w4mcorcov: w4mcorcov.xml annotate

annotate w4mcorcov.xml @ 3:61935618f92c draft

planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582

author	eschen42
date	Sun, 12 Nov 2017 16:40:57 -0500
parents	a06344808ffc
children	d3bb34e764fe

rev	line source
3 61935618f92c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 2 diff changeset	1 <tool id="w4mcorcov" name="OPLS-DA_Contrasts" version="0.98.5">
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	2
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	3 <description>OPLS-DA Contrasts of Univariate Results</description>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	4
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	5 <requirements>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	6 <requirement type="package">r-batch</requirement>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	7 <requirement type="package">bioconductor-ropls</requirement>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	8 <!-- <requirement type="package">r-foreach</requirement> -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	9 </requirements>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	10
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	11 <stdio>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	12 <exit_code range="1:" level="fatal" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	13 </stdio>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	14
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	15 <command><![CDATA[
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	16 cd $__tool_directory__; Rscript w4mcorcov_wrapper.R
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	17 dataMatrix_in "$dataMatrix_in"
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	18 sampleMetadata_in "$sampleMetadata_in"
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	19 variableMetadata_in "$variableMetadata_in"
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	20 tesC "$tesC"
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	21 facC "$facC"
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	22 pairSigFeatOnly "$pairSigFeatOnly"
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	23 levCSV '$levCSV'
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	24 matchingC '$matchingC'
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	25 labelFeatures '$labelFeatures'
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	26 labelOrthoFeatures '$labelOrthoFeatures'
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	27 contrast_detail '$contrast_detail'
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	28 contrast_corcov '$contrast_corcov'
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	29 contrast_salience '$contrast_salience'
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	30 ]]></command>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	31
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	32 <inputs>
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	33 <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="Features x samples (tabular data - decimal: '.'; missing: NA; mode: numerical; separator: tab character)" />
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	34 <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="Samples x metadata (tabular data - decimal: '.'; missing: NA; mode: character or numerical; separator: tab character)" />
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	35 <param name="variableMetadata_in" label="Variable metadata file (ideally from Univariate)" type="data" format="tabular" help="Features x metadata (tabular data - decimal: '.'; missing: NA; mode: character or numerical; separator: tab character)" />
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	36 <param name="facC" label="Factor of interest" type="text" help="REQUIRED - The name of the column of sampleMetadata corresponding to the qualitative variable used to define the contrasts. Except when the 'Univariate Significance-test' is set to 'none', this also must be a portion of the column names in the variableMetadata file."/>
3 61935618f92c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 2 diff changeset	37 <param name="tesC" label="Univariate significance-test" type="select" help="Either 'none' or the name of the statistical test that was run by the 'Univariate' tool to produce the variableMetadata file; that name must also be a portion of the column names in that file.">
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	38 <option value="none">none - Display all features from variableMetadata (rather than choosing a subset based on significance in univariate testing)</option>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	39 <option value="ttest">ttest - Student's t-test (parametric test, qualitative factor with exactly 2 levels)</option>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	40 <option value="anova">anova - Analysis of variance (parametric test, qualitative factor with more than 2 levels)</option>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	41 <option value="wilcoxon">wilcoxon - Wilcoxon rank test (nonparametric test, qualitative factor with exactly 2 levels)</option>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	42 <option value="kruskal">kruskal - Kruskal-Wallis rank test (nonparametric test, qualitative factor with more than 2 levels)</option>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	43 </param>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	44 <param
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	45 name="pairSigFeatOnly"
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	46 type="boolean"
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	47 checked="true"
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	48 truevalue="TRUE"
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	49 falsevalue="FALSE"
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	50 label="Retain only pairwise-significant features"
3 61935618f92c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 2 diff changeset	51 help="When 'none' is chosen as the test, all features are included in the analysis (i. e., this parameter is ignored). Otherwise, when this option is set to 'Yes', analysis will be performed including only features that differ significantly for the pair of levels being contrasted; when set to 'No', any feature that varies significantly across all levels will be included (i.e., exclude any feature that is not significantly different across all levels). See examples below."/>
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	52 <param name="levCSV" label="Levels of interest" type="text" value = "*" help="Comma-separated level-names (or comma-less regular expressions to match level-names) to consider in analysis; must match at least two levels; levels must be non-numeric; may include wild cards or regular expressions. Note that extra space characters will affect results - 'a,b' is correct, but 'a , b' is not and may fail or give different results.">
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	53 <sanitizer>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	54 <valid initial="string.letters">
