w4mclassfilter: w4mclassfilter.xml annotate

annotate w4mclassfilter.xml @ 16:c0bb5667f5cd draft default tip

"planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit aaac8e2f8de03c01e5064abf8a2e30020fabe7ca-dirty"

author	eschen42
date	Thu, 11 Mar 2021 21:14:05 +0000
parents	08d4ca8bc6dd
children

rev	line source
15 08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1 <tool id="w4mclassfilter" name="W4m Data Subset" version="0.98.19">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	2 <description>Filter W4M data by values or metadata</description>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	3 <requirements>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	4 <requirement type="package" version="4.0.3">r-base</requirement>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	5 <requirement type="package" version="1.1_5">r-batch</requirement>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	6 <requirement type="package" version="0.98.19">w4mclassfilter</requirement>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	7 </requirements>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	8 <command detect_errors="aggressive"><![CDATA[
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	9 unset R_HOME;
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	10 if [ '$centering' == 'medoid' -a '$imputation' == 'none' ]; then
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	11 (echo 'medoid' centering may not be chosen with imputation 'none' 1>&2);
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	12 [ ! 1 ];
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	13 else
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	14 Rscript
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	15 $__tool_directory__/w4mclassfilter_wrapper.R
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	16 dataMatrix_in '$dataMatrix_in'
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	17 sampleMetadata_in '$sampleMetadata_in'
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	18 variableMetadata_in '$variableMetadata_in'
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	19 sampleclassNames '$sampleclassNames'
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	20 inclusive '$inclusive'
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	21 wildcards '$wildcards'
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	22 classnameColumn '$classnameColumn'
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	23 samplenameColumn 'sampleMetadata'
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	24 variable_range_filter '$variableRangeFilter'
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	25 transformation '$transformation'
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	26 imputation '$imputation'
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	27 dataMatrix_out '$dataMatrix_out'
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	28 sampleMetadata_out '$sampleMetadata_out'
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	29 variableMetadata_out '$variableMetadata_out'
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	30 order_vrbl '$order_vrbl'
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	31 order_smpl '$order_smpl'
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	32 centering '$centering';
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	33 fi
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	34 ]]></command>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	35 <inputs>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	36 <param name="dataMatrix_in" format="tabular" label="Data matrix" type="data"
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	37 help="Choose data-matrix file (tab-separated values with sample names in first row and feature names in first column)." />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	38 <param name="sampleMetadata_in" format="tabular" label="Sample metadata" type="data"
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	39 help="Choose sample-metadata file (tab-separated values with one row per sample, sample name in first column)." />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	40 <param name="variableMetadata_in" format="tabular" label="Variable metadata" type="data"
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	41 help="Choose variable-metadata file (tab-separated values with one row per feature, feature name in first column)." />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	42 <param name="classnameColumn" label="Column containing the sample-class names (or treatment names)" type="text" value = "class"
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	43 help="Name the column in 'Sample metadata' that has the values to be referenced by 'Sample-class names' and 'Compute centers for classes'. [default: 'class']">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	44 <sanitizer>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	45 <valid initial="string.letters">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	46 <add preset="string.digits"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	47 <add value="." /> <!-- dot, period -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	48 <add value="_" /> <!-- underscore -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	49 </valid>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	50 </sanitizer>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	51 </param>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	52 <param name="sampleclassNames" label="Sample-class names (or patterns)" type="text" value = ""
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	53 help="List of names (or patterns to match names) of sample classes to include or exclude. List should be comma-separated with no stray space characters. (Leave this empty to match no names.) [default: empty]">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	54 <sanitizer>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	55 <valid initial="string.letters">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	56 <add preset="string.digits"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	57 <add value="{" /> <!-- l-curb, left-curly-bracket -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	58 <add value="\|" /> <!-- pipe -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	59 <add value="}" /> <!-- r-curb, right-curly-bracket -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	60 <add value="$" /> <!-- dollar, dollar-sign -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	61 <add value="(" /> <!-- left-paren -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	62 <add value=")" /> <!-- right-paren -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	63 <add value="*" /> <!-- splat, asterisk -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	64 <add value="+" /> <!-- plus -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	65 <add value="-" /> <!-- dash, hyphen -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	66 <add value="," /> <!-- comma -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	67 <add value="." /> <!-- dot, period -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	68 <add value=":" /> <!-- colon -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	69 <add value=";" /> <!-- semi, semicolon -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	70 <add value="?" /> <!-- what, question mark -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	71 <add value="[" /> <!-- l-squib, left-square-bracket -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	72 <add value="\" /> <!-- whack, backslash -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	73 <add value="]" /> <!-- r-squib, right-square-bracket -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	74 <add value="^" /> <!-- hat, caret -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	75 <add value="_" /> <!-- underscore -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	76 </valid>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	77 </sanitizer>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	78 </param>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	79 <param name="inclusive" label="Exclude/include named (or matched) sample classes" type="select" help="Indicate meaning of preceding list: either to identify classes to exclude from output or to identify classes to include in output. [default: 'filter-out']">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	80 <option value="TRUE">filter-in:    Include only the named sample classes.</option>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	81 <option value="FALSE" selected="true">filter-out:    Exclude only the named sample classes.</option>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	82 </param>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	83 <param name="wildcards" label="Use 'wild card patterns' or 'regular expression patterns' to match sample-class names" type="select"
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	84 help="See '<i>Wild-card patterns to match class names</i>' and '<i>Regular-expression patterns to match sample-class names</i>' sections below. [default: 'wild-card patterns']">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	85 <option value="TRUE" selected="true">wild-card patterns:    Use '*' and '?' to match sample-class names.</option>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	86 <option value="FALSE">regular-expression patterns:    Use regular expressions to match sample-class names.</option>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	87 </param>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	88 <param name="variableRangeFilter" label="Variable-range filters" type="text" value = ""
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	89 help="List of filters, each specifying the range of permitted values in a column of 'Variable metadata' (specified as 'column:min:max'), as described in '<i>Variable-range filters</i>' section below. List should be comma-separated with no stray space characters. (Leave this empty for no filtering.) [default: empty]">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	90 <sanitizer>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	91 <valid initial="string.letters">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	92 <add preset="string.digits"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	93 <add value="," /> <!-- comma -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	94 <add value="." /> <!-- dot, period -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	95 <add value=":" /> <!-- colon -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	96 <add value="_" /> <!-- underscore -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	97 </valid>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	98 </sanitizer>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	99 </param>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	100 <param name="transformation" label="Data transformation" type="select"
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	101 help="Choose transformation. In all cases, negative intensities become missing values. See '<i>Data transformation and imputation</i>' section below. [default: 'none']">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	102 <option value="none" selected="true">none:    Do not transform data.</option>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	103 <option value="log2">log2:    Perform log base 2 transformation of data.</option>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	104 <option value="log10">log10:    Perform log base 10 transformation of data.</option>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	105 </param>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	106 <param name="imputation" label="Imputation of missing values" type="select"
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	107 help="Choose imputation for missing values. See '<i>Data transformation and imputation</i>' section below. [default: 'zero']">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	108 <option value="zero" selected="true">zero:    Replace missing values with zero.</option>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	109 <option value="center">center:    Replace missing values with feature-median.</option>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	110 <option value="none">none:    Perform no imputation. Note that 'compute centers' cannot be set to 'medoid'.</option>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	111 </param>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	112 <param name="order_smpl" label="Columns that specify order for samples" type="text" value = "sampleMetadata"
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	113 help="List of sample-metadata column names for sorting samples. List should be comma-separated with no stray space characters. (This is ignored when 'Compute centers for classes' is set to either 'centroid' or 'median'.) [default: 'sampleMetadata']">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	114 <sanitizer>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	115 <valid initial="string.letters">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	116 <add preset="string.digits"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	117 <add value="." /> <!-- dot, period -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	118 <add value="_" /> <!-- underscore -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	119 <add value="," /> <!-- comma -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	120 </valid>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	121 </sanitizer>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	122 </param>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	123 <param name="order_vrbl" label="Columns that specify order for features" type="text" value = "variableMetadata"
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	124 help="List of feature-metadata column names for sorting features. List should be comma-separated with no stray space characters. [default: 'variableMetadata']">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	125 <sanitizer>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	126 <valid initial="string.letters">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	127 <add preset="string.digits"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	128 <add value="." /> <!-- dot, period -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	129 <add value="_" /> <!-- underscore -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	130 <add value="," /> <!-- comma -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	131 </valid>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	132 </sanitizer>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	133 </param>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	134 <param name="centering" label="Compute centers for classes (e.g., treatments)" type="select" help="[default: 'none']">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	135 <option value="none" selected="true">none:    Do not compute centers for classes/treatments.</option>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	136 <option value="centroid">centroid:    For each class, compute the mean for each feature.</option>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	137 <option value="median">median:    For each class, compute the median for each feature.</option>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	138 <option value="medoid">medoid:    For each class, select only the most central member. Note that 'Imputation of missing values' cannot be 'none'.</option>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	139 </param>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	140 </inputs>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	141 <outputs>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	142 <data name="dataMatrix_out" format="tabular" label="${dataMatrix_in.name}.subset" ></data>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	143 <data name="sampleMetadata_out" format="tabular" label="${sampleMetadata_in.name}.subset" ></data>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	144 <data name="variableMetadata_out" format="tabular" label="${variableMetadata_in.name}.subset" ></data>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	145 </outputs>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	146 <tests>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	147 <!-- test 1 -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	148 <test>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	149 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	150 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	151 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	152 <param name="classnameColumn" value="gender"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	153 <param name="sampleclassNames" value="M"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	154 <param name="wildcards" value="FALSE"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	155 <param name="inclusive" value="TRUE"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	156 <param name="variableRangeFilter" value="FEATMAX:2e6:,mz:200:,rt::800"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	157 <param name="transformation" value="none"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	158 <output name="dataMatrix_out">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	159 <assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	160 <has_text text="747080" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	161 <not_has_text text="13420742" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	162 <not_has_text text="47259" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	163 </assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	164 </output>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	165 <output name="sampleMetadata_out">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	166 <assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	167 <has_text text="HU_017" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	168 <has_text text="HU_034" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	169 <has_text text="HU_078" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	170 <has_text text="HU_091" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	171 <has_text text="HU_093" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	172 <has_text text="HU_099" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	173 <has_text text="HU_130" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	174 <has_text text="HU_134" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	175 <has_text text="HU_138" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	176 <not_has_text text="HU_028" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	177 <not_has_text text="HU_051" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	178 <not_has_text text="HU_060" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	179 <not_has_text text="HU_110" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	180 <not_has_text text="HU_149" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	181 <not_has_text text="HU_152" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	182 <not_has_text text="HU_175" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	183 <not_has_text text="HU_178" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	184 <not_has_text text="HU_185" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	185 <not_has_text text="HU_204" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	186 <not_has_text text="HU_208" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	187 </assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	188 </output>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	189 <output name="variableMetadata_out">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	190 <assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	191 <has_text text="HMDB00208" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	192 <has_text text="HMDB01032" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	193 <has_text text="HMDB01101.1" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	194 <has_text text="HMDB13189" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	195 <not_has_text text="HMDB00191" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	196 <not_has_text text="HMDB00251" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	197 <not_has_text text="HMDB00299" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	198 <not_has_text text="HMDB00512" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	199 <not_has_text text="HMDB00518" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	200 <not_has_text text="HMDB00715" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	201 <not_has_text text="HMDB00822" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	202 <not_has_text text="HMDB03193" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	203 <not_has_text text="HMDB04824" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	204 <not_has_text text="HMDB10348" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	205 <not_has_text text="HMDB59717" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	206 </assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	207 </output>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	208 </test>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	209 <!-- test 2 -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	210 <test>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	211 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	212 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	213 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	214 <!-- test that hyphens in regular expressions work -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	215 <param name="sampleclassNames" value="HU_[0-9][0-9][0-9]"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	216 <param name="inclusive" value="TRUE"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	217 <param name="wildcards" value="FALSE"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	218 <param name="classnameColumn" value="sampleMetadata"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	219 <!-- test that variableRangeFilter works with tranformation -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	220 <param name="variableRangeFilter" value="FEATMAX:6.30103:,mz:200:,rt::800"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	221 <param name="transformation" value="log10"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	222 <param name="imputation" value="zero"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	223 <output name="dataMatrix_out" md5="5644d2ea01d072ee1d0c40e29e9d0089">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	224 <assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	225 <has_text text="5.8733671" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	226 </assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	227 </output>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	228 <output name="sampleMetadata_out">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	229 <assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	230 <has_text text="HU_017" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	231 <has_text text="HU_028" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	232 <has_text text="HU_034" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	233 <has_text text="HU_051" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	234 <has_text text="HU_060" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	235 <has_text text="HU_078" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	236 <has_text text="HU_091" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	237 <has_text text="HU_093" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	238 <has_text text="HU_099" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	239 <has_text text="HU_110" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	240 <has_text text="HU_130" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	241 <has_text text="HU_134" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	242 <has_text text="HU_138" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	243 <has_text text="HU_149" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	244 <has_text text="HU_152" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	245 <has_text text="HU_175" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	246 <has_text text="HU_178" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	247 <has_text text="HU_185" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	248 <has_text text="HU_208" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	249 <not_has_text text="HU_204" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	250 </assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	251 </output>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	252 <output name="variableMetadata_out">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	253 <assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	254 <has_text text="HMDB00191" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	255 <has_text text="HMDB00208" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	256 <has_text text="HMDB01032" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	257 <has_text text="HMDB01101.1" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	258 <has_text text="HMDB13189" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	259 <not_has_text text="HMDB00251" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	260 <not_has_text text="HMDB00299" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	261 <not_has_text text="HMDB00512" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	262 <not_has_text text="HMDB00518" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	263 <not_has_text text="HMDB00715" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	264 <not_has_text text="HMDB00822" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	265 <not_has_text text="HMDB03193" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	266 <not_has_text text="HMDB04824" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	267 <not_has_text text="HMDB10348" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	268 <not_has_text text="HMDB59717" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	269 </assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	270 </output>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	271 </test>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	272 <!-- test 3 -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	273 <test>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	274 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	275 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	276 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	277 <param name="classnameColumn" value="gender"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	278 <param name="sampleclassNames" value="M"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	279 <param name="inclusive" value="TRUE"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	280 <param name="transformation" value="none"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	281 <output name="dataMatrix_out">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	282 <assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	283 <not_has_text text="HU_028" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	284 <not_has_text text="HU_051" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	285 <not_has_text text="HU_060" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	286 <not_has_text text="HU_110" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	287 <not_has_text text="HU_149" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	288 <not_has_text text="HU_152" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	289 <not_has_text text="HU_175" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	290 <not_has_text text="HU_178" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	291 <not_has_text text="HU_185" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	292 <not_has_text text="HU_204" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	293 <not_has_text text="HU_208" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	294 <has_text text="HU_017" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	295 <has_text text="HU_034" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	296 <has_text text="HU_078" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	297 <has_text text="HU_091" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	298 <has_text text="HU_093" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	299 <has_text text="HU_099" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	300 <has_text text="HU_130" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	301 <has_text text="HU_134" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	302 <has_text text="HU_138" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	303 <has_text text="HMDB03193" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	304 <not_has_text text="HMDB00822" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	305 <has_text text="HMDB01101" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	306 <has_text text="HMDB01101.1" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	307 <has_text text="HMDB10348" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	308 <has_text text="HMDB59717" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	309 <has_text text="HMDB13189" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	310 <has_text text="HMDB00299" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	311 <has_text text="HMDB00191" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	312 <has_text text="HMDB00518" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	313 <has_text text="HMDB00715" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	314 <has_text text="HMDB01032" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	315 <has_text text="HMDB00208" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	316 <has_text text="HMDB04824" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	317 <has_text text="HMDB00512" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	318 <has_text text="HMDB00251" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	319 </assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	320 </output>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	321 </test>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	322 <!-- test 4 -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	323 <test>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	324 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	325 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	326 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	327 <param name="classnameColumn" value="gender"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	328 <param name="sampleclassNames" value="*"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	329 <param name="wildcards" value="TRUE"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	330 <param name="inclusive" value="TRUE"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	331 <param name="imputation" value="zero"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	332 <output name="dataMatrix_out" md5="b2eac4946d3803a07606286b50451af4">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	333 <assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	334 <not_has_text text="NA" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	335 </assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	336 </output>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	337 <output name="sampleMetadata_out">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	338 <assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	339 <not_has_text text="HU_204" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	340 <has_text text="HU_028" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	341 <has_text text="HU_051" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	342 <has_text text="HU_060" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	343 <has_text text="HU_110" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	344 <has_text text="HU_149" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	345 <has_text text="HU_152" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	346 <has_text text="HU_175" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	347 <has_text text="HU_178" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	348 <has_text text="HU_185" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	349 <has_text text="HU_208" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	350 <has_text text="HU_017" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	351 <has_text text="HU_034" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	352 <has_text text="HU_078" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	353 <has_text text="HU_091" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	354 <has_text text="HU_093" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	355 <has_text text="HU_099" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	356 <has_text text="HU_130" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	357 <has_text text="HU_134" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	358 <has_text text="HU_138" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	359 </assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	360 </output>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	361 </test>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	362 <!-- test 5 -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	363 <test>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	364 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	365 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	366 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	367 <param name="classnameColumn" value="gender"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	368 <param name="sampleclassNames" value="M"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	369 <param name="wildcards" value="FALSE"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	370 <param name="inclusive" value="TRUE"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	371 <output name="sampleMetadata_out">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	372 <assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	373 <not_has_text text="HU_028" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	374 <not_has_text text="HU_051" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	375 <not_has_text text="HU_060" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	376 <not_has_text text="HU_110" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	377 <not_has_text text="HU_149" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	378 <not_has_text text="HU_152" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	379 <not_has_text text="HU_175" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	380 <not_has_text text="HU_178" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	381 <not_has_text text="HU_185" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	382 <not_has_text text="HU_204" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	383 <not_has_text text="HU_208" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	384 <has_text text="HU_017" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	385 <has_text text="HU_034" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	386 <has_text text="HU_078" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	387 <has_text text="HU_091" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	388 <has_text text="HU_093" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	389 <has_text text="HU_099" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	390 <has_text text="HU_130" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	391 <has_text text="HU_134" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	392 <has_text text="HU_138" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	393 </assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	394 </output>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	395 </test>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	396 <!-- test 6 -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	397 <test>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	398 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	399 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	400 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	401 <param name="classnameColumn" value="gender"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	402 <param name="sampleclassNames" value="M"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	403 <param name="wildcards" value="FALSE"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	404 <param name="inclusive" value="TRUE"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	405 <output name="variableMetadata_out">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	406 <assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	407 <has_text text="HMDB03193" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	408 <not_has_text text="HMDB00822" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	409 <has_text text="HMDB01101" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	410 <has_text text="HMDB01101.1" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	411 <has_text text="HMDB10348" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	412 <has_text text="HMDB59717" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	413 <has_text text="HMDB13189" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	414 <has_text text="HMDB00299" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	415 <has_text text="HMDB00191" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	416 <has_text text="HMDB00518" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	417 <has_text text="HMDB00715" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	418 <has_text text="HMDB01032" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	419 <has_text text="HMDB00208" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	420 <has_text text="HMDB04824" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	421 <has_text text="HMDB00512" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	422 <has_text text="HMDB00251" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	423 </assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	424 </output>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	425 </test>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	426 <!-- test 7 -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	427 <test>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	428 <param name="dataMatrix_in" value="input_nofilter_dataMatrix.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	429 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	430 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	431 <param name="classnameColumn" value="gender"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	432 <param name="sampleclassNames" value="M"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	433 <param name="wildcards" value="FALSE"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	434 <param name="inclusive" value="TRUE"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	435 <output name="variableMetadata_out">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	436 <assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	437 <has_text text="HMDB03193" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	438 <not_has_text text="HMDB00822" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	439 <has_text text="HMDB01101" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	440 <has_text text="HMDB01101.1" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	441 <has_text text="HMDB10348" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	442 <has_text text="HMDB59717" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	443 <not_has_text text="HMDB13189" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	444 <has_text text="HMDB00299" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	445 <has_text text="HMDB00191" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	446 <has_text text="HMDB00518" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	447 <has_text text="HMDB00715" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	448 <has_text text="HMDB01032" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	449 <has_text text="HMDB00208" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	450 <has_text text="HMDB04824" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	451 <has_text text="HMDB00512" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	452 <has_text text="HMDB00251" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	453 </assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	454 </output>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	455 </test>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	456 <!-- test 8 -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	457 <test>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	458 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	459 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	460 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	461 <param name="classnameColumn" value="gender"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	462 <param name="sampleclassNames" value="[Mm],[fF]"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	463 <param name="wildcards" value="FALSE"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	464 <param name="inclusive" value="TRUE"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	465 <output name="sampleMetadata_out">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	466 <assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	467 <has_text text="HU_028" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	468 <has_text text="HU_051" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	469 <has_text text="HU_060" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	470 <has_text text="HU_110" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	471 <has_text text="HU_149" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	472 <has_text text="HU_152" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	473 <has_text text="HU_175" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	474 <has_text text="HU_178" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	475 <has_text text="HU_185" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	476 <not_has_text text="HU_204" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	477 <has_text text="HU_208" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	478 <has_text text="HU_017" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	479 <has_text text="HU_034" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	480 <has_text text="HU_078" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	481 <has_text text="HU_091" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	482 <has_text text="HU_093" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	483 <has_text text="HU_099" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	484 <has_text text="HU_130" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	485 <has_text text="HU_134" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	486 <has_text text="HU_138" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	487 </assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	488 </output>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	489 </test>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	490 <!-- test 9 -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	491 <test>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	492 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	493 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	494 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	495 <param name="classnameColumn" value=""/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	496 <param name="sampleclassNames" value="M"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	497 <param name="wildcards" value="FALSE"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	498 <param name="inclusive" value="TRUE"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	499 <output name="sampleMetadata_out">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	500 <assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	501 <has_text text="HU_028" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	502 <has_text text="HU_051" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	503 <has_text text="HU_060" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	504 <has_text text="HU_110" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	505 <has_text text="HU_149" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	506 <has_text text="HU_152" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	507 <has_text text="HU_175" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	508 <has_text text="HU_178" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	509 <has_text text="HU_185" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	510 <not_has_text text="HU_204" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	511 <has_text text="HU_208" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	512 <has_text text="HU_017" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	513 <has_text text="HU_034" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	514 <has_text text="HU_078" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	515 <has_text text="HU_091" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	516 <has_text text="HU_093" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	517 <has_text text="HU_099" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	518 <has_text text="HU_130" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	519 <has_text text="HU_134" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	520 <has_text text="HU_138" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	521 </assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	522 </output>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	523 </test>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	524 <!-- test 10 - extends test4 with no imputation rather than zero imputation -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	525 <test>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	526 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	527 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	528 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	529 <param name="classnameColumn" value="gender"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	530 <param name="sampleclassNames" value="*"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	531 <param name="wildcards" value="TRUE"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	532 <param name="inclusive" value="TRUE"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	533 <param name="imputation" value="none"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	534 <output name="dataMatrix_out" md5="6200dfa77d09c56e434f80b1a23b3393">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	535 <assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	536 <not_has_text text="HU_204" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	537 <has_text text="NA" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	538 <has_text text="HU_028" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	539 </assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	540 </output>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	541 <output name="sampleMetadata_out">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	542 <assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	543 <not_has_text text="HU_204" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	544 <has_text text="HU_028" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	545 </assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	546 </output>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	547 </test>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	548 <!-- test 11 - extends test4 with center imputation rather than zero imputation -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	549 <test>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	550 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	551 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	552 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	553 <param name="classnameColumn" value="gender"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	554 <param name="sampleclassNames" value="*"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	555 <param name="wildcards" value="TRUE"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	556 <param name="inclusive" value="TRUE"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	557 <param name="imputation" value="center"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	558 <output name="dataMatrix_out" md5="a404278c5c9ffd5bdadf346c4f8a0184">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	559 <assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	560 <not_has_text text="HU_204" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	561 <not_has_text text="NA" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	562 <has_text text="HU_028" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	563 </assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	564 </output>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	565 <output name="sampleMetadata_out">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	566 <assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	567 <not_has_text text="HU_204" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	568 <has_text text="HU_028" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	569 </assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	570 </output>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	571 </test>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	572 <!