w4mcorcov: w4mcorcov.xml annotate

annotate w4mcorcov.xml @ 10:9a52306991b3 draft

planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552

author	eschen42
date	Sat, 01 Sep 2018 11:33:03 -0400
parents	06c51af11531
children	ddcc33ff3205

rev	line source
10 9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	1 <tool id="w4mcorcov" name="OPLS-DA_Contrasts" version="0.98.14">
8 342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	2 <description>OPLS-DA Contrasts of Univariate Results</description>
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	3 <macros>
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	4 <xml name="paramPairSigFeatOnly">
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	5 <param name="pairSigFeatOnly" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE"
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	6 label="Retain only pairwise-significant features"
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	7 help="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." />
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	8 </xml>
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	9 <xml name="cplots">
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	10 <param name="cplot_y" label="C-plot Y-axis" type="select" help="Choose the Y-axis for C-plots.">
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	11 <option value="correlation">Plot VIP versus correlation</option>
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	12 <option value="covariance">Plot VIP versus covariance</option>
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	13 </param>
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	14 <param name="cplot_p" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE"
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	15 label="Produce predictor C-plot"
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	16 help="When this option is set to 'Yes', correlation will be plotted against vip4 for predictor loadings." />
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	17 <param name="cplot_o" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE"
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	18 label="Produce orthogonal C-plot"
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	19 help="When this option is set to 'Yes', correlation will be plotted against vip4 for orthogonal loadings." />
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	20 </xml>
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	21 </macros>
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	22 <requirements>
9 06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	23 <!--
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	24 <requirement type="package" version="3.4.1">r-base</requirement>
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	25 <requirement type="package" version="1.1_4">r-batch</requirement>
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	26 <requirement type="package" version="1.2.14">bioconductor-ropls</requirement>
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	27 -->
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	28 <requirement type="package">r-base</requirement>
8 342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	29 <requirement type="package">r-batch</requirement>
9 06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	30 <requirement type="package" version="1.10.0">bioconductor-ropls</requirement>
8 342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	31 </requirements>
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	32 <command detect_errors="aggressive"><![CDATA[
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	33 Rscript '$__tool_directory__/w4mcorcov_wrapper.R'
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	34 dataMatrix_in '$dataMatrix_in'
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	35 sampleMetadata_in '$sampleMetadata_in'
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	36 variableMetadata_in '$variableMetadata_in'
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	37 facC '$facC'
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	38 #if str( $signif_test.tesC ) == "none":
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	39 tesC "none"
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	40 pairSigFeatOnly "FALSE"
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	41 #else:
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	42 tesC '$signif_test.tesC'
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	43 pairSigFeatOnly '$signif_test.pairSigFeatOnly'
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	44 #end if
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	45 levCSV '$levCSV'
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	46 matchingC '$matchingC'
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	47 labelFeatures '$labelFeatures'
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	48 #if str( $xplots.expPlot ) == "none":
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	49 cplot_p "FALSE"
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	50 cplot_o "FALSE"
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	51 cplot_y "correlation"
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	52 #else if str( $xplots.expPlot ) == "cplot":
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	53 cplot_p '$xplots.cplot_p'
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	54 cplot_o '$xplots.cplot_o'
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	55 cplot_y '$xplots.cplot_y'
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	56 #end if
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	57 contrast_detail '$contrast_detail'
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	58 contrast_corcov '$contrast_corcov'
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	59 contrast_salience '$contrast_salience'
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	60 ]]></command>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	61
8 342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	62 <inputs>
9 06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	63 <param name="dataMatrix_in" format="tabular" label="Data matrix file" type="data"
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	64 help="variables ✖ samples" />
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	65 <param name="sampleMetadata_in" format="tabular" label="Sample metadata file" type="data"
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	66 help="sample metadata, one row per sample" />
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	67 <param name="variableMetadata_in" format="tabular" label="Variable metadata file (ideally from Univariate)"
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	68 type="data" help="variable metadata, one row per variable" />
8 342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	69 <param name="facC" type="text"
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	70 label="Factor of interest"
10 9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	71 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.">
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	72 <sanitizer>
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	73 <valid initial="string.letters">
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	74 <add preset="string.digits"/>
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	75 <add value="." /> <!-- dot, period -->
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	76 <add value="_" /> <!-- underscore -->
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	77 <!-- R does not permit dashes in column names; neither does SQL -->
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	78 </valid>
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	79 </sanitizer>
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	80 </param>
8 342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	81 <conditional name="signif_test">
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	82 <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.">
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	83 <option value="none">none - Display all features from variableMetadata (rather than choosing a subset based on significance in univariate testing)</option>
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	84 <option value="ttest">ttest - Student's t-test (parametric test, qualitative factor with exactly 2 levels)</option>
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	85 <option value="anova">anova - Analysis of variance (parametric test, qualitative factor with more than 2 levels)</option>
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	86 <option value="wilcoxon">wilcoxon - Wilcoxon rank test (nonparametric test, qualitative factor with exactly 2 levels)</option>
