Mercurial > repos > eschen42 > w4mcorcov
comparison w4mcorcov.xml @ 9:06c51af11531 draft
planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
author | eschen42 |
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date | Fri, 10 Aug 2018 11:15:31 -0400 |
parents | 342570ad880c |
children | 9a52306991b3 |
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1 <tool id="w4mcorcov" name="OPLS-DA_Contrasts" version="0.98.12"> | 1 <tool id="w4mcorcov" name="OPLS-DA_Contrasts" version="0.98.13"> |
2 <description>OPLS-DA Contrasts of Univariate Results</description> | 2 <description>OPLS-DA Contrasts of Univariate Results</description> |
3 <macros> | 3 <macros> |
4 <xml name="paramPairSigFeatOnly"> | 4 <xml name="paramPairSigFeatOnly"> |
5 <param name="pairSigFeatOnly" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" | 5 <param name="pairSigFeatOnly" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" |
6 label="Retain only pairwise-significant features" | 6 label="Retain only pairwise-significant features" |
18 label="Produce orthogonal C-plot" | 18 label="Produce orthogonal C-plot" |
19 help="When this option is set to 'Yes', correlation will be plotted against vip4 for orthogonal loadings." /> | 19 help="When this option is set to 'Yes', correlation will be plotted against vip4 for orthogonal loadings." /> |
20 </xml> | 20 </xml> |
21 </macros> | 21 </macros> |
22 <requirements> | 22 <requirements> |
23 <!-- | |
24 <requirement type="package" version="3.4.1">r-base</requirement> | |
25 <requirement type="package" version="1.1_4">r-batch</requirement> | |
26 <requirement type="package" version="1.2.14">bioconductor-ropls</requirement> | |
27 --> | |
28 <requirement type="package">r-base</requirement> | |
23 <requirement type="package">r-batch</requirement> | 29 <requirement type="package">r-batch</requirement> |
24 <requirement type="package">bioconductor-ropls</requirement> | 30 <requirement type="package" version="1.10.0">bioconductor-ropls</requirement> |
25 </requirements> | 31 </requirements> |
26 <command detect_errors="aggressive"><![CDATA[ | 32 <command detect_errors="aggressive"><![CDATA[ |
27 Rscript '$__tool_directory__/w4mcorcov_wrapper.R' | 33 Rscript '$__tool_directory__/w4mcorcov_wrapper.R' |
28 dataMatrix_in '$dataMatrix_in' | 34 dataMatrix_in '$dