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comparison w4mcorcov.xml @ 5:50f60f94c034 draft

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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
author eschen42
date Fri, 30 Mar 2018 14:59:19 -0400
parents 8bba31f628da
children 7bd523ca1f9a
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4:8bba31f628da 5:50f60f94c034
1 <tool id="w4mcorcov" name="OPLS-DA_Contrasts" version="0.98.7"> 1 <tool id="w4mcorcov" name="OPLS-DA_Contrasts" version="0.98.8">
2 2
3 <description>OPLS-DA Contrasts of Univariate Results</description> 3 <description>OPLS-DA Contrasts of Univariate Results</description>
4 4
5 <macros>
6 <xml name="paramPairSigFeatOnly">
7 <param
8 name="pairSigFeatOnly"
9 type="boolean"
10 checked="true"
11 truevalue="TRUE"
12 falsevalue="FALSE"
13 label="Retain only pairwise-significant features"
14 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." />
15 </xml>
16 </macros>
17
5 <requirements> 18 <requirements>
6 <requirement type="package">r-batch</requirement> 19 <requirement type="package">r-batch</requirement>
7 <requirement type="package">bioconductor-ropls</requirement> 20 <requirement type="package">bioconductor-ropls</requirement>
8 <!-- <requirement type="package">r-foreach</requirement> -->
9 </requirements> 21 </requirements>
10 22
11 <stdio> 23 <stdio>
12 <exit_code range="1:" level="fatal" /> 24 <exit_code range="1:" level="fatal" />
13 </stdio> 25 </stdio>
15 <command><![CDATA[ 27 <command><![CDATA[
16 cd $__tool_directory__; Rscript w4mcorcov_wrapper.R 28 cd $__tool_directory__; Rscript w4mcorcov_wrapper.R
17 dataMatrix_in "$dataMatrix_in" 29 dataMatrix_in "$dataMatrix_in"
18 sampleMetadata_in "$sampleMetadata_in" 30 sampleMetadata_in "$sampleMetadata_in"
19 variableMetadata_in "$variableMetadata_in" 31 variableMetadata_in "$variableMetadata_in"
20 tesC "$tesC"
21 facC "$facC" 32 facC "$facC"
22 pairSigFeatOnly "$pairSigFeatOnly" 33 #if str( $signif_test.tesC ) == "none":
34 tesC "none"
35 pairSigFeatOnly "FALSE"
36 #else:
37 tesC "$signif_test.tesC"
38 pairSigFeatOnly "$signif_test.pairSigFeatOnly"
39 #end if
23 levCSV '$levCSV' 40 levCSV '$levCSV'
24 matchingC '$matchingC' 41 matchingC '$matchingC'
25 labelFeatures '$labelFeatures' 42 labelFeatures '$labelFeatures'
26 labelOrthoFeatures '$labelOrthoFeatures'
27 contrast_detail '$contrast_detail' 43 contrast_detail '$contrast_detail'
28 contrast_corcov '$contrast_corcov' 44 contrast_corcov '$contrast_corcov'
29 contrast_salience '$contrast_salience' 45 contrast_salience '$contrast_salience'
30 ]]></command> 46 ]]></command>
31 47
32 <inputs> 48 <inputs>
33 <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="Features x samples (tabular data - decimal: '.'; missing: NA; mode: numerical; separator: tab character)" /> 49 <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="Features x samples (tabular data - decimal: '.'; missing: NA; mode: numerical; separator: tab character)" />
34 <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="Samples x metadata (tabular data - decimal: '.'; missing: NA; mode: character or numerical; separator: tab character)" /> 50 <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="Samples x metadata (tabular data - decimal: '.'; missing: NA; mode: character or numerical; separator: tab character)" />
35 <param name="variableMetadata_in" label="Variable metadata file (ideally from Univariate)" type="data" format="tabular" help="Features x metadata (tabular data - decimal: '.'; missing: NA; mode: character or numerical; separator: tab character)" /> 51 <param name="variableMetadata_in" label="Variable metadata file (ideally from Univariate)" type="data" format="tabular" help="Features x metadata (tabular data - decimal: '.'; missing: NA; mode: character or numerical; separator: tab character)" />