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	87 <option value="kruskal">kruskal - Kruskal-Wallis rank test (nonparametric test, qualitative factor with more than 2 levels)</option>
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	88 </param>
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	89 <when value="none" />
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	90 <when value="ttest">
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	91 <expand macro="paramPairSigFeatOnly" />
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	92 </when>
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	93 <when value="anova">
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	94 <expand macro="paramPairSigFeatOnly" />
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	95 </when>
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	96 <when value="wilcoxon">
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	97 <expand macro="paramPairSigFeatOnly" />
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	98 </when>
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	99 <when value="kruskal">
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	100 <expand macro="paramPairSigFeatOnly" />
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	101 </when>
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	102 </conditional>
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	103 <param name="levCSV" type="text" value="*" label="Levels of interest"
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	104 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.">
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	105 <sanitizer>
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	106 <valid initial="string.letters">
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	107 <add preset="string.digits"/>
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	108 <add value="$" /> <!-- $ dollar, dollar-sign -->
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	109 <add value="(" /> <!-- ( left-paren -->
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	110 <add value=")" /> <!-- ) right-paren -->
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	111 <add value="" /> <!-- splat, asterisk -->
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	112 <add value="+" /> <!-- + plus -->
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	113 <add value="," /> <!-- , comma -->
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	114 <add value="-" /> <!-- - dash, minus-sign -->
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	115 <add value="." /> <!-- . dot, period -->
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	116 <add value=":" /> <!-- : colon -->
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	117 <add value=";" /> <!-- ; semi, semicolon -->
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	118 <add value="?" /> <!-- ? what, question mark -->
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	119 <add value="[" /> <!-- [ l-squib, left-squre-bracket -->
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	120 <add value="\" /> <!-- \ whack, backslash -->
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	121 <add value="]" /> <!-- ] r-squib, right-squre-bracket -->
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	122 <add value="^" /> <!-- ^ hat, caret -->
10 9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	123 <add value="_" /> <!-- underscore -->
8 342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	124 <add value="{" /> <!-- { l-cube, left-curly-bracket -->
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	125 <add value="\|" /> <!-- \| pipe -->
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	126 <add value="}" /> <!-- } r-cube, right-curly-bracket -->
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	127 <!-- 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. -->
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	128 </valid>
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	129 </sanitizer>
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	130 </param>
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	131 <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.)">
10 9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	132 <option value="none">do no generic matching</option>
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	133 <option value="wildcard" selected="true">use wild-cards for matching level-names (default)</option>
8 342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	134 <option value="regex">use regular expressions for matching level-names</option>
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	135 </param>
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	136 <param name="labelFeatures" type="text" value="3"
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	137 label="How many features having extreme loadings should be labelled on cov-vs.-cor plot"
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	138 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."/>
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	139 <conditional name="xplots">
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	140 <param name="expPlot" label="Extra plots to include" type="select" help="Choosing 'none' hides further choices.">
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	141 <option value="none">Do not include additonal extra plots.</option>
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	142 <option value="cplot">Include C-plots (predictor-loading vs. 'vip4p' and orthogonal-loading versus 'vip4o')</option>
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	143 </param>
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	144 <when value="none" />
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	145 <when value="cplot">
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	146 <expand macro="cplots" />
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	147 </when>
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	148 </conditional>
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	149 </inputs>
342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	150 <outputs>
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	151 <!--
2 e03582f26617 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 1 diff changeset	152 pdf1: summaries of each contrasts, clearly labelled by level=pair name
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	153 * first PCA score-plot
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	154 * then PLS score-plot
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	155 * then PLS S-PLOT; color in red features with VIP > 1; color in grey any non-pairwise-significant features, if these are included
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	156 -->
8 342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	157 <data name="contrast_detail" format="pdf" label="${tool.name}_${variableMetadata_in.name}_detail" />
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	158 <!--
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	159 tsv1: cor and cov table with columns:
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	160 * feature-ID
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	161 * factor-level 1
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	162 * factor-level 2, lexically greater than level 1
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	163 * Wiklund_2008 correlation
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	164 * Wiklund_2008 covariance
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	165 * Galindo_Prieto_2014 VIP for predictive components, VIP[4,p]
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	166 * Galindo_Prieto_2014 VIP for orthogonal components, VIP[4,o]
9 06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	167 * 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.
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	168 -->
8 342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	169 <data name="contrast_corcov" format="tabular" label="${tool.name}_${variableMetadata_in.name}_corcov" />
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	170 <!--
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	171 tsv2: salience table with columns (experimental feature):
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	172 * feature-ID
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	173 * Salient level, i.e., for the feature, the class-level having the greatest median intensity
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	174 * 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
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	175 * 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.
