampleclassNames\'\n- inclusive \'$inclusive\'\n- wildcards \'$wildcards\'\n- classnameColumn \'$classnameColumn\'\n- samplenameColumn \'sampleMetadata\'\n- variable_range_filter \'$variableRangeFilter\'\n-\ttransformation \'$transformation\'\n- dataMatrix_out \'$dataMatrix_out\'\n- sampleMetadata_out \'$sampleMetadata_out\'\n- variableMetadata_out \'$variableMetadata_out\'\n- ]]></command>\n-\n- <inputs>\n- <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: \'.\', missing: NA, mode: numerical, separator: tab" />\n- <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata columns, separator: tab" />\n- <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata columns, separator: tab" />\n- <param name="classnameColumn" label="Column that names the sample-class" type="text" value = "class" help="name of the column in sample metadata that has the values to be tested against the \'Names of sample-classes\' input parameter - defaults to \'class\'">\n- <sanitizer>\n- <valid initial="string.letters">\n- <add preset="string.digits"/>\n- <add value="-" /> <!-- dash, hyphen -->\n- <add value="." /> <!-- dot, period -->\n- <add value="_" /> <!-- underscore -->\n- </valid>\n- </sanitizer>\n- </param>\n- <param name="sampleclassNames" label="Names of sample-classes" type="text" value = "" help="comma-separated names (or regular expressions to match names) of sample-classes to filter in or out; defaults to no names">\n- <sanitizer>\n- <valid initial="string.letters">\n- <add preset="string.digits"/>\n- <add value="{" /> <!-- l-cube, left-curly-bracket -->\n- <add value="|" /> <!-- pipe -->\n- <add value="}" /> <!-- r-cube, right-curly-bracket -->\n- <add value="$" /> <!-- dollar, dollar-sign -->\n- <add value="(" /> <!-- left-paren -->\n- <add value=")" /> <!-- right-paren -->\n- <add value="*" /> <!-- splat, asterisk -->\n- <add value="+" /> <!-- plus -->\n- <add value="-" /> <!-- dash, hyphen -->\n- <add value="," /> <!-- comma -->\n- <add value="." /> <!-- dot, period -->\n- <add value=":" /> <!-- colon -->\n- <add value=";" /> <!-- semi, semicolon -->\n- <add value="?" /> <!-- what, question mark -->\n- <add value="[" /> <!-- l-squib, left-squre-bracket -->\n- <add value="\" /> <!-- whack, backslash -->\n- <add value="]" /> <!-- r-squib, right-squre-bracket -->\n- <add value="^" /> <!-- hat, caret -->\n- <add value="_" /> <!-- underscore -->\n- </valid>\n- </sanitizer>\n- </param>\n-\n- <param name="wildcards" label="Use \'wild cards\' or \'regular expressions\'" type="sele'..b' 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.\n-\n-Changes in version 0.98.3\n-=========================\n-\n-Internal modifications\n-\n-- Improved input handling.\n-- Now uses w4mclassfilter R package v0.98.3, although that version has no functional implications for this tool.\n-- Improved reference-list.\n-\n-Changes in version 0.98.2\n-=========================\n-\n-New features\n-\n-- Added support for R-flavored regular expression pattern-matching when selecting names of sample-classes.\n-- Empty classes argument or zero-length class_column result in no samples filtered out.\n-\n-Internal modifications\n-\n-- Support and tests for new features.\n-\n-Changes in version 0.98.1\n-=========================\n-\n-First release - Wrap the w4mclassfilter R package that implements filtering of W4m data matrix, variable metadata, and sample metadata by class of sample.\n-\n-New features\n-\n-- Output *dataMatrix* is input dataMatrix as modified by the tool\n-- Output *sampleMetadata* is input sampleMetadata as modified by the tool\n-- Output *variableMetadata* is input variableMetadata as modified by the tool\n-\n- ]]></help>\n- <citations>\n- <!-- Giacomoni_2014 W4m 2.5 -->\n- <citation type="doi">10.1093/bioinformatics/btu813</citation>\n- <!-- Guitton_2017 W4m 3.0 -->\n- <citation type="doi">10.1016/j.biocel.2017.07.002</citation>\n- <!-- Kuhl_2012 CAMERA -->\n- <citation type="doi">10.1021/ac202450g</citation>\n- <!-- Smith_2006 XCMS -->\n- <citation type="doi">10.1021/ac051437y</citation>\n- <!-- Thevenot_2015 Urinary metabolome statistics -->\n- <citation type="doi">10.1021/acs.jproteome.5b00354</citation>\n- </citations>\n- <!--\n- vim:noet:sw=2:ts=2\n++-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+\n+| Expected Output | Download from URL |\n++===================+===================================================================================================================================================+\n+| Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/rangefilter_dataMatrix.tsv |\n++-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+\n+| Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/rangefilter_sampleMetadata.tsv |\n++-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+\n+| Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/rangefilter_variableMetadata.tsv |\n++-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+\n+ ]]></help>\n+ <citations>\n+ <!-- Giacomoni_2014 W4m 2.5 -->\n+ <citation type="doi">10.1093/bioinformatics/btu813</citation>\n+ <!-- Guitton_2017 W4m 3.0 -->\n+ <citation type="doi">10.1016/j.biocel.2017.07.002</citation>\n+ <!-- Kuhl_2012 CAMERA -->\n+ <citation type="doi">10.1021/ac202450g</citation>\n+ <!-- Smith_2006 XCMS -->\n+ <citation type="doi">10.1021/ac051437y</citation>\n+ <!-- Thevenot_2015 Urinary metabolome statistics -->\n+ <citation type="doi">10.1021/acs.jproteome.5b00354</citation>\n+ </citations>\n+ <!--\n+ vim:noet:sw=4:ts=4\n --> </tool>\n' |