36 <param name="facC" label="Factor of interest" type="text" help="REQUIRED - The name of the column of sampleMetadata corresponding to the qualitative variable used to define the contrasts. Except when the 'Univariate Significance-test' is set to 'none', this also must be a portion of the column names in the variableMetadata file."/> 52 <param name="facC" label="Factor of interest" type="text" help="REQUIRED - The name of the column of sampleMetadata corresponding to the qualitative variable used to define the contrasts. Except when the 'Univariate Significance-test' is set to 'none', this also must be a portion of the column names in the variableMetadata file."/>
37 <param name="tesC" label="Univariate significance-test" type="select" help="Either 'none' or the name of the statistical test that was run by the 'Univariate' tool to produce the variableMetadata file; that name must also be a portion of the column names in that file."> 53 <conditional name="signif_test">
38 <option value="none">none - Display all features from variableMetadata (rather than choosing a subset based on significance in univariate testing)</option> 54 <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.">
39 <option value="ttest">ttest - Student's t-test (parametric test, qualitative factor with exactly 2 levels)</option> 55 <option value="none">none - Display all features from variableMetadata (rather than choosing a subset based on significance in univariate testing)</option>
40 <option value="anova">anova - Analysis of variance (parametric test, qualitative factor with more than 2 levels)</option> 56 <option value="ttest">ttest - Student's t-test (parametric test, qualitative factor with exactly 2 levels)</option>
41 <option value="wilcoxon">wilcoxon - Wilcoxon rank test (nonparametric test, qualitative factor with exactly 2 levels)</option> 57 <option value="anova">anova - Analysis of variance (parametric test, qualitative factor with more than 2 levels)</option>
42 <option value="kruskal">kruskal - Kruskal-Wallis rank test (nonparametric test, qualitative factor with more than 2 levels)</option> 58 <option value="wilcoxon">wilcoxon - Wilcoxon rank test (nonparametric test, qualitative factor with exactly 2 levels)</option>
43 </param> 59 <option value="kruskal">kruskal - Kruskal-Wallis rank test (nonparametric test, qualitative factor with more than 2 levels)</option>
44 <param 60 </param>
45 name="pairSigFeatOnly" 61 <when value="none" />
46 type="boolean" 62 <when value="ttest">
47 checked="true" 63 <expand macro="paramPairSigFeatOnly" />
48 truevalue="TRUE" 64 </when>
49 falsevalue="FALSE" 65 <when value="anova">
50 label="Retain only pairwise-significant features" 66 <expand macro="paramPairSigFeatOnly" />
51 help="When 'none' is chosen as the test, all features are included in the analysis (i. e., this parameter is ignored). Otherwise, when this option is set to 'Yes', analysis will be performed including only features that differ significantly for the pair of levels being contrasted; when set to 'No', any feature that varies significantly across all levels will be included (i.e., exclude any feature that is not significantly different across all levels). See examples below."/> 67 </when>
68 <when value="wilcoxon">
69 <expand macro="paramPairSigFeatOnly" />
70 </when>
71 <when value="kruskal">
72 <expand macro="paramPairSigFeatOnly" />
73 </when>
74 </conditional>
52 <param name="levCSV" label="Levels of interest" type="text" value = "*" help="Comma-separated level-names (or comma-less regular expressions to match level-names) to consider in analysis; must match at least two levels; levels must be non-numeric; may include wild cards or regular expressions. Note that extra space characters will affect results - 'a,b' is correct, but 'a , b' is not and may fail or give different results."> 75 <param name="levCSV" label="Levels of interest" type="text" value = "*" help="Comma-separated level-names (or comma-less regular expressions to match level-names) to consider in analysis; must match at least two levels; levels must be non-numeric; may include wild cards or regular expressions. Note that extra space characters will affect results - 'a,b' is correct, but 'a , b' is not and may fail or give different results.">