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	176 -->
8 342570ad880c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab eschen42 parents: 7 diff changeset	177 <data name="contrast_salience" format="tabular" label="${tool.name}_${variableMetadata_in.name}_salience" />
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	178 </outputs>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	179 <tests>
6 7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	180 <!-- test #1 -->
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	181 <test>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	182 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	183 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	184 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	185 <param name="tesC" value="kruskal"/>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	186 <param name="facC" value="k10"/>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	187 <param name="pairSigFeatOnly" value="FALSE"/>
2 e03582f26617 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 1 diff changeset	188 <param name="labelFeatures" value="3"/>
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	189 <param name="levCSV" value="k[12],k[3-4]"/>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	190 <param name="matchingC" value="regex"/>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	191 <output name="contrast_corcov">
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	192 <assert_contents>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	193 <!-- column-labels line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	194 <has_text text="featureID" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	195 <has_text text="factorLevel1" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	196 <has_text text="factorLevel2" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	197 <has_text text="correlation" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	198 <has_text text="covariance" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	199 <has_text text="vip4p" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	200 <has_text text="vip4o" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	201 <has_text text="level1Level2Sig" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	202 <!-- first matched line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	203 <has_text text="M349.2383T700" />
7 066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066 eschen42 parents: 6 diff changeset	204 <has_text text="-0.3704185" />
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066 eschen42 parents: 6 diff changeset	205 <has_text text="-36.6668927" />
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066 eschen42 parents: 6 diff changeset	206 <has_text text="0.4914638" />
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066 eschen42 parents: 6 diff changeset	207 <has_text text="0.01302117" />
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	208 <!-- second matched line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	209 <has_text text="M207.9308T206" />
7 066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066 eschen42 parents: 6 diff changeset	210 <has_text text="0.3235022" />
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066 eschen42 parents: 6 diff changeset	211 <has_text text="5.97529097" />
6 7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	212 <has_text text="0.207196379" />
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	213 <has_text text="0.04438632" />
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	214 </assert_contents>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	215 </output>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	216 <output name="contrast_salience">
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	217 <assert_contents>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	218 <!-- column-labels line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	219 <has_text text="featureID" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	220 <has_text text="salientLevel" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	221 <has_text text="salientRCV" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	222 <has_text text="salience" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	223 <!-- first matched line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	224 <has_text text="M349.2383T700" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	225 <has_text text="0.659554" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	226 <has_text text="8.81866595" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	227 <!-- second matched line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	228 <has_text text="M207.9308T206" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	229 <has_text text="0.0578578" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	230 <has_text text="2.27527985" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	231 <!-- third matched line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	232 <has_text text="M211.0607T263" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	233 <has_text text="9999" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	234 <has_text text="12.87766096" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	235 </assert_contents>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	236 </output>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	237 </test>
6 7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	238 <!-- test #2 -->
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	239 <test>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	240 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	241 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	242 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	243 <param name="tesC" value="kruskal"/>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	244 <param name="facC" value="k10"/>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	245 <param name="pairSigFeatOnly" value="TRUE"/>
2 e03582f26617 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 1 diff changeset	246 <param name="labelFeatures" value="3"/>
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	247 <param name="levCSV" value="k[12],k[3-4]"/>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	248 <param name="matchingC" value="regex"/>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	249 <output name="contrast_corcov">
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	250 <assert_contents>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	251 <!-- column-labels line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	252 <has_text text="featureID" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	253 <has_text text="factorLevel1" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	254 <has_text text="factorLevel2" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	255 <has_text text="correlation" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	256 <has_text text="covariance" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	257 <has_text text="vip4p" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	258 <has_text text="vip4o" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	259 <has_text text="level1Level2Sig" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	260 <!-- first matched line -->
6 7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	261 <has_text text="M200.005T296" />
7 066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066 eschen42 parents: 6 diff changeset	262 <has_text text="-0.24533821" />
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066 eschen42 parents: 6 diff changeset	263 <has_text text="-3.3573953" />
6 7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	264 <has_text text="0.1157346" />
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	265 <has_text text="0.0647860" />
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	266 </assert_contents>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	267 </output>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	268 <output name="contrast_salience">
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	269 <assert_contents>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	270 <!-- column-labels line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	271 <has_text text="featureID" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	272 <has_text text="salientLevel" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	273 <has_text text="salientRCV" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	274 <has_text text="salience" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	275 <!-- first matched line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	276 <has_text text="M349.2383T700" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	277 <has_text text="0.659554" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	278 <has_text text="8.81866595" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	279 <!-- second matched line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	280 <has_text text="M207.9308T206" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	281 <has_text text="0.0578578" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	282 <has_text text="2.27527985" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	283 <!-- third matched line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	284 <has_text text="M211.0607T263" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	285 <has_text text="9999" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	286 <has_text text="12.87766096" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	287 </assert_contents>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	288 </output>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	289 </test>
6 7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	290 <!-- test #3 -->
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	291 <test>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	292 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	293 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	294 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	295 <param name="tesC" value="none"/>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	296 <param name="facC" value="k10"/>