-- test 12 - select medoid for class -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	573 <test>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	574 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	575 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	576 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	577 <param name="classnameColumn" value="gender"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	578 <param name="sampleclassNames" value=""/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	579 <param name="wildcards" value="TRUE"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	580 <param name="inclusive" value="FALSE"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	581 <param name="imputation" value="zero"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	582 <param name="order_vrbl" value="rt"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	583 <param name="order_smpl" value="gender"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	584 <param name="centering" value="medoid"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	585 <output name="dataMatrix_out" md5="c91bbfbf30004fa24b05a67ec479bfb1">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	586 <assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	587 <not_has_text text="1013302" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	588 <has_text text="4763576" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	589 <has_text text="2003278" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	590 <has_text text="26222916" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	591 </assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	592 </output>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	593 <output name="sampleMetadata_out">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	594 <assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	595 <not_has_text text="HU_099" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	596 <not_has_text text="HU_185" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	597 <has_text text="HU_110" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	598 <has_text text="HU_078" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	599 </assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	600 </output>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	601 </test>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	602 <!-- test 13 -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	603 <test>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	604 <param name="dataMatrix_in" value="input_med1_dm.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	605 <param name="sampleMetadata_in" value="input_med1_sm.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	606 <param name="variableMetadata_in" value="input_med1_vm.tsv"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	607 <param name="classnameColumn" value="pcgroup"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	608 <param name="sampleclassNames" value=""/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	609 <param name="wildcards" value="TRUE"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	610 <param name="inclusive" value="FALSE"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	611 <param name="imputation" value="zero"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	612 <param name="order_vrbl" value="sample"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	613 <param name="order_smpl" value="pcgroup"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	614 <param name="centering" value="medoid"/>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	615 <output name="sampleMetadata_out">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	616 <assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	617 <has_text text="X10" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	618 <has_text text="M70T1043" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	619 <has_text text="70.01229" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	620 <has_text text="1042.837" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	621 <has_text text="X345" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	622 <has_text text="M74T33" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	623 <not_has_text text="M70T1042_1" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	624 <not_has_text text="M74T34" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	625 </assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	626 </output>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	627 <output name="dataMatrix_out">
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	628 <assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	629 <has_text text="X10" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	630 <has_text text="X345" />
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	631 </assert_contents>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	632 </output>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	633 </test>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	634 </tests>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	635 <!-- Here is the hyphenation standard that I try to apply consistently in my documentation:
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	636 https://web.archive.org/web/20161014025757/http://www.sandranoonan.com/dont-let-hyphenation-drive-crazy/
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	637 -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	638 <help><![CDATA[
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	639
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	640
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	641 Author Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu)
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	642
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	643 --------------------------------------------------------------------------
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	644
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	645
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	646 R package
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	647
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	648 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).
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	649
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	650 -----------------------------------------------------------------------------------------------------------------------------------------
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	651
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	652
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	653 Tool updates
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	654
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	655 See https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper#news
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	656
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	657 ---------------------------------------------------
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	658
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	659 ======================================================
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	660 "W4M Data Subset" - Filter Workflow4Metabolomics data
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	661 ======================================================
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	662
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	663 ----------
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	664 Motivation
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	665 ----------
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	666
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	667 LC-MS metabolomics experiments seek to resolve "features", i.e., species that have distinct chromatographic retention time ("rt") and (after ionization) mass-to-charge ratio ("m/z" or "mz").
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	668 (If a chemical is fragmented or may have a variety of adducts, several features will result.)
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	669 Data for a sample are collected as mass-spectral intensities, each of which is associated with a position on a 2D plane with dimensions of rt and m/z.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	670 Ideally, features would be sufficiently reproducible among sample-runs to distinguish features that are similar among samples from those that differ.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	671
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	672 For liquid chromatography, the retention time for a species can vary considerably from one chromatography run to the next.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	673 The Workflow4Metabolomics suite of Galaxy tools (W4M, [Giacomoni et al., 2014, Guitton et al. 2017])
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	674 uses the XCMS preprocessing tools [Smith et al., 2006]
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	675 for "retention-time correction" to align features among samples.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	676 Features may be better aligned if pooled samples and blanks are included.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	677
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	678 Multivariate statistical tools may be used to discover clusters of similar samples [Th]]>é<![CDATA[venot et al., 2015].
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	679 However, once retention-time alignment of features has been achieved among samples in LC-MS datasets:
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	680
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	681 - The presence of pools and blanks may confound identification and separation of sample clusters.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	682 - Multivariate statistical algorithms may be impacted by missing values or dimensions that have zero variance.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	683
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	684 -----------
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	685 Description
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	686 -----------
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	687
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	688 The W4M Data Subset tool selects subsets of samples, features, or data values and conditions the data for further analysis.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	689
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	690 - The tool takes as input the dataMatrix, sampleMetadata, and variableMetadata datasets produced by W4M's XCMS and CAMERA [Kuhl et al., 2012] tools.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	691 - The tool produces the same trio of output datasets, modified as described below.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	692
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	693 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):
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	694
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	695 - Sample filtering: Samples may be selected by designating a "sample class" column in sampleMetadata and specifying criteria to include or exclude samples based on the contents of this column.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	696 - Feature filtering: Features may be selected by specifying minimum or maximum value (or both) allowable in columns of variableMetadata.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	697 - Intensity filtering: To exclude minimal features from consideration, a lower bound may be specified for the maximum intensity for a feature across all samples (i.e., for a row in dataMatrix).
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	698
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	699 This tool also conditions data for statistical analysis:
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	700
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	701 - Samples that are missing from either sampleMetadata or dataMatrix are eliminated.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	702 - Features that are missing from either variableMetadata or dataMatrix are eliminated.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	703 - Features and samples that have zero variance are eliminated.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	704 - Samples and features are ordered consistently in variableMetadata, sampleMetadata, and dataMatrix.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	705 (The columns for sorting variableMetadata or sampleMetadata may be specified.)
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	706 - The names of the first columns of variableMetadata and sampleMetadata are set respectively to "variableMetadata" and "sampleMetadata".
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	707 - If desired, the values in dataMatrix may be log-transformed.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	708 - Negative intensities become missing values (before missing-value replacement is performed).