53 <sanitizer> 76 <sanitizer>
54 <valid initial="string.letters"> 77 <valid initial="string.letters">
55 <add preset="string.digits"/> 78 <add preset="string.digits"/>
56 <add value="&#36;" /> <!-- $ dollar, dollar-sign --> 79 <add value="&#36;" /> <!-- $ dollar, dollar-sign -->
79 <option value="none">do no generic matching (default)</option> 102 <option value="none">do no generic matching (default)</option>
80 <option value="wildcard" selected="true">use wild-cards for matching level-names</option> 103 <option value="wildcard" selected="true">use wild-cards for matching level-names</option>
81 <option value="regex">use regular expressions for matching level-names</option> 104 <option value="regex">use regular expressions for matching level-names</option>
82 </param> 105 </param>
83 <param name="labelFeatures" type="text" value="3" label="How many features having extreme loadings should be labelled on cov-vs.-cor plot" help="Specify the number of features at each of the loading-extremes that should be labelled (with the name of the feature) on the covariance-vs.-correlation plot; specify 'ALL' to label all features or '0' to label no features; this choice has no effect on the OPLS-DA loadings plot."/> 106 <param name="labelFeatures" type="text" value="3" label="How many features having extreme loadings should be labelled on cov-vs.-cor plot" help="Specify the number of features at each of the loading-extremes that should be labelled (with the name of the feature) on the covariance-vs.-correlation plot; specify 'ALL' to label all features or '0' to label no features; this choice has no effect on the OPLS-DA loadings plot."/>
84 <param
85 name="labelOrthoFeatures"
86 type="boolean"
87 checked="false"
88 truevalue="TRUE"
89 falsevalue="FALSE"
90 label="Label features having extreme orthogonal loadings"
91 help="When using the preceding parameter to label only features at the loading-extremess in the cor-vs.-cov plot, use 'no' here to label only features having extreme parallel loadings (loadp); this is the default. Choose 'yes' to add labels also to features having extreme orthogonal loadings (both loado and loadp); this may clutter the plot."/>
92 </inputs> 107 </inputs>
93 108
94 <outputs> 109 <outputs>
95 <!-- 110 <!--
96 pdf1: summaries of each contrasts, clearly labelled by level=pair name 111 pdf1: summaries of each contrasts, clearly labelled by level=pair name
128 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/> 143 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
129 <param name="tesC" value="kruskal"/> 144 <param name="tesC" value="kruskal"/>
130 <param name="facC" value="k10"/> 145 <param name="facC" value="k10"/>
131 <param name="pairSigFeatOnly" value="FALSE"/> 146 <param name="pairSigFeatOnly" value="FALSE"/>
132 <param name="labelFeatures" value="3"/> 147 <param name="labelFeatures" value="3"/>
133 <param name="labelOrthogonalFeatures" value="FALSE"/>
134 <param name="levCSV" value="k[12],k[3-4]"/> 148 <param name="levCSV" value="k[12],k[3-4]"/>
135 <param name="matchingC" value="regex"/> 149 <param name="matchingC" value="regex"/>
136 <output name="contrast_corcov"> 150 <output name="contrast_corcov">
137 <assert_contents> 151 <assert_contents>
138 <!-- column-labels line --> 152 <!-- column-labels line -->
192 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/> 206 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
193 <param name="tesC" value="kruskal"/> 207 <param name="tesC" value="kruskal"/>
194 <param name="facC" value="k10"/> 208 <param name="facC" value="k10"/>
195 <param name="pairSigFeatOnly" value="TRUE"/> 209 <param name="pairSigFeatOnly" value="TRUE"/>
196 <param name="labelFeatures" value="3"/> 210 <param name="labelFeatures" value="3"/>
197 <param name="labelOrthogonalFeatures" value="TRUE"/>
198 <param name="levCSV" value="k[12],k[3-4]"/> 211 <param name="levCSV" value="k[12],k[3-4]"/>