2 e03582f26617 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 1 diff changeset	297 <param name="labelFeatures" value="3"/>
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	298 <param name="levCSV" value="k[12],k[3-4]"/>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	299 <param name="matchingC" value="regex"/>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	300 <output name="contrast_corcov">
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	301 <assert_contents>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	302 <!-- column-labels line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	303 <has_text text="featureID" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	304 <has_text text="factorLevel1" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	305 <has_text text="factorLevel2" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	306 <has_text text="correlation" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	307 <has_text text="covariance" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	308 <has_text text="vip4p" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	309 <has_text text="vip4o" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	310 <!-- first matched line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	311 <has_text text="M349.2383T700" />
7 066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066 eschen42 parents: 6 diff changeset	312 <has_text text="-0.37867079" />
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066 eschen42 parents: 6 diff changeset	313 <has_text text="-37.71066" />
6 7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	314 <has_text text="0.5246766" />
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	315 <has_text text="0.0103341" />
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	316 <!-- second matched line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	317 <has_text text="M207.9308T206" />
7 066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066 eschen42 parents: 6 diff changeset	318 <has_text text="0.31570433" />
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066 eschen42 parents: 6 diff changeset	319 <has_text text="5.86655640" />
6 7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	320 <has_text text="0.2111623" />
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	321 <has_text text="0.0488654" />
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	322 </assert_contents>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	323 </output>
10 9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	324 <!-- test #4 -->
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	325 <output name="contrast_salience">
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	326 <assert_contents>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	327 <!-- column-labels line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	328 <has_text text="featureID" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	329 <has_text text="salientLevel" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	330 <has_text text="salientRCV" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	331 <has_text text="salience" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	332 <!-- first matched line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	333 <has_text text="M349.2383T700" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	334 <has_text text="0.659554" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	335 <has_text text="8.81866595" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	336 <!-- second matched line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	337 <has_text text="M207.9308T206" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	338 <has_text text="0.0578578" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	339 <has_text text="2.27527985" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	340 <!-- third matched line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	341 <has_text text="M211.0607T263" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	342 <has_text text="9999" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	343 <has_text text="12.87766096" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	344 </assert_contents>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	345 </output>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	346 </test>
6 7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	347 <!-- test #4 -->
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	348 <test>
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	349 <param name="dataMatrix_in" value="issue1_input_dataMatrix.tsv"/>
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	350 <param name="sampleMetadata_in" value="issue1_input_sampleMetadata.tsv"/>
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	351 <param name="variableMetadata_in" value="issue1_input_variableMetadata.tsv"/>
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	352 <param name="tesC" value="none"/>
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	353 <param name="facC" value="tissue_flowering"/>
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	354 <param name="labelFeatures" value="3"/>
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	355 <param name="levCSV" value="*"/>
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	356 <param name="matchingC" value="wildcard"/>
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	357 <output name="contrast_corcov">
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	358 <assert_contents>
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	359 <!-- column-labels line -->
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	360 <has_text text="featureID" />
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	361 <has_text text="factorLevel1" />
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	362 <has_text text="factorLevel2" />
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	363 <has_text text="correlation" />
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	364 <has_text text="covariance" />
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	365 <has_text text="vip4p" />
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	366 <has_text text="vip4o" />
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	367 <!-- first matched line -->
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	368 <has_text text="NM516T251" />
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	369 <has_text text="flower_yes" />
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	370 <has_text text="other" />
7 066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066 eschen42 parents: 6 diff changeset	371 <has_text text="0.03402807" />
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066 eschen42 parents: 6 diff changeset	372 <has_text text="0.03526926" />
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066 eschen42 parents: 6 diff changeset	373 <has_text text="0.43664386" />
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066 eschen42 parents: 6 diff changeset	374 <has_text text="0.587701897" />
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066 eschen42 parents: 6 diff changeset	375 <has_text text="0.026082688" />
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066 eschen42 parents: 6 diff changeset	376 <has_text text="0.0437742145" />
6 7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	377 <has_text text="516.0845" />
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	378 <has_text text="250.8762" />
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	379 </assert_contents>
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	380 </output>
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	381 <output name="contrast_salience">
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	382 <assert_contents>
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	383 <!-- column-labels line -->
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	384 <has_text text="featureID" />
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	385 <has_text text="salientLevel" />
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	386 <has_text text="salientRCV" />
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	387 <has_text text="salience" />
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	388 <has_text text="mz" />
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	389 <has_text text="rt" />
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	390 <!-- first matched line -->
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	391 <has_text text="PM518T369" />
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	392 <has_text text="flower_yes" />
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	393 <has_text text="0.58655260" />
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	394 <has_text text="4.414469" />
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	395 <has_text text="518.1656" />
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	396 <has_text text="368.59817" />
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	397 </assert_contents>
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	398 </output>
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	399 </test>
10 9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	400 <!-- test #5 -->
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	401 <test>
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	402 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	403 <param name="sampleMetadata_in" value="issue6_input_sampleMetadata.tsv"/>
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	404 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	405 <param name="tesC" value="none"/>
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	406 <param name="facC" value="k._10"/>
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	407 <param name="labelFeatures" value="3"/>
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	408 <param name="levCSV" value="k1,k.2"/>
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	409 <param name="matchingC" value="none"/>
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	410 <output name="contrast_corcov">
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	411 <assert_contents>
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	412 <!-- column-labels line -->
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	413 <has_text text="featureID" />