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	709 - If desired, each missing value in dataMatrix may be replaced with zero or the median value observed for the corresponding feature.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	710 - If desired, a "center" for each treatment can be computed in lieu of the samples for that treatment.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	711
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	712 This tool may be applied several times sequentially, which may be useful for:
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	713
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	714 - analyzing subsets of samples for progressively smaller sets of treatment levels, or
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	715 - choosing subsets of samples or features, respectively based on criteria in columns of sampleMetadata or variableMetadata.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	716
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	717 -----------------
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	718 Workflow Position
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	719 -----------------
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	720
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	721 This tool can be used at any point downstream of Preprocessing.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	722
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	723 - Possible upstream tool categories: Preprocessing, Quality Control, Statistical Analysis, Filter and Sort
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	724 - Possible downstream tool categories: Normalisation, Statistical Analysis, Quality Control, Filter and Sort
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	725
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	726 -----------
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	727 Input files
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	728 -----------
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	729
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	730 +------------------------+---------------------------------------+------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	731 \| File \| Contents \| Format \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	732 +========================+=======================================+============+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	733 \| Data matrix \| per-feature, per-sample intensities \| tabular \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	734 +------------------------+---------------------------------------+------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	735 \| Sample metadata \| metadata for samples \| tabular \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	736 +------------------------+---------------------------------------+------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	737 \| Variable metadata \| metadata for features \| tabular \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	738 +------------------------+---------------------------------------+------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	739
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	740
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	741 ----------
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	742 Parameters
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	743 ----------
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	744
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	745 Data matrix
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	746 \| feature x sample dataMatrix (tab-separated values) file of the numeric data matrix, with period-character ('.') as decimal, and 'NA' for missing values.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	747 \| The file must not contain metadata apart from the required row and column names.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	748 \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	749
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	750 Sample metadata
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	751 \| sample x metadata sampleMetadata (tab-separated values) file of the numeric and/or character sample metadata, with period-character ('.') as decimal, and 'NA' for missing values.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	752 \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	753
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	754 Variable metadata
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	755 \| variable x metadata variableMetadata (tab-separated values) file of the numeric and/or character variable metadata, with period-character ('.') as decimal, and 'NA' for missing values.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	756 \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	757
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	758 Column containing the sample-class names (default = '``class``')
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	759 \| name of the column in sampleMetadata that has the values to be tested against the '``Sample-class names``' input parameter or to be referenced by the '``Compute centers for classes``' input parameter.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	760 \| Only letters, digits, periods, and underscores are permitted.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	761 \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	762
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	763 Sample-class names (default = no names)
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	764 \| names (or regular expressions to match names) of sample-classes to include or exclude
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	765 \| (Separate names with commas, without any extra space characters.)
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	766 \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	767
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	768 Exclude/include named (or matched) classes (default = '``filter-out``')
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	769 \| '``filter-in``' - include only the named sample-classes
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	770 \| '``filter-out``' - exclude only the named sample-classes
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	771 \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	772
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	773 Use 'wild card patterns' or 'regular expression patterns' (default = '``wild-card patterns``')
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	774 \| '``wild-card patterns``' - use wild cards to match names of sample-classes (see the 'Wild-card patterns to match class names' section below.)
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	775 \| '``regular-expression patterns``' - use regular expressions to match the named sample-classes (see the 'Regular-expression patterns to match class names' section below.)
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	776 \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	777
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	778 Variable-range filters (default = no filters)
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	779 \| variable-range filters (see the 'Variable-range filters' section below)
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	780 \| (Separate filter expressions with commas, without any extra space characters.)
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	781 \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	782
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	783 Data transformation (default = '``none``')
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	784 \| '``none``' - Do not transform data matrix values.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	785 \| '``log2``' - Take the log base 2 of the values in the data matrix.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	786 \| '``log10``' - Take the log base 10 of the values in the data matrix.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	787 \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	788 \| Note that negative intensities become missing values regardless of the choice made here.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	789 \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	790
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	791 Imputation of missing values (default = '``zero``')
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	792 \| '``none``' - Do not impute data matrix values.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	793 \| '``zero``' - Negative and missing values are imputed to zero.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	794 \| '``center``' - For each feature, negative and missing values are imputed to the median of other values.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	795 \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	796 \| Note well: For '``none``' option, '``Compute centers for classes``' cannot be set to '``medoid``'.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	797 \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	798
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	799 Columns that specify order for samples (default = '``sampleMetadata``')
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	800 \| names of the columns in sampleMetadata that is used to sort samples; only letters, digits, periods, and underscores are permitted.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	801 \| (Separate column names with commas, without any extra space characters.)
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	802 \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	803
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	804 Columns that specify order for features (default = '``variableMetadata``')
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	805 \| names of the columns in variableMetadata that is used to sort features; only letters, digits, periods, and underscores are permitted.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	806 \| (Separate column names with commas, without any extra space characters.)
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	807 \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	808
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	809 Compute centers for classes, e.g., treatments (default = '``none``')
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	810 \| '``none``' - Return all samples; do not compute centers for classes/treatments.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	811 \| '``centroid``' - For each treatment, return only the centroid (the treatment-center computed as the mean intensity for each feature).
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	812 \| '``median``' - For each treatment, return only the treatment-center computed as the median intensity for each feature.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	813 \| '``medoid``' - For each treatment, return only the medoid (the sample most similar to the other samples for that treatment).
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	814 \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	815 \| Note well: For '``medoid``' option, '``Imputation of missing values``' cannot be set to '``none``'.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	816 \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	817
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	818 ------------
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	819 Output files
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	820 ------------
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	821
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	822 sampleMetadata
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	823 \| (tab-separated values) file.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	824 \| If centering is '``none``' or '``medoid``', this will be 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)