199 <param name="matchingC" value="regex"/> 212 <param name="matchingC" value="regex"/>
200 <output name="contrast_corcov"> 213 <output name="contrast_corcov">
201 <assert_contents> 214 <assert_contents>
202 <!-- column-labels line --> 215 <!-- column-labels line -->
252 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/> 265 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
253 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/> 266 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
254 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/> 267 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
255 <param name="tesC" value="none"/> 268 <param name="tesC" value="none"/>
256 <param name="facC" value="k10"/> 269 <param name="facC" value="k10"/>
257 <param name="pairSigFeatOnly" value="TRUE"/>
258 <param name="labelFeatures" value="3"/> 270 <param name="labelFeatures" value="3"/>
259 <param name="labelOrthogonalFeatures" value="FALSE"/>
260 <param name="levCSV" value="k[12],k[3-4]"/> 271 <param name="levCSV" value="k[12],k[3-4]"/>
261 <param name="matchingC" value="regex"/> 272 <param name="matchingC" value="regex"/>
262 <output name="contrast_corcov"> 273 <output name="contrast_corcov">
263 <assert_contents> 274 <assert_contents>
264 <!-- column-labels line --> 275 <!-- column-labels line -->
310 <has_text text="12.87766096" /> 321 <has_text text="12.87766096" />
311 </assert_contents> 322 </assert_contents>
312 </output> 323 </output>
313 </test> 324 </test>
314 </tests> 325 </tests>
315 <!--
316 .. |reg| unicode:: U+000AE .. REGISTERED SIGN - see http://docutils.sourceforge.net/docutils/parsers/rst/include/isonum.txt or /usr/share/docutils/parsers/rst/include/isonum.txt
317 -->
318 <help><![CDATA[ 326 <help><![CDATA[
319 327
320 **Run PLS-DA Contrasts of Univariate Results** 328 **Run PLS-DA Contrasts of Univariate Results**
321 ---------------------------------------------- 329 ----------------------------------------------
322 330
423 [IN] Factor of interest 431 [IN] Factor of interest
424 | Name of the **column of sampleMetadata** corresponding to the qualitative or quantitative variable 432 | Name of the **column of sampleMetadata** corresponding to the qualitative or quantitative variable
425 | 433 |
426 434
427 [IN] Retain only pairwise-significant features 435 [IN] Retain only pairwise-significant features
436 | *Note that when 'Test' is 'none', all features are included in the analysis and this parameter is not settable.*
428 | When **true**, for each contrast of two levels, include only those features which pass the significance threshold for that contrast. Choosing true results in an OPLS-DA model that better reflects and visualizes the difference detected by univariate analysis, with somewhat increased reliability of prediction (as assessed by cross-validation). 437 | 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).
429 | When **false**, include all features that pass the significance threshold when testing for difference across all factor-levels. This choice produces a plot that displays more features but is not necessarily more informative. 438 | 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.
430 | *Note that when 'Test' is 'none', all features are included in the analysis and this parameter has no effect.*
431 | 439 |
432 440
433 [IN] Levels of interest 441 [IN] Levels of interest
434 | Comma-separated **level-names** (or comma-less regular expressions to match level-names) to consider in analysis; must match at least two levels; may include wild cards or regular expressions. 442 | 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.
435 | 443 |
438 | Indicator of **how levels are to be specified generically** (if at all) - wild cards, regular expressions, or none (no generic matching). 446 | Indicator of **how levels are to be specified generically** (if at all) - wild cards, regular expressions, or none (no generic matching).