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	414 <has_text text="factorLevel1" />
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	415 <has_text text="factorLevel2" />
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	416 <has_text text="correlation" />
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	417 <has_text text="covariance" />
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	418 <has_text text="vip4p" />
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	419 <has_text text="vip4o" />
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	420 <!-- first matched line -->
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	421 <has_text text="M349.2383T700" />
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	422 <has_text text="-0.37867079" />
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	423 <has_text text="-37.71066" />
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	424 <has_text text="0.5246766" />
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	425 <has_text text="0.0103341" />
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	426 <!-- second matched line -->
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	427 <has_text text="M207.9308T206" />
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	428 <has_text text="0.31570433" />
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	429 <has_text text="5.86655640" />
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	430 <has_text text="0.2111623" />
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	431 <has_text text="0.0488654" />
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	432 </assert_contents>
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	433 </output>
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	434 </test>
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	435 <!-- test #6 -->
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	436 <test>
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	437 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	438 <param name="sampleMetadata_in" value="issue6_input_sampleMetadata.tsv"/>
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	439 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	440 <param name="tesC" value="none"/>
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	441 <param name="facC" value="k._10"/>
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	442 <param name="labelFeatures" value="3"/>
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	443 <param name="levCSV" value="k_3,k-4"/>
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	444 <param name="matchingC" value="none"/>
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	445 <output name="contrast_corcov">
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	446 <assert_contents>
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	447 <!-- column-labels line -->
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	448 <has_text text="featureID" />
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	449 <has_text text="factorLevel1" />
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	450 <has_text text="factorLevel2" />
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	451 <has_text text="correlation" />
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	452 <has_text text="covariance" />
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	453 <has_text text="vip4p" />
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	454 <has_text text="vip4o" />
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	455 <!-- first matched line -->
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	456 <has_text text="M349.2383T700" />
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	457 <has_text text="-0.0435663" />
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	458 <has_text text="-1.9068114" />
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	459 <has_text text="0.0304592" />
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	460 <has_text text="0.104748883" />
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	461 </assert_contents>
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	462 </output>
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	463 </test>
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	464 </tests>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	465 <help><![CDATA[
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	466
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	467 Run PLS-DA Contrasts of Univariate Results
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	468 ----------------------------------------------
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	469
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	470 Author - Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu)
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	471
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	472
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	473 Motivation
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	474 ----------
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	475
4 8bba31f628da planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 8f2dc8b66666340275cd8967e09c504720528462 eschen42 parents: 3 diff changeset	476 OPLS-DA and the SIMCA S-PLOT (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 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	477
1 0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	478 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 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	479
1 0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	480 The primary aims of this tool are:
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	481
1 0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	482 - To compute and visualize multiple contrasts with OPLS-DA and the covariance vs. correlation plot.
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	483 - To write the results to data files for use in further multivariate analysis or visualization.
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	484
1 0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	485 Note: This tool only supports categorical factors with non-numeric level-names.
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	486
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	487 Description
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	488 -----------
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	489
1 0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	490 The purpose of the 'PLS-DA Contrasts' tool is to visualize GC-MS or LC-MS features that are possible biomarkers.
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	491
4 8bba31f628da planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 8f2dc8b66666340275cd8967e09c504720528462 eschen42 parents: 3 diff changeset	492 The W4M 'Univariate' tool (Th]]>é<![CDATA[venot et al., 2015) adds the results of family-wise corrected pairwise significance-tests as columns of the variableMetadata dataset.
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	493 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.
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	494
2 e03582f26617 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 1 diff changeset	495 - 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.
e03582f26617 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 1 diff changeset	496 - 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.
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	497
6 7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	498 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.
1 0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	499
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	500 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).
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	501
6 7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	502 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 may be to use univariate testing to exclude features that are not significantly different and then to use OPLS-DA to visualize the differences identified in univariate testing (Th]]>é<![CDATA[venot et al., 2015); an appropriate exception would be to visualize contrasts of a specific list of metabolites.
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	503
2 e03582f26617 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 1 diff changeset	504 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:
e03582f26617 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 1 diff changeset	505
e03582f26617 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 1 diff changeset	506 - picking features with maximum loadings along the projection parallel to the predictor (loadp),
9 06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	507 - examining extreme values on S-PLOTs
2 e03582f26617 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 1 diff changeset	508 - examining "variable importance in projection VIP for OPLS-DA" (Galindo-Prieto et al. 2014), and
e03582f26617 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 1 diff changeset	509 - examining a feature's "selectivity ratio" (Rajalahti et al., 2009).
e03582f26617 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 1 diff changeset	510
6 7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	511 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.
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	512
1 0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	513 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.
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	514
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	515 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.
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	516
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	517
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	518 W4M Workflow Position
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	519 ---------------------
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	520
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	521 - Upstream tool: Univariate (category: Statistical Analysis) or (not generally recommended) any Preprocessing tool that produces or updates a 'variableMetadata' file.