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	55 <add preset="string.digits"/>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	56 <add value="$" /> <!-- $ dollar, dollar-sign -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	57 <add value="(" /> <!-- ( left-paren -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	58 <add value=")" /> <!-- ) right-paren -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	59 <add value="" /> <!-- splat, asterisk -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	60 <add value="+" /> <!-- + plus -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	61 <add value="," /> <!-- , comma -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	62 <add value="-" /> <!-- - dash, minus-sign -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	63 <add value="." /> <!-- . dot, period -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	64 <add value=":" /> <!-- : colon -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	65 <add value=";" /> <!-- ; semi, semicolon -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	66 <add value="?" /> <!-- ? what, question mark -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	67 <add value="[" /> <!-- [ l-squib, left-squre-bracket -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	68 <add value="\" /> <!-- \ whack, backslash -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	69 <add value="]" /> <!-- ] r-squib, right-squre-bracket -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	70 <add value="^" /> <!-- ^ hat, caret -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	71 <add value="{" /> <!-- { l-cube, left-curly-bracket -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	72 <add value="\|" /> <!-- \| pipe -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	73 <add value="}" /> <!-- } r-cube, right-curly-bracket -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	74 <!-- IMPORTANT - Note that single and double quotes are not part of this list; they have the potential to make the 'command' section insecure or broken. -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	75 </valid>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	76 </sanitizer>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	77 </param>
3 61935618f92c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 2 diff changeset	78 <param name="matchingC" label="Level-name matching" type="select" help="How to specify level-names generically. (See help below for details on using wild cards or regular expressions.)">
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	79 <option value="none">do no generic matching (default)</option>
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	80 <option value="wildcard" selected="true">use wild-cards for matching level-names</option>
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	81 <option value="regex">use regular expressions for matching level-names</option>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	82 </param>
3 61935618f92c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 2 diff changeset	83 <param name="labelFeatures" type="text" value="3" label="How many features having extreme loadings should be labelled on cov-vs.-cor plot" help="Specify the number of features at each of the loading-extremes that should be labelled (with the name of the feature) on the covariance-vs.-correlation plot; specify 'ALL' to label all features or '0' to label no features; this choice has no effect on the OPLS-DA loadings plot."/>
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	84 <param
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	85 name="labelOrthoFeatures"
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	86 type="boolean"
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	87 checked="false"
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	88 truevalue="TRUE"
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	89 falsevalue="FALSE"
3 61935618f92c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 2 diff changeset	90 label="Label features having extreme orthogonal loadings"
61935618f92c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 2 diff changeset	91 help="When using the preceding parameter to label only features at the loading-extremess in the cor-vs.-cov plot, use 'no' here to label only features having extreme parallel loadings (loadp); this is the default. Choose 'yes' to add labels also to features having extreme orthogonal loadings (both loado and loadp); this may clutter the plot."/>
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	92 </inputs>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	93
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	94 <outputs>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	95 <!--
3 61935618f92c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 2 diff changeset	96 pdf1: summaries of each contrasts, clearly labelled by level=pair name
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	97 * first PCA score-plot
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	98 * then PLS score-plot
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	99 * then PLS S-PLOT; color in red features with VIP > 1; color in grey any non-pairwise-significant features, if these are included
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	100 -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	101 <data name="contrast_detail" label="${tool.name}_${variableMetadata_in.name}_detail" format="pdf" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	102 <!--
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	103 tsv1: cor and cov table with columns:
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	104 * feature-ID
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	105 * factor-level 1
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	106 * factor-level 2, lexically greater than level 1
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	107 * Wiklund_2008 correlation
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	108 * Wiklund_2008 covariance
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	109 * Galindo_Prieto_2014 VIP for predictive components, VIP[4,p]
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	110 * Galindo_Prieto_2014 VIP for orthogonal components, VIP[4,o]
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	111 * (When filtering on significance of univariate tests) Significance of test of null hypothesis that there is no difference between the two classes, i.e, the pair-wise test.
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	112 -->
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	113 <data name="contrast_corcov" label="${tool.name}_${variableMetadata_in.name}_corcov" format="tabular" />
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	114 <!--
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	115 tsv2: salience table with columns (experimental feature):
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	116 * feature-ID
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	117 * Salient level, i.e., for the feature, the class-level having the greatest median intensity
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	118 * Salient robust coefficient of variation, i.e., for the feature, the mean absolute deviation of the intensity for the salient level divided by the median intensity for the salient level
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	119 * Salience, i.e., for the feature, the median of the class-level having the greatest intensity divided by the mean of the medians for all class-levels.