439 | 447 |
440 448
441 [IN] Label how many extreme features 449 [IN] Label how many extreme features
442 | Specify the number of features at each of the loading-extremes that should be labelled (with the name of the feature) on the covariance-vs.-correlation plot; specify 'ALL' to label all features; this choice has no effect on the OPLS-DA loadings plot. 450 | 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.
443 |
444
445 [IN] Label features with extreme loado
446 | If the previous parameter has limited the the number of features to be labelled at each of the loading-extremes, then the extreme values for both loado and loadp will be labelled when this parameter is set to 'yes'; otherwise (in the default case) only extreme values for loadp will be lableld. The default was chosen to make the plot less cluttered.
447 | 451 |
448 452
449 [OUT] Contrast-detail output PDF 453 [OUT] Contrast-detail output PDF
450 | Several plots for each two-projection OPLS-DA analysis: 454 | Several plots for each two-projection OPLS-DA analysis:
451 455
560 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 564 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
561 | Level-name matching | use regular expressions for matching level-names | 565 | Level-name matching | use regular expressions for matching level-names |
562 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 566 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
563 | Number of features having extreme loadings | ALL | 567 | Number of features having extreme loadings | ALL |
564 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 568 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
565 | Label feat. having extreme orth. loadings | Yes |
566 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
567 | Output primary table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_corcov.tsv | 569 | Output primary table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_corcov.tsv |
568 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 570 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
569 | Output salience table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_salience.tsv | 571 | Output salience table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_salience.tsv |
570 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 572 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
571 | Output figures PDF | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_detail.pdf | 573 | Output figures PDF | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_detail.pdf |
586 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 588 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
587 | Level-name matching | use wild cards for matching level-names | 589 | Level-name matching | use wild cards for matching level-names |
588 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 590 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
589 | Number of features having extreme loadings | 5 | 591 | Number of features having extreme loadings | 5 |
590 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 592 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
591 | Label feat. having extreme orth. loadings | No |
592 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
593 | Output primary table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_corcov_all.tsv | 593 | Output primary table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_corcov_all.tsv |
594 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 594 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
595 | Output salience table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_salience_all.tsv | 595 | Output salience table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_salience_all.tsv |
596 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 596 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
597 | Output figures PDF | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_detail_all.pdf | 597 | Output figures PDF | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_detail_all.pdf |
604 +============================================+========================================================================================================================================+ 604 +============================================+========================================================================================================================================+
605 | Factor of interest | k10 | 605 | Factor of interest | k10 |
606 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 606 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
607 | Univariate Significance-Test | none | 607 | Univariate Significance-Test | none |
608 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 608 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
609 | Retain only pairwise-significant features | No |
610 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
611 | Levels of interest | k[12],k[3-4] | 609 | Levels of interest | k[12],k[3-4] |
612 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 610 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
613 | Level-name matching | use regular expressions for matching level-names | 611 | Level-name matching | use regular expressions for matching level-names |
614 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 612 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
615 | Number of features having extreme loadings | 0 | 613 | Number of features having extreme loadings | 0 |
616 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
617 | Label feat. having extreme orth. loadings | Yes |
618 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 614 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
619 | Output primary table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_corcov_global.tsv | 615 | Output primary table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_corcov_global.tsv |
620 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 616 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
621 | Output salience table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_salience_global.tsv | 617 | Output salience table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_salience_global.tsv |
622 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 618 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
630 +============================================+========================================================================================================================================+ 626 +============================================+========================================================================================================================================+
631 | Factor of interest | lohi | 627 | Factor of interest | lohi |
632 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 628 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
633 | Univariate Significance-Test | none | 629 | Univariate Significance-Test | none |
634 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 630 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
635 | Retain only pairwise-significant features | No |
636 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
637 | Levels of interest | low,high | 631 | Levels of interest | low,high |
638 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 632 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
639 | Level-name matching | use regular expressions for matching level-names | 633 | Level-name matching | use regular expressions for matching level-names |
640 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 634 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
641 | Number of features having extreme loadings | 3 | 635 | Number of features having extreme loadings | 3 |
642 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
643 | Label feat. having extreme orth. loadings | Yes |
644 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 636 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
645 | Output primary table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_corcov_lohi.tsv | 637 | Output primary table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_corcov_lohi.tsv |
646 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 638 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
647 | Output salience table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_salience_lohi.tsv | 639 | Output salience table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_salience_lohi.tsv |
648 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 640 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
657 649
658 650
659 Release notes 651 Release notes
660 ------------- 652 -------------
661 653
654 0.98.8
655
656 - new feature: Replace loadings plot with correlation-versus-covariance plot for orthogonal features, i.e., the consistency of features influencing within-treatment variation (which is linearly related to the loading of the orthogonal projection) versus consistency. This eliminates the need for the parameter to suppress labels for features with extreme orthogonal loadings
657
662 0.98.7 658 0.98.7
663 659
664 - bug fix: handle case of a treatment level with only one sample. 660 - bug fix: Handle case of a treatment level with only one sample.