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	522 - Downstream tool categories: Statistical Analysis
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	523
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	524 Input files
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	525 -----------
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	526
1 0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	527 +----------------------+-----------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	528 \| File \| Format \|
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	529 +======================+===========+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	530 \| Data matrix \| tabular \|
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	531 +----------------------+-----------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	532 \| Sample metadata \| tabular \|
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	533 +----------------------+-----------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	534 \| Variable metadata \| tabular \|
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	535 +----------------------+-----------+
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	536
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	537 Output files
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	538 ------------
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	539
1 0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	540 +-------------------------------------------+-----------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	541 \| File \| Format \|
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	542 +===========================================+===========+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	543 \| Contrast detail \| pdf \|
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	544 +-------------------------------------------+-----------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	545 \| Contrast "corrlation and covariance" data \| tabular \|
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	546 +-------------------------------------------+-----------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	547 \| Feature "salience" data \| tabular \|
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	548 +-------------------------------------------+-----------+
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	549
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	550 Parameters
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	551 ----------
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	552
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	553 [IN] Data matrix file
1 0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	554 \| 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)
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	555 \|
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	556
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	557 [IN] Sample metadata file
1 0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	558 \| sample x metadata sampleMetadata (tabular separated values) file of the numeric and/or character sample metadata, with '.' as decimal and 'NA' for missing values
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	559 \|
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	560
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	561 [IN] Variable metadata file
1 0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	562 \| variable x metadata variableMetadata (tabular separated values) file of the numeric and/or character variable metadata, with '.' as decimal and 'NA' for missing values
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	563 \|
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	564
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	565 [IN] Test
1 0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	566 \| Name of the statistical test - a component of column names in variable metadata table
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	567 \| May be one of 'none', 'ttest', 'gwilcoxon', 'anova', 'kruskal', 'pearson', 'spearman'
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	568 \|
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	569
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	570 [IN] Factor of interest
1 0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	571 \| Name of the column of sampleMetadata corresponding to the qualitative or quantitative variable
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	572 \|
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	573
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	574 [IN] Retain only pairwise-significant features
5 50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f eschen42 parents: 4 diff changeset	575 \| Note that when 'Test' is 'none', all features are included in the analysis and this parameter is not settable.
1 0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	576 \| 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).
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	577 \| 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.
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	578 \|
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	579
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	580 [IN] Levels of interest
1 0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	581 \| 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.
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	582 \|
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	583
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	584 [IN] Level-name matching
1 0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	585 \| Indicator of how levels are to be specified generically (if at all) - wild cards, regular expressions, or none (no generic matching).
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	586 \|
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	587
2 e03582f26617 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 1 diff changeset	588 [IN] Label how many extreme features
e03582f26617 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 1 diff changeset	589 \| 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.
e03582f26617 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 1 diff changeset	590 \|
e03582f26617 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 1 diff changeset	591
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	592 [OUT] Contrast-detail output PDF
1 0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	593 \| Several plots for each two-projection OPLS-DA analysis:
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	594
6 7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	595 - (first row, 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), for use to identify features for consideration as biomarkers.
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	596 - (second row, 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 (Th]]>é<![CDATA[venot, 2017)
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	597 - (first row, right) OPLS-DA scores-plot for the two projections (Th]]>é<![CDATA[venot et al., 2015)
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	598 - (second row, right) correlation-versus-covariance plot of OPLS-DA results orthogonal to the predictor (see section "S-Plot of Orthogonal Component" in Wiklund, op. cit., pp. 120-121; this characterizes features with the greatest variation independent of the predictor).
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	599 - (third row, left, when "predictor C-plot" is chosen under "Extra plots to include") plot of the covariance or correlation vs. the VIP for the projection parallel to the predictor, for use to identify features for consideration as biomarkers.
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	600 - (third row, right, when "orthogonal C-plot" is chosen under "Extra plots to include") plotof the covariance or correlation vs. the VIP for the projection orthogonal to the predictor, for use to identify features varying considerably without regard to the predictor.
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	601
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	602 [OUT] Contrast Correlation-Covarinace data TABULAR
1 0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	603 \| A tab-separated values file of metadata for each feature for each contrast in which it was included.
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	604 \| Thus, a given feature may appear many times, but the combination of featureID, factorLevel1, and factorLevel2 will be unique.
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	605 \| This file has the following columns:
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	606
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	607 - featureID - feature-identifier
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	608 - factorLevel1 - factor-level 1
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	609 - factorLevel2 - factor-level 2 (or "other" when contrasting factor-level 1 with all other levels)
2 e03582f26617 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 1 diff changeset	610 - 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'.
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	611 - covariance - covariance of the features projection explaining the difference between the features, < 0 when intensity for level 1 is greater (from formula in ibid.)
1 0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	612 - vip4p - "variable importance in projection" to the predictive projection, VIP\ :subscript:`4,p` (Galindo-Prieto op. cit.)
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	613 - vip4o - "variable importance in projection" to the orthogonal projection, VIP\ :subscript:`4,o` (ibid.)
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	614 - loadp - variable loading for the predictive projection (Wiklund op. cit.)
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	615 - loado - variable loading for the orthogonal projection (ibid.)
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	616 - 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
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	617
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	618 [OUT] Feature "Salience" data TABULAR
6 7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d eschen42 parents: 5 diff changeset	619 \| 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 way to discover features for consideration as potential biomarkers without dimensionally reducting the data. This is a tab-separated values file having the following columns:
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	620
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	621 - featureID - feature identifier
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	622 - salientLevel - salient level, i.e., for the feature, the class-level having the greatest median intensity
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	623 - 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
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	624 - 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
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	625
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	626 Wild card patterns to match level-names
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	627 ---------------------------------------
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	628
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	629 "wild card" patterns may be used to select level-names.