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	120 -->
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	121 <data name="contrast_salience" label="${tool.name}_${variableMetadata_in.name}_salience" format="tabular" />
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	122 </outputs>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	123
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	124 <tests>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	125 <test>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	126 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	127 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	128 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	129 <param name="tesC" value="kruskal"/>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	130 <param name="facC" value="k10"/>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	131 <param name="pairSigFeatOnly" value="FALSE"/>
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	132 <param name="labelFeatures" value="3"/>
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	133 <param name="labelOrthogonalFeatures" value="FALSE"/>
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	134 <param name="levCSV" value="k[12],k[3-4]"/>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	135 <param name="matchingC" value="regex"/>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	136 <output name="contrast_corcov">
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	137 <assert_contents>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	138 <!-- column-labels line -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	139 <has_text text="featureID" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	140 <has_text text="factorLevel1" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	141 <has_text text="factorLevel2" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	142 <has_text text="correlation" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	143 <has_text text="covariance" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	144 <has_text text="vip4p" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	145 <has_text text="vip4o" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	146 <has_text text="level1Level2Sig" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	147 <!-- first matched line -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	148 <has_text text="M349.2383T700" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	149 <has_text text="-0.05007" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	150 <has_text text="-5.8455" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	151 <has_text text="0.0961269" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	152 <has_text text="0.1848301" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	153 <!-- second matched line -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	154 <has_text text="M207.9308T206" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	155 <has_text text="-0.2967565" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	156 <has_text text="-19.56942" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	157 <has_text text="1.6023" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	158 <has_text text="1.35368" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	159 <!-- third matched line -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	160 <has_text text="M211.0607T263" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	161 <has_text text="0.47052" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	162 <has_text text="15.910087" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	163 <has_text text="0.89838" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	164 <has_text text="0.125372" />
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	165 </assert_contents>
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	166 </output>
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	167 <output name="contrast_salience">
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	168 <assert_contents>
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	169 <!-- column-labels line -->
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	170 <has_text text="featureID" />
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	171 <has_text text="salientLevel" />
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	172 <has_text text="salientRCV" />
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	173 <has_text text="salience" />
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	174 <!-- first matched line -->
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	175 <has_text text="M349.2383T700" />
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	176 <has_text text="0.659554" />
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	177 <has_text text="8.81866595" />
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	178 <!-- second matched line -->
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	179 <has_text text="M207.9308T206" />
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	180 <has_text text="0.0578578" />
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	181 <has_text text="2.27527985" />
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	182 <!-- third matched line -->
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	183 <has_text text="M211.0607T263" />
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	184 <has_text text="9999" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	185 <has_text text="12.87766096" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	186 </assert_contents>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	187 </output>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	188 </test>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	189 <test>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	190 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	191 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	192 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	193 <param name="tesC" value="kruskal"/>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	194 <param name="facC" value="k10"/>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	195 <param name="pairSigFeatOnly" value="TRUE"/>
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	196 <param name="labelFeatures" value="3"/>
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	197 <param name="labelOrthogonalFeatures" value="TRUE"/>
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	198 <param name="levCSV" value="k[12],k[3-4]"/>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	199 <param name="matchingC" value="regex"/>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	200 <output name="contrast_corcov">
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	201 <assert_contents>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	202 <!-- column-labels line -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	203 <has_text text="featureID" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	204 <has_text text="factorLevel1" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	205 <has_text text="factorLevel2" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	206 <has_text text="correlation" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	207 <has_text text="covariance" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	208 <has_text text="vip4p" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	209 <has_text text="vip4o" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	210 <has_text text="level1Level2Sig" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	211 <!-- first matched line -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	212 <has_text text="M349.2383T700" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	213 <has_text text="-0.99601577" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	214 <has_text text="-947.55795176" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	215 <!-- second matched line -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	216 <has_text text="M207.9308T206" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	217 <has_text text="0.688549" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	218 <has_text text="58.22352" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	219 <has_text text="1.394687" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	220 <has_text text="0.06049885" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	221 <!-- third matched line -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	222 <has_text text="M211.0607T263" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	223 <has_text text="-0.572018" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	224 <has_text text="-14.57769" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	225 <has_text text="0.7780899" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	226 <has_text text="0.3678166776" />
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	227 </assert_contents>
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	228 </output>
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	229 <output name="contrast_salience">
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	230 <assert_contents>
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	231 <!-- column-labels line -->
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	232 <has_text text="featureID" />
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	233 <has_text text="salientLevel" />
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	234 <has_text text="salientRCV" />
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	235 <has_text text="salience" />
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	236 <!-- first matched line -->
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	237 <has_text text="M349.2383T700" />
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	238 <has_text text="0.659554" />
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	239 <has_text text="8.81866595" />
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	240 <!-- second matched line -->
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	241 <has_text text="M207.9308T206" />
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	242 <has_text text="0.0578578" />
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	243 <has_text text="2.27527985" />
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	244 <!-- third matched line -->
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	245 <has_text text="M211.0607T263" />
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	246 <has_text text="9999" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	247 <has_text text="12.87766096" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	248 </assert_contents>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	249 </output>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	250 </test>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	251 <test>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	252 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	253 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	254 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	255 <param name="tesC" value="none"/>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	256 <param name="facC" value="k10"/>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	257 <param name="pairSigFeatOnly" value="TRUE"/>
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	258 <param name="labelFeatures" value="3"/>
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	259 <param name="labelOrthogonalFeatures" value="FALSE"/>
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	260 <param name="levCSV" value="k[12],k[3-4]"/>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	261 <param name="matchingC" value="regex"/>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	262 <output name="contrast_corcov">
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	263 <assert_contents>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	264 <!-- column-labels line -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	265 <has_text text="featureID" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	266 <has_text text="factorLevel1" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	267 <has_text text="factorLevel2" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	268 <has_text text="correlation" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	269 <has_text text="covariance" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	270 <has_text text="vip4p" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	271 <has_text text="vip4o" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	272 <!-- first matched line -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	273 <has_text text="M349.2383T700" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	274 <has_text text="-0.64331257" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	275 <has_text text="-161.82220" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	276 <has_text text="1.862455" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	277 <has_text text="0.2105143" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	278 <!-- second matched line -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	279 <has_text text="M207.9308T206" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	280 <has_text text="-0.313507" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	281 <has_text text="-20.0476" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	282 <has_text text="1.6956987" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	283 <has_text text="1.19247" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	284 <!-- third matched line -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	285 <has_text text="M211.0607T263" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	286 <has_text text="-0.38986114" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	287 <has_text text="-23.747718" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	288 <has_text text="1.064296856" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	289 <has_text text="1.16507455" />
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	290 </assert_contents>
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	291 </output>
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	292 <output name="contrast_salience">
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	293 <assert_contents>
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	294 <!-- column-labels line -->
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	295 <has_text text="featureID" />
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	296 <has_text text="salientLevel" />
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	297 <has_text text="salientRCV" />
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	298 <has_text text="salience" />
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	299 <!-- first matched line -->
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	300 <has_text text="M349.2383T700" />
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	301 <has_text text="0.659554" />
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	302 <has_text text="8.81866595" />
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	303 <!-- second matched line -->
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	304 <has_text text="M207.9308T206" />
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	305 <has_text text="0.0578578" />
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	306 <has_text text="2.27527985" />
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	307 <!-- third matched line -->
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	308 <has_text text="M211.0607T263" />
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	309 <has_text text="9999" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	310 <has_text text="12.87766096" />
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	311 </assert_contents>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	312 </output>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	313 </test>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	314 </tests>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	315 <!--
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	316 .. \|reg\| unicode:: U+000AE .. REGISTERED SIGN - see http://docutils.sourceforge.net/docutils/parsers/rst/include/isonum.txt or /usr/share/docutils/parsers/rst/include/isonum.txt
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	317 -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	318 <help><![CDATA[
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	319
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	320 Run PLS-DA Contrasts of Univariate Results
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	321 ----------------------------------------------
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	322
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	323 Author - Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu)
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	324
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	325
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	326 Motivation
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	327 ----------
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	328
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	329 OPLS-DA\ :superscript:`®` and the SIMCA\ :superscript:`®` S-PLOT\ :superscript:`®` (Wiklund et al., 2008) may be employed to draw attention to metabolomic features that are potential biomarkers, i.e. features that are potentially useful to discriminate to which class a sample should be assigned (e.g. Sun et al., 2016). Workflow4Metabolomics (W4M, Giacomoni et al., 2014, Guitton et al., 2017) provides a suite of tools for preprocessing and statistical analysis of LC-MS, GC-MS, and NMR metabolomics data; however, it does not (as of release 3.0) include a tool for making the equivalent of an S-PLOT.
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	330
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	331 The S-PLOT is computed from mean-centered, pareto-scaled data. This plot presents the correlation of the first score vector from an OPLS-DA model with the sample-variables used to produce that model versus the covariance of the scores with the sample-variables. For OPLS-DA, the first score vector represents the variation among the sample-variables that is related to the predictor (i.e., the contrasting factor).
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	332
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	333 The primary aims of this tool are:
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	334
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	335 - To compute and visualize multiple contrasts with OPLS-DA and the covariance vs. correlation plot.
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	336 - To write the results to data files for use in further multivariate analysis or visualization.
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	337
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	338 Note: This tool only supports categorical factors with non-numeric level-names.
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	339
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	340 Description
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	341 -----------
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	342
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	343 The purpose of the 'PLS-DA Contrasts' tool is to visualize GC-MS or LC-MS features that are possible biomarkers.
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	344
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	345 The W4M 'Univariate' tool (Thévenot et al., 2015) adds the results of family-wise corrected pairwise significance-tests as columns of the variableMetadata dataset.
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	346 For instance, suppose that you ran Kruskal-Wallis testing for a column named 'cluster' in sampleMetadata that has values 'k1' and 'k2' and at least one other value.
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	347
3 61935618f92c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 2 diff changeset	348 - A column of variableMetadata would be labelled 'cluster_kruskal_sig' and would have values '1' and '0'; when the samples are grouped by 'cluster', '1' means that there is strong evidence against the hypothesis that there is no difference among the intensities for the feature across all sample-groups.
61935618f92c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 2 diff changeset	349 - A column of variableMetadata would be labelled 'cluster_kruskal_k1.k2_sig' and would have values '1' and '0', where '1' means that there is significant evidence against the hypothesis that samples from sampleMetadata whose 'cluster' column contains 'k1' or 'k2' have the same intensity for that feature.
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	350
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	351 The 'PLS-DA Contrasts' tool produces graphics and data for OPLS-DA contrasts of feature-intensities between significantly different pairs of factor-levels. For each factor-level, the tool performs a contrast with all other factor-levels combined and then separately with each other factor-level.
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	352
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	353 Along the left-to-right axis, the plots show the supervised projection of the variation explained by the predictor (i.e., the factor specified when invoking the tool); the top-to-bottom axis displays the variation that is orthogonal to the predictor level (i.e., independent of it).