665 661
666 0.98.6 662 0.98.6
667 663
668 - bug fix: set 'crossvalI' param (of R function 'ropls::opls') to the number of samples when the there are fewer than seven samples. 664 - bug fix: Set 'crossvalI' param (of R function 'ropls::opls') to the number of samples when the there are fewer than seven samples.
669 665
670 0.98.5 666 0.98.5
671 667
672 - bug fix: fit feature-labels within clipping region of cor-vs.cov plot 668 - bug fix: Fit feature-labels within clipping region of cor-vs.cov plot
673 - new feature: optionally (and by default) suppress labels for features with extreme orthogonal loadings 669 - new feature: optionally (and by default) suppress labels for features with extreme orthogonal loadings
674 670
675 0.98.3 671 0.98.3
676 672
677 - add support for two-level factors 673 - Add support for two-level factors
678 - add adjusted mz and rt to output tables 674 - Add adjusted mz and rt to output tables
679 - allow explicitly setting the number of features with extreme loadings to be labelled on the correlation vs. covariance plot 675 - Allow explicitly setting the number of features with extreme loadings to be labelled on the correlation vs. covariance plot
680 - add loadings to corcov table 676 - Add loadings to corcov table
681 677
682 0.98.2 678 0.98.2
683 679
684 - first release 680 - first release
685 681
686 682
687 ]]></help> 683 ]]></help>
688 <citations> 684 <citations>
685 <!-- this tool -->
689 <citation type="doi">10.5281/zenodo.1034784</citation> 686 <citation type="doi">10.5281/zenodo.1034784</citation>
690 <!-- Galindo_Prieto_2014 Variable influence on projection (VIP) for OPLS --> 687 <!-- Galindo_Prieto_2014 Variable influence on projection (VIP) for OPLS -->
691 <citation type="doi">10.1002/cem.2627</citation> 688 <citation type="doi">10.1002/cem.2627</citation>
692 <!-- Giacomoni_2014 W4M 2.5 --> 689 <!-- Giacomoni_2014 W4M 2.5 -->
693 <citation type="doi">10.1093/bioinformatics/btu813</citation> 690 <citation type="doi">10.1093/bioinformatics/btu813</citation>
717 ]]></citation> 714 ]]></citation>
718 <!-- Wiklund_2008 OPLS PLS-DA and S-PLOT --> 715 <!-- Wiklund_2008 OPLS PLS-DA and S-PLOT -->
719 <citation type="doi">10.1021/ac0713510</citation> 716 <citation type="doi">10.1021/ac0713510</citation>
720 </citations> 717 </citations>
721 <!-- 718 <!--
722 vim:noet:sw=4:ts=4 719 vim:noet:sw=2:ts=2
723 --> 720 -->
724 </tool> 721 </tool>