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	630
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	631 - use '``?``' to match a single character
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	632 - use '``*``' to match zero or more characters
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	633 - the entire pattern must match the level name
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	634
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	635 For example
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	636
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	637 - '``??.le*``' matches '``my.level``' but not '``my.own.level``'
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	638 - '``*.level``' matches '``my.level``' and '``my.own.level``'
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	639 - '``*.level``' matches neither '``my.level``' nor '``my.own.level``'
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	640
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	641 Regular expression patterns to match level-names
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	642 ------------------------------------------------
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	643
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	644 "regular expression" patterns may be used to select level-names.
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	645
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	646 POSIX 1003.2 standard regular expressions allow precise pattern-matching and are exhaustively defined at:
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	647 http://pubs.opengroup.org/onlinepubs/9699919799/basedefs/V1_chap09.html
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	648
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	649 However, only a few basic building blocks of regular expressions need to be mastered for most cases:
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	650
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	651 - '``^``' matches the beginning of a level-name
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	652 - '``$``' matches the end of a level-name
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	653 - '``.``' outside of square brackets matches a single character
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	654 - '``*``' matches character specified immediately before zero or more times
1 0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	655 - Square brackets specify a set of characters to be matched. Within square brackets:
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	656
1 0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	657 - '``^``' as the first character specifies that the list of characters are those that should not be matched.
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	658 - '``-``' is used to specify ranges of characters
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	659
1 0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	660 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 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	661
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	662 First Example: Consider a field of level-names consisting of '``marq3,marq6,marq9,marq12,front3,front6,front9,front12``'
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	663
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	664 - The regular expression '``^front[0-9][0-9]*$``' will match the same sample-levels as '``front3,front6,front9,front12``'
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	665 - The regular expression '``^[a-z][a-z]3$``' will match the same sample-levels as '``front3,marq3``'
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	666 - The regular expression '``^[a-z][a-z]12$``' will match the same sample-levels as '``front12,marq12``'
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	667 - The regular expression '``^[a-z][a-z][0-9]$``' will match the same sample-levels as '``front3,front6,front9,marq3,marq6,marq9``'
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	668
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	669 Second Example: Consider these regular expression patterns as possible matches to a sample-level name '``AB0123``':
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	670
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	671 - '``^[A-Z][A-Z][0-9][0-9]$``' - MATCHES '``^AB0123$*``'
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	672 - '``^[A-Z][A-Z][0-9][0-9]$``' - MATCHES '``^AB0123$``'
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	673 - '``^[A-Z][0-9]``' - MATCHES '``^A* B0123$``' - first character is a letter, '``*``' can specify zero characters, and end of line did not need to be matched.
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	674 - '``^[A-Z][A-Z][0-9]``' - MATCHES '``^AB0 123$``' - first two characters are letters aind the third is a digit.
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	675 - '``^[A-Z][A-Z]*[0-9][0-9]$``' - NO MATCH - the name does not end with the pattern '``[A-Z][0-9][0-9]$``', i.e., it ends with four digits, not two.
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	676 - '``^[A-Z][0-9]*$``' - NO MATCH - the pattern specifies that second character and all those that follow, if present, must be digits.
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	677
1 0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	678 Working examples
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	679 ----------------
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	680
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	681 Input files
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	682
9 06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	683 +-----------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	684 \| Download from URL \|
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	685 +===============================================================================================================================================+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	686 \| https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/input_dataMatrix.tsv \|
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	687 +-----------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	688 \| https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/input_sampleMetadata.tsv \|
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	689 +-----------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	690 \| https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/input_variableMetadata.tsv \|
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	691 +-----------------------------------------------------------------------------------------------------------------------------------------------+
1 0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	692
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	693 Example 1: Include in the analysis only features identified as pair-wise significant in the Univariate test.
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	694
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	695 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	696 \| Input Parameter or Result \| Value \|
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	697 +============================================+========================================================================================================================================+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	698 \| Factor of interest \| k10 \|
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	699 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	700 \| Univariate Significance-Test \| kruskal \|
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	701 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	702 \| Retain only pairwise-significant features \| Yes \|
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	703 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	704 \| Levels of interest \| k[12],k[3-4] \|
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	705 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	706 \| Level-name matching \| use regular expressions for matching level-names \|
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	707 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	708 \| Number of features having extreme loadings \| ALL \|
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	709 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
9 06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	710 \| Output primary table \| https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_corcov.tsv \|
1 0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	711 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
9 06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	712 \| Output salience table \| https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_salience.tsv \|
1 0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	713 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
9 06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	714 \| Output figures PDF \| https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_detail.pdf \|
1 0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	715 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	716
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	717 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 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	718
9 06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	719 +--------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	720 \| Input Parameter or Result \| Value \|
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	721 +============================================+============================================================================================================================================+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	722 \| Factor of interest \| k10 \|
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	723 +--------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	724 \| Univariate Significance-Test \| kruskal \|
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	725 +--------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	726 \| Retain only pairwise-significant features \| No \|
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	727 +--------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	728 \| Levels of interest \| ``*`` \|
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	729 +--------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	730 \| Level-name matching \| use wild cards for matching level-names \|
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	731 +--------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	732 \| Number of features having extreme loadings \| 5 \|
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	733 +--------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	734 \| Output primary table \| https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_corcov_all.tsv \|
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	735 +--------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	736 \| Output salience table \| https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_salience_all.tsv \|
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	737 +--------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	738 \| Output figures PDF \| https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_detail_all.pdf \|
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	739 +--------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------+
1 0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	740
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	741 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 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	742
9 06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	743 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	744 \| Input Parameter or Result \| Value \|
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	745 +============================================+==============================================================================================================================================+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	746 \| Factor of interest \| k10 \|
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	747 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	748 \| Univariate Significance-Test \| none \|
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	749 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	750 \| Levels of interest \| k[12],k[3-4] \|
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	751 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	752 \| Level-name matching \| use regular expressions for matching level-names \|
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	753 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	754 \| Number of features having extreme loadings \| 0 \|
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	755 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	756 \| Output primary table \| https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_corcov_global.tsv \|
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	757 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	758 \| Output salience table \| https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_salience_global.tsv \|
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	759 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	760 \| Output figures PDF \| https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_detail_global.pdf \|
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	761 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
1 0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	762
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	763 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".