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	825 \| If centering is '``centroid``' or '``median``', most columns will be replaced with the treatment name and the number of samples for that treatment.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	826 \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	827
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	828 variableMetadata
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	829 \| (tab-separated values) file identical to the variableMetadata file given as an input argument, excepting lacking rows for variables (LC-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)
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	830 \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	831
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	832 dataMatrix
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	833 \| (tab-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
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	834 \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	835
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	836
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	837 -----------------------------------------
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	838 Wild-card patterns to match class names
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	839 -----------------------------------------
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	840
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	841 W4M Data Subset supports use of "wild card" patterns to select class-names.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	842
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	843 - use '``?``' to match a single character
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	844 - use '``*``' to match zero or more characters
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	845 - the entire pattern must match the sample name
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	846
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	847 For example
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	848
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	849 - '``??.samp*``' matches '``my.sample``' but not '``my.own.sample``'
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	850 - '``*.sample``' matches '``my.sample``' and '``my.own.sample``'
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	851 - '``*.sampl``' matches neither '``my.sample``' nor '``my.own.sample``'
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	852
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	853 --------------------------------------------------
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	854 Regular-expression patterns to match class names
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	855 --------------------------------------------------
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	856
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	857 W4M Data Subset supports use of R "extended regular expression" patterns to select class-names.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	858
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	859 R extended regular expressions, which allow precise pattern-matching and are exhaustively defined at
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	860 https://stat.ethz.ch/R-manual/R-devel/library/base/html/regex.html
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	861
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	862 However, only a few basic building blocks of regular expressions need to be mastered for most cases:
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	863
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	864 - '``^``' matches the beginning of a class-name
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	865 - '``$``' matches the end of a class-name
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	866 - '``.``' outside of square brackets matches a single character
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	867 - '``*``' matches character specified immediately before zero or more times
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	868 - square brackets specify a set of characters to be matched.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	869
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	870 Within square brackets
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	871
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	872 - '``^``' as the first character specifies that the list of characters are those that should not be matched.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	873 - '``-``' is used to specify ranges of characters
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	874
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	875 Caveat: The tool wrapper uses the comma ('``,``') to split a list of sample-class names, so commas may not be used within regular expressions for this tool
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	876
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	877 First Example: Consider a field of class-names consisting of '``marq3,marq6,marq9,marq12,front3,front6,front9,front12``'
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	878
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	879 - The regular expression '``^front[0-9][0-9]*$``' will match the same sample-classes as '``front3,front6,front9,front12``'
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	880 - The regular expression '``^[a-z][a-z]3$``' will match the same sample-classes as '``front3,marq3``'
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	881 - The regular expression '``^[a-z][a-z]12$``' will match the same sample-classes as '``front12,marq12``'
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	882 - The regular expression '``^[a-z][a-z][0-9]$``' will match the same sample-classes as '``front3,front6,front9,marq3,marq6,marq9``'
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	883
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	884 Second Example: Consider these regular expression patterns as possible matches to a sample-class name '``AB0123``':
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	885
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	886 - '``^[A-Z][A-Z][0-9][0-9]$``' MATCHES '``^AB0123$*``'
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	887 - '``^[A-Z][A-Z][0-9][0-9]$``' MATCHES '``^AB0123$``'
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	888 - '``^[A-Z][0-9]``' MATCHES '``^A* B0123$``' - first character is a letter, '``*``' can specify zero characters, and end of line did not need to be matched.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	889 - '``^[A-Z][A-Z][0-9]``' MATCHES '``^AB0 123$``' - first two characters are letters aind the third is a digit.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	890 - '``^[A-Z][A-Z]*[0-9][0-9]$``' DOES NOT MATCH - the name does not end with the pattern '``[A-Z][0-9][0-9]$``', i.e., it ends with four digits, not two.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	891 - '``^[A-Z][0-9]*$``' DOES NOT MATCH - the pattern specifies that second character and all those that follow, if present, must be digits.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	892
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	893 ----------------------
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	894 Variable-range filters
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	895 ----------------------
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	896
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	897 An array of range-specification strings may be supplied in the '``Variable-range filters``'
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	898 argument. If supplied, only features having numerical values in the specified column
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	899 of variableMetadata that fall within the specified ranges will be retained
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	900 in the output. Each range is a string of three colon-separated values (e.g., '``mz:200:800``') in the
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	901 following order:
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	902
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	903 - the name of a column of variableMetadata which must have numerical data (only letters, digits, periods, and underscores are permitted in the name itself), e.g., '``mz``';
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	904 - the minimum allowed value in that column for the feature to be retained, e.g., '``200``';
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	905 - the maximum allowed value, e.g., '``800``'.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	906
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	907 Note for the range specification strings:
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	908
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	909 - 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)
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	910 - If the name supplied in the first field is '``FEATMAX``', then the string is defining the threshold for the maximum intensity for each feature in the dataMatrix.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	911
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	912 - For example, '``FEATMAX:1e6:``' would specify that any feature would be excluded if no sample had an intensity for that feature greater than 1,000,000.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	913 - Although a maximum may be specified, it seems unlikely that this would be useful. Note that when the "maximum" is less than the "minimum" for the FEATMAX range specification, then the specification is ignored.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	914
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	915 ----------------------------------
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	916 Data transformation and imputation
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	917 ----------------------------------
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	918
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	919 Data may optionally be log2- or log10-transformed.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	920
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	921 Negative intensities are always substituted with missing values before imputation, even when no transformation is chosen.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	922
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	923 Missing intensity data values may optionally be imputed. Missing values may be substituted:
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	924
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	925 - with zeros (as may be appropriate for univariate analysis)
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	926 - with the median for the feature (as may be appropriate for multivariate analysis).
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	927
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	928 - Note that the median feature-intensity is computed for the samples before variable-range filters are applied.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	929
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	930 -----------------------------------------
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	931 Optional Computation of Treatment Centers
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	932 -----------------------------------------
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	933
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	934 A "center" for each treatment may be computed in lieu of all the samples for each treatment.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	935
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	936 - '``none``' - Return all samples; do not compute centers.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	937 - '``centroid``' - For each treatment, return only the centroid (the treatment-center computed as the mean intensity for each feature).