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	354
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	355 Although this tool can be used in a purely exploratory manner by supplying the variableMetadata file without the columns added by the W4M 'Univariate' tool, the preferred workflow is to use univariate testing to exclude features that are not significantly different and use OPLS-DA to visualize the differences identified in univariate testing (Thévenot et al., 2015); an appropriate exception would be to visualize contrasts of a specific list of metabolites.
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	356
3 61935618f92c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 2 diff changeset	357 It must be stressed that there may be no single definitive computational approach to select features that are reliable biomarkers, especially from a small number of samples or experiments. A few possible choices are:
61935618f92c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 2 diff changeset	358
61935618f92c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 2 diff changeset	359 - picking features with maximum loadings along the projection parallel to the predictor (loadp),
61935618f92c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 2 diff changeset	360 - examining extreme values on S-PLOTs (for which covariance is linearly related to loadp),
61935618f92c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 2 diff changeset	361 - examining "variable importance in projection VIP for OPLS-DA" (Galindo-Prieto et al. 2014), and
61935618f92c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 2 diff changeset	362 - examining a feature's "selectivity ratio" (Rajalahti et al., 2009).
61935618f92c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 2 diff changeset	363
61935618f92c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 2 diff changeset	364 In this spirit, this tool reports the S-PLOT covariance and correlation (Wiklund op. cit.) and VIP metrics, and it introduces an informal "salience" metric to flag features that may merit attention without dimensional reduction; future versions may add selectivity ratio.
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	365
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	366 For a more systematic approach to biomarker identification, please consider the W4M 'biosigner' tool (Rinuardo et al. 2016), which applies three different identification metrics to the selection process.
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	367
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	368 Regardless of how any potential biomarker is identified, further validation analysis (e.g., independent confirmatory experiments) is needed before it is recommended for general application.
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	369
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	370
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	371 W4M Workflow Position
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	372 ---------------------
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	373
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	374 - Upstream tool: Univariate (category: Statistical Analysis) or (not generally recommended) any Preprocessing tool that produces or updates a 'variableMetadata' file.
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	375 - Downstream tool categories: Statistical Analysis
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	376
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	377 Input files
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	378 -----------
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	379
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	380 +----------------------+-----------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	381 \| File \| Format \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	382 +======================+===========+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	383 \| Data matrix \| tabular \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	384 +----------------------+-----------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	385 \| Sample metadata \| tabular \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	386 +----------------------+-----------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	387 \| Variable metadata \| tabular \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	388 +----------------------+-----------+
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	389
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	390 Output files
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	391 ------------
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	392
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	393 +-------------------------------------------+-----------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	394 \| File \| Format \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	395 +===========================================+===========+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	396 \| Contrast detail \| pdf \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	397 +-------------------------------------------+-----------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	398 \| Contrast "corrlation and covariance" data \| tabular \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	399 +-------------------------------------------+-----------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	400 \| Feature "salience" data \| tabular \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	401 +-------------------------------------------+-----------+
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	402
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	403 Parameters
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	404 ----------
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	405
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	406 [IN] Data matrix file
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	407 \| variable x sample dataMatrix (tabular separated values) file of the numeric data matrix, with '.' as decimal, and 'NA' for missing values; the table must not contain metadata apart from row and column names; the row and column names must be identical to the rownames of the sample and variable metadata, respectively (see below)
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	408 \|
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	409
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	410 [IN] Sample metadata file
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	411 \| sample x metadata sampleMetadata (tabular separated values) file of the numeric and/or character sample metadata, with '.' as decimal and 'NA' for missing values
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	412 \|
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	413
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	414 [IN] Variable metadata file
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	415 \| variable x metadata variableMetadata (tabular separated values) file of the numeric and/or character variable metadata, with '.' as decimal and 'NA' for missing values
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	416 \|
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	417
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	418 [IN] Test
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	419 \| Name of the statistical test - a component of column names in variable metadata table
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	420 \| May be one of 'none', 'ttest', 'gwilcoxon', 'anova', 'kruskal', 'pearson', 'spearman'
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	421 \|
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	422
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	423 [IN] Factor of interest
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	424 \| Name of the column of sampleMetadata corresponding to the qualitative or quantitative variable
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	425 \|
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	426
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	427 [IN] Retain only pairwise-significant features
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	428 \| When true, for each contrast of two levels, include only those features which pass the significance threshold for that contrast. Choosing true results in an OPLS-DA model that better reflects and visualizes the difference detected by univariate analysis, with somewhat increased reliability of prediction (as assessed by cross-validation).
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	429 \| When false, include all features that pass the significance threshold when testing for difference across all factor-levels. This choice produces a plot that displays more features but is not necessarily more informative.
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	430 \| Note that when 'Test' is 'none', all features are included in the analysis and this parameter has no effect.
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	431 \|
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	432
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	433 [IN] Levels of interest
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	434 \| Comma-separated level-names (or comma-less regular expressions to match level-names) to consider in analysis; must match at least two levels; may include wild cards or regular expressions.