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	764
9 06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	765 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	766 \| Input Parameter or Result \| Value \|
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	767 +============================================+==============================================================================================================================================+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	768 \| Factor of interest \| lohi \|
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	769 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	770 \| Univariate Significance-Test \| none \|
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	771 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	772 \| Levels of interest \| low,high \|
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	773 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	774 \| Level-name matching \| use regular expressions for matching level-names \|
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	775 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	776 \| Number of features having extreme loadings \| 3 \|
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	777 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	778 \| Output primary table \| https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_corcov_lohi.tsv \|
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	779 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	780 \| Output salience table \| https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_salience_lohi.tsv \|
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	781 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	782 \| Output figures PDF \| https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_detail_lohi.pdf \|
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0 eschen42 parents: 8 diff changeset	783 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	784
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	785
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	786 Trademarks
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	787 ----------
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	788
4 8bba31f628da planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 8f2dc8b66666340275cd8967e09c504720528462 eschen42 parents: 3 diff changeset	789 OPLS-DA, SIMCA, and S-PLOT are registered trademarks of the Umetrics company. http://umetrics.com/about-us/trademarks
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	790
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	791
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	792 ]]></help>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	793 <citations>
5 50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f eschen42 parents: 4 diff changeset	794 <!-- this tool -->
2 e03582f26617 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582 eschen42 parents: 1 diff changeset	795 <citation type="doi">10.5281/zenodo.1034784</citation>
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	796 <!-- Galindo_Prieto_2014 Variable influence on projection (VIP) for OPLS -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	797 <citation type="doi">10.1002/cem.2627</citation>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	798 <!-- Giacomoni_2014 W4M 2.5 -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	799 <citation type="doi">10.1093/bioinformatics/btu813</citation>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	800 <!-- Guitton_2017 W4M 3.0 -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	801 <citation type="doi">10.1016/j.biocel.2017.07.002</citation>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	802 <!-- Mehmood_2012 PLS-based variable-selection -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	803 <citation type="doi">10.1186/1748-7188-6-27</citation>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	804 <!-- Rajalahti_2009 Biomarker discovery using selectivity ratio -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	805 <citation type="doi">10.1016/j.chemolab.2008.08.004</citation>
1 0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	806 <!-- Rinuardo 2016 -->
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	807 <citation type="doi">10.3389/fmolb.2016.00026</citation>
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	808 <!-- Sun_2016 Urinary Biomarkers for adolescent idiopathic scoliosis -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	809 <citation type="doi">10.1038/srep22274</citation>
4 8bba31f628da planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 8f2dc8b66666340275cd8967e09c504720528462 eschen42 parents: 3 diff changeset	810 <!-- Thevenot_2015 Urinary metabolome statistics -->
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	811 <citation type="doi">10.1021/acs.jproteome.5b00354</citation>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	812 <!-- ropls package -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	813 <citation type="bibtex"><![CDATA[
1 0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	814 @incollection{Thevenot_ropls_2017,
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	815 author = {Th{\'{e}}venot, Etienne A.},
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	816 title = {ropls: PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data},
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	817 publisher = {bioconductor.org},
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	818 year = {2017},
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	819 doi = {10.18129/B9.bioc.ropls},
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	820 booktitle = {Bioconductor: Open source software for bioinformatics},
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	821 address = {Roswell Park Cancer Institute},
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92 eschen42 parents: 0 diff changeset	822 }
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	823 ]]></citation>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	824 <!-- Wiklund_2008 OPLS PLS-DA and S-PLOT -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	825 <citation type="doi">10.1021/ac0713510</citation>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	826 </citations>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	827 <!--
10 9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552 eschen42 parents: 9 diff changeset	828 vim:et:sw=4:ts=4
0 23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	829 -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: diff changeset	830 </tool>

Mercurial > repos > eschen42 > w4mcorcov

annotate w4mcorcov.xml @ 10:9a52306991b3 draft