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	938 - '``median``' - For each treatment, return only the treatment-center computed as the median intensity for each feature.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	939 - '``medoid``' - For each treatment, return only the medoid (the sample most similar to the other samples for that treatment). This choice requires that the '``Imputation of missing values``' argument must not be set to '``none``'.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	940
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	941 The medoid is the sample having the smallest sum of its distances from other samples in the treatment:
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	942
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	943 - Because principal components are uncorrelated, distances are computed in the space defined by the principal-component scores to minimize the distortion of computed distances by correlated features.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	944 - Because principal components are used to compute distances, no missing values are permitted, which is why the '``Imputation of missing values``' argument must not be set to '``none``'.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	945 - The distances are used to identify the medoid using code adapted from https://web.archive.org/web/20191231012914/https://www.biostars.org/p/11987/#11989
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	946
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	947 -----------------------------------------------------------------------------
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	948
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	949 ----------------
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	950 WORKING EXAMPLES
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	951 ----------------
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	952
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	953 -----------
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	954 Input Files
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	955 -----------
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	956
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	957 +------------------------------------------------------------------------------------------------------------------------------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	958 \| Input File URL \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	959 +======================================================================================================================================================+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	960 \| https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/input_dataMatrix.tsv \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	961 +------------------------------------------------------------------------------------------------------------------------------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	962 \| https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/input_sampleMetadata.tsv \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	963 +------------------------------------------------------------------------------------------------------------------------------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	964 \| https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/input_variableMetadata.tsv \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	965 +------------------------------------------------------------------------------------------------------------------------------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	966
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	967 -------------------------------
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	968 Example without Range-Filtering
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	969 -------------------------------
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	970
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	971 This example retains only samples whose '``gender``' attribute is '``M``'.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	972
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	973 Input parameters
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	974
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	975 +---------------------------------------------+-------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	976 \| Input Parameter \| Value \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	977 +=============================================+===============================+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	978 \| Column that names the sample class \| gender \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	979 +---------------------------------------------+-------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	980 \| Sample-class names \| M \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	981 +---------------------------------------------+-------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	982 \| Exclude/include named classes \| filter-in \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	983 +---------------------------------------------+-------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	984 \| Use 'wild-cards' or 'regular expressions' \| wild-cards \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	985 +---------------------------------------------+-------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	986 \| Variable range-filters \| (Leave this field empty.) \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	987 +---------------------------------------------+-------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	988 \| Data transformation \| none \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	989 +---------------------------------------------+-------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	990 \| Missing-value imputation \| center \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	991 +---------------------------------------------+-------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	992 \| Sample-sort column \| sampleMetadata \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	993 +---------------------------------------------+-------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	994 \| Feature-sort column \| variableMetadata \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	995 +---------------------------------------------+-------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	996 \| Compute centers for classes \| none \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	997 +---------------------------------------------+-------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	998
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	999 Expected outputs
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1000
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1001 +-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1002 \| Expected Output \| Download from URL \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1003 +===================+=================================================================================================================================================+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1004 \| Data matrix \| https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/expected_dataMatrix.tsv \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1005 +-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1006 \| Sample metadata \| https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/expected_sampleMetadata.tsv \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1007 +-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1008 \| Variable metadata \| https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/expected_variableMetadata.tsv \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1009 +-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1010
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1011 ----------------------------
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1012 Example with Range-Filtering
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1013 ----------------------------
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1014
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1015 This example retains only features whose ``mz`` is greater than 200, whose ``rt`` is less than 800, and whose maximum intensity across all samples is 2,000,000.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1016 This example retains all samples (except those having zero variance for all feature), although it would be possible to filter on samples as well.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1017
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1018 Input parameters
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1019
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1020 +---------------------------------------------+-----------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1021 \| Input Parameter \| Value \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1022 +=============================================+===================================+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1023 \| Column that names the sample class \| sampleMetadata \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1024 +---------------------------------------------+-----------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1025 \| Sample-class names \| HU_13[48] \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1026 +---------------------------------------------+-----------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1027 \| Exclude/include named classes \| filter-out \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1028 +---------------------------------------------+-----------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1029 \| Use 'wild-cards' or 'regular expressions' \| regular-expressions \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1030 +---------------------------------------------+-----------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1031 \| Variable range-filters \| FEATMAX:20.93157:,mz:200:,rt::800 \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1032 +---------------------------------------------+-----------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1033 \| Data transformation \| log2 \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1034 +---------------------------------------------+-----------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1035 \| Missing-value imputation \| zero \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1036 +---------------------------------------------+-----------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1037 \| Sample-sort column \| sampleMetadata \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1038 +---------------------------------------------+-----------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1039 \| Feature-sort column \| variableMetadata \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1040 +---------------------------------------------+-----------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1041 \| Compute centers for classes \| none \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1042 +---------------------------------------------+-----------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1043
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1044 Expected outputs
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1045
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1046 +-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1047 \| Expected Output \| Download from URL \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1048 +===================+===================================================================================================================================================+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1049 \| Data matrix \| https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/rangefilter_dataMatrix.tsv \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1050 +-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1051 \| Sample metadata \| https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/rangefilter_sampleMetadata.tsv \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1052 +-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1053 \| Variable metadata \| https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/rangefilter_variableMetadata.tsv \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1054 +-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1055
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1056 --------------------------------
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1057 Example with Treatment-Centering
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1058 --------------------------------
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1059
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1060 This example retains only the samples that are medoids for their gender.
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1061
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1062 Input parameters
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1063
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1064 +---------------------------------------------+-----------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1065 \| Input Parameter \| Value \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1066 +=============================================+===================================+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1067 \| Column that names the sample class \| gender \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1068 +---------------------------------------------+-----------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1069 \| Sample-class names \| (Leave this field empty.) \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1070 +---------------------------------------------+-----------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1071 \| Exclude/include named classes \| filter-out \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1072 +---------------------------------------------+-----------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1073 \| Use 'wild-cards' or 'regular expressions' \| wild-cards \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1074 +---------------------------------------------+-----------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1075 \| Variable range-filters \| (Leave this field empty.) \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1076 +---------------------------------------------+-----------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1077 \| Data transformation \| none \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1078 +---------------------------------------------+-----------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1079 \| Missing-value imputation \| zero \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1080 +---------------------------------------------+-----------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1081 \| Sample-sort column \| gender \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1082 +---------------------------------------------+-----------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1083 \| Feature-sort column \| rt \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1084 +---------------------------------------------+-----------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1085 \| Compute centers for classes \| medoid \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1086 +---------------------------------------------+-----------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1087
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1088 Expected outputs
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1089
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1090 +-------------------+----------------------------------------------------------------------------------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1091 \| Expected Output \| Download from URL \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1092 +===================+==========================================================================================================+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1093 \| Data matrix \| https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/exp_cent_medoid_dm.tsv \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1094 +-------------------+----------------------------------------------------------------------------------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1095 \| Sample metadata \| https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/exp_cent_medoid_sm.tsv \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1096 +-------------------+----------------------------------------------------------------------------------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1097 \| Variable metadata \| https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/exp_cent_medoid_vm.tsv \|
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1098 +-------------------+----------------------------------------------------------------------------------------------------------+
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1099 ]]></help>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1100 <citations>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1101 <!-- Giacomoni_2014 W4M 2.5 -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1102 <citation type="doi">10.1093/bioinformatics/btu813</citation>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1103 <!-- Guitton_2017 W4M 3.0 -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1104 <citation type="doi">10.1016/j.biocel.2017.07.002</citation>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1105 <!-- Kuhl_2012 CAMERA -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1106 <citation type="doi">10.1021/ac202450g</citation>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1107 <!-- Smith_2006 XCMS -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1108 <citation type="doi">10.1021/ac051437y</citation>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1109 <!-- Thevenot_2015 Urinary metabolome statistics -->
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1110 <citation type="doi">10.1021/acs.jproteome.5b00354</citation>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1111 </citations>
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1112 <!--
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1113 vim:noet:sw=4:ts=4
08d4ca8bc6dd "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" eschen42 parents: diff changeset	1114 --> </tool>

Mercurial > repos > eschen42 > w4mclassfilter

annotate w4mclassfilter.xml @ 16:c0bb5667f5cd draft default tip