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	435 \|
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	436
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	437 [IN] Level-name matching
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	438 \| Indicator of how levels are to be specified generically (if at all) - wild cards, regular expressions, or none (no generic matching).
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	439 \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	440
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	441 [IN] Label how many extreme features
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	442 \| Specify the number of features at each of the loading-extremes that should be labelled (with the name of the feature) on the covariance-vs.-correlation plot; specify 'ALL' to label all features; this choice has no effect on the OPLS-DA loadings plot.
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	443 \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	444
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	445 [IN] Label features with extreme loado
3 61935618f92c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 2 diff changeset	446 \| If the previous parameter has limited the the number of features to be labelled at each of the loading-extremes, then the extreme values for both loado and loadp will be labelled when this parameter is set to 'yes'; otherwise (in the default case) only extreme values for loadp will be lableld. The default was chosen to make the plot less cluttered.
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	447 \|
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	448
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	449 [OUT] Contrast-detail output PDF
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	450 \| Several plots for each two-projection OPLS-DA analysis:
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	451
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	452 - (top-left) correlation-versus-covariance plot of OPLS-DA results (a work-alike for the S-PLOT, computed using formula in Supplement to Wiklund, op. cit.); point-color becomes saturated as the "variable importance in projection to the predictive components" (VIP\ :subscript:`4,p` from Galindo-Prieto et al. 2014) ranges from 0.83 and 1.21 (Mehmood et al. 2012)
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	453 - (bottom-left) model-overview plot for the two projections; grey bars are the correlation coefficient for the fitted data; black bars indicate performance in cross-validation tests (Thévenot, 2017)
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	454 - (top-right) OPLS-DA scores-plot for the two projections (Thévenot et al., 2015)
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	455 - (bottom-right) OPLS-DA loadings-plot for the two projections (ibid.)
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	456
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	457 [OUT] Contrast Correlation-Covarinace data TABULAR
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	458 \| A tab-separated values file of metadata for each feature for each contrast in which it was included.
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	459 \| Thus, a given feature may appear many times, but the combination of featureID, factorLevel1, and factorLevel2 will be unique.
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	460 \| This file has the following columns:
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	461
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	462 - featureID - feature-identifier
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	463 - factorLevel1 - factor-level 1
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	464 - factorLevel2 - factor-level 2 (or "other" when contrasting factor-level 1 with all other levels)
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	465 - correlation - correlation of the features projection explaining the difference between the features, < 0 when intensity for level 1 is greater (from formula in Supplement to Wiklund, op. cit.). Note that, for a given contrast, there is a linear relationship between 'loadp' and 'correlation'.
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	466 - covariance - covariance of the features projection explaining the difference between the features, < 0 when intensity for level 1 is greater (from formula in ibid.)
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	467 - vip4p - "variable importance in projection" to the predictive projection, VIP\ :subscript:`4,p` (Galindo-Prieto op. cit.)
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	468 - vip4o - "variable importance in projection" to the orthogonal projection, VIP\ :subscript:`4,o` (ibid.)
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	469 - loadp - variable loading for the predictive projection (Wiklund op. cit.)
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	470 - loado - variable loading for the orthogonal projection (ibid.)
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	471 - level1Level2Sig - (Only present when a test other than "none" is chosen) '1' when feature varies significantly across all classes (i.e., not pair-wise); '0' otherwise
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	472
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	473 [OUT] Feature "Salience" data TABULAR
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	474 \| Metrics for the "salient level" for each feature, i.e., the level at which the feature is more prominent than any other level. This is not at all related to the SIMCA OPLS-DA S-PLOT; rather, it is intended as a potential (and unproven) way to identify features that may suggest potential biomarkers without dimensional reduction of data. This is a tab-separated values file having the following columns:
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	475
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	476 - featureID - feature identifier
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	477 - salientLevel - salient level, i.e., for the feature, the class-level having the greatest median intensity
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	478 - salientRCV - salient robust coefficient of variation, i.e., for the feature, the mean absolute deviation of the intensity for the salient level divided by the median intensity for the salient level
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	479 - salience - salience, i.e., for the feature, the median of the class-level having the greatest intensity divided by the mean of the medians for all class-levels
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	480
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	481 Wild card patterns to match level-names
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	482 ---------------------------------------
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	483
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	484 "wild card" patterns may be used to select level-names.
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	485
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	486 - use '``?``' to match a single character
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	487 - use '``*``' to match zero or more characters
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	488 - the entire pattern must match the level name
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	489
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	490 For example
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	491
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	492 - '``??.le*``' matches '``my.level``' but not '``my.own.level``'
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	493 - '``*.level``' matches '``my.level``' and '``my.own.level``'
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	494 - '``*.level``' matches neither '``my.level``' nor '``my.own.level``'
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	495
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	496 Regular expression patterns to match level-names
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	497 ------------------------------------------------
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	498
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	499 "regular expression" patterns may be used to select level-names.
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	500
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	501 POSIX 1003.2 standard regular expressions allow precise pattern-matching and are exhaustively defined at:
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	502 http://pubs.opengroup.org/onlinepubs/9699919799/basedefs/V1_chap09.html
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	503
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	504 However, only a few basic building blocks of regular expressions need to be mastered for most cases:
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	505
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	506 - '``^``' matches the beginning of a level-name
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	507 - '``$``' matches the end of a level-name
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	508 - '``.``' outside of square brackets matches a single character
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	509 - '``*``' matches character specified immediately before zero or more times
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	510 - Square brackets specify a set of characters to be matched. Within square brackets:
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	511
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	512 - '``^``' as the first character specifies that the list of characters are those that should not be matched.
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	513 - '``-``' is used to specify ranges of characters
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	514
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	515 Caveat: The tool wrapper uses the comma ('``,``') to split a list of sample-level names, so commas may not be used within regular expressions for this tool.
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	516
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	517 First Example: Consider a field of level-names consisting of '``marq3,marq6,marq9,marq12,front3,front6,front9,front12``'
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	518
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	519 - The regular expression '``^front[0-9][0-9]*$``' will match the same sample-levels as '``front3,front6,front9,front12``'
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	520 - The regular expression '``^[a-z][a-z]3$``' will match the same sample-levels as '``front3,marq3``'
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	521 - The regular expression '``^[a-z][a-z]12$``' will match the same sample-levels as '``front12,marq12``'
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	522 - The regular expression '``^[a-z][a-z][0-9]$``' will match the same sample-levels as '``front3,front6,front9,marq3,marq6,marq9``'
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	523
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	524 Second Example: Consider these regular expression patterns as possible matches to a sample-level name '``AB0123``':
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	525
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	526 - '``^[A-Z][A-Z][0-9][0-9]$``' - MATCHES '``^AB0123$*``'
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	527 - '``^[A-Z][A-Z][0-9][0-9]$``' - MATCHES '``^AB0123$``'
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	528 - '``^[A-Z][0-9]``' - MATCHES '``^A* B0123$``' - first character is a letter, '``*``' can specify zero characters, and end of line did not need to be matched.
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	529 - '``^[A-Z][A-Z][0-9]``' - MATCHES '``^AB0 123$``' - first two characters are letters aind the third is a digit.
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	530 - '``^[A-Z][A-Z]*[0-9][0-9]$``' - NO MATCH - the name does not end with the pattern '``[A-Z][0-9][0-9]$``', i.e., it ends with four digits, not two.
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	531 - '``^[A-Z][0-9]*$``' - NO MATCH - the pattern specifies that second character and all those that follow, if present, must be digits.
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	532
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	533 Working examples
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	534 ----------------
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	535
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	536 Input files
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	537
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	538 +-------------------+-------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	539 \| Input File \| Download from URL \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	540 +===================+===================================================================================================================+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	541 \| Data matrix \| https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/input_dataMatrix.tsv \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	542 +-------------------+-------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	543 \| Sample metadata \| https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/input_sampleMetadata.tsv \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	544 +-------------------+-------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	545 \| Variable metadata \| https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/input_variableMetadata.tsv \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	546 +-------------------+-------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	547
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	548 Example 1: Include in the analysis only features identified as pair-wise significant in the Univariate test.
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	549
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	550 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	551 \| Input Parameter or Result \| Value \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	552 +============================================+========================================================================================================================================+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	553 \| Factor of interest \| k10 \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	554 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	555 \| Univariate Significance-Test \| kruskal \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	556 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	557 \| Retain only pairwise-significant features \| Yes \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	558 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	559 \| Levels of interest \| k[12],k[3-4] \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	560 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	561 \| Level-name matching \| use regular expressions for matching level-names \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	562 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	563 \| Number of features having extreme loadings \| ALL \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	564 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	565 \| Output primary table \| https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_corcov.tsv \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	566 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	567 \| Output salience table \| https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_salience.tsv \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	568 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	569 \| Output figures PDF \| https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_detail.pdf \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	570 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	571
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	572 Example 2: Include in the analysis only features identified as overall-significant in the Univariate test. Note that this even includes these features in contrasts where they were not determined to be pair-wise significant in the Univariate test. Thus, more features are included than in Example 1.
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	573
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	574 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	575 \| Input Parameter or Result \| Value \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	576 +============================================+========================================================================================================================================+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	577 \| Factor of interest \| k10 \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	578 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	579 \| Univariate Significance-Test \| kruskal \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	580 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	581 \| Retain only pairwise-significant features \| No \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	582 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	583 \| Levels of interest \| ``*`` \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	584 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	585 \| Level-name matching \| use wild cards for matching level-names \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	586 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	587 \| Number of features having extreme loadings \| 5 \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	588 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	589 \| Output primary table \| https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_corcov_all.tsv \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	590 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	591 \| Output salience table \| https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_salience_all.tsv \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	592 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	593 \| Output figures PDF \| https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_detail_all.pdf \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	594 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	595
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	596 Example 3: Include all features in the analysis without regard to Univariate testing. Univariate testing is not even a pre-requisite to using the tool when 'none' is selected for the test. Thus, more features are included than in Example 2.
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	597
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	598 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	599 \| Input Parameter or Result \| Value \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	600 +============================================+========================================================================================================================================+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	601 \| Factor of interest \| k10 \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	602 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	603 \| Univariate Significance-Test \| none \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	604 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	605 \| Retain only pairwise-significant features \| No \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	606 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	607 \| Levels of interest \| k[12],k[3-4] \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	608 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	609 \| Level-name matching \| use regular expressions for matching level-names \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	610 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	611 \| Number of features having extreme loadings \| 0 \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	612 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	613 \| Output primary table \| https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_corcov_global.tsv \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	614 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	615 \| Output salience table \| https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_salience_global.tsv \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	616 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	617 \| Output figures PDF \| https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_detail_global.pdf \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	618 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	619
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	620 Example 4: Analysis of a two-level factor (including all features). This suppresses the contrasts of "each factor vs. the aggregate of all the others".
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	621
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	622 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	623 \| Input Parameter or Result \| Value \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	624 +============================================+========================================================================================================================================+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	625 \| Factor of interest \| lohi \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	626 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	627 \| Univariate Significance-Test \| none \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	628 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	629 \| Retain only pairwise-significant features \| No \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	630 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	631 \| Levels of interest \| low,high \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	632 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	633 \| Level-name matching \| use regular expressions for matching level-names \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	634 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	635 \| Number of features having extreme loadings \| 3 \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	636 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	637 \| Output primary table \| https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_corcov_lohi.tsv \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	638 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	639 \| Output salience table \| https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_salience_lohi.tsv \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	640 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	641 \| Output figures PDF \| https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_detail_lohi.pdf \|
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	642 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	643
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	644
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	645 Trademarks
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	646 ----------
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	647
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	648 OPLS-DA\ :superscript:`®`, SIMCA\ :superscript:`®`, and S-PLOT\ :superscript:`®` are registered trademarks of the Umetrics company. http://umetrics.com/about-us/trademarks
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	649
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	650
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	651 Release notes
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	652 -------------
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	653
3 61935618f92c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 2 diff changeset	654 0.98.5
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	655
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	656 - bug fix: fit feature-labels within clipping region of cor-vs.cov plot
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	657 - new feature: optionally (and by default) suppress labels for features with extreme orthogonal loadings
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	658
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	659 0.98.3
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	660
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	661 - add support for two-level factors
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	662 - add adjusted mz and rt to output tables
3 61935618f92c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 2 diff changeset	663 - allow explicitly setting the number of features with extreme loadings to be labelled on the correlation vs. covariance plot
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	664 - add loadings to corcov table
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	665
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	666 0.98.2
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	667
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	668 - first release
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	669
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	670
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	671 ]]></help>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	672 <citations>
3 61935618f92c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 2 diff changeset	673 <citation type="doi">10.5281/zenodo.1034784</citation>
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	674 <!-- Galindo_Prieto_2014 Variable influence on projection (VIP) for OPLS -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	675 <citation type="doi">10.1002/cem.2627</citation>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	676 <!-- Giacomoni_2014 W4M 2.5 -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	677 <citation type="doi">10.1093/bioinformatics/btu813</citation>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	678 <!-- Guitton_2017 W4M 3.0 -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	679 <citation type="doi">10.1016/j.biocel.2017.07.002</citation>
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	680 <!-- Mehmood_2012 PLS-based variable-selection -->
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	681 <citation type="doi">10.1186/1748-7188-6-27</citation>
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	682 <!-- Rajalahti_2009 Biomarker discovery using selectivity ratio -->
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	683 <citation type="doi">10.1016/j.chemolab.2008.08.004</citation>
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	684 <!-- Rinuardo 2016 -->
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	685 <citation type="doi">10.3389/fmolb.2016.00026</citation>
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	686 <!-- Sun_2016 Urinary Biomarkers for adolescent idiopathic scoliosis -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	687 <citation type="doi">10.1038/srep22274</citation>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	688 <!-- Th_venot_2015 Urinary metabolome statistics -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	689 <citation type="doi">10.1021/acs.jproteome.5b00354</citation>
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	690 <!-- ropls package -->
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	691 <citation type="bibtex"><![CDATA[
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	692 @incollection{Thevenot_ropls_2017,
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	693 author = {Th{\'{e}}venot, Etienne A.},
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	694 title = {ropls: PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data},
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	695 publisher = {bioconductor.org},
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	696 year = {2017},
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	697 doi = {10.18129/B9.bioc.ropls},
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	698 booktitle = {Bioconductor: Open source software for bioinformatics},
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	699 address = {Roswell Park Cancer Institute},
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	700 }
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	701 ]]></citation>
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	702 <!-- Wiklund_2008 OPLS PLS-DA and S-PLOT -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	703 <citation type="doi">10.1021/ac0713510</citation>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	704 </citations>
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	705 <!--
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	706 vim:noet:sw=4:ts=4
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	707 -->
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	708 </tool>

Mercurial > repos > eschen42 > w4mcorcov

annotate w4mcorcov.xml @ 3:61935618f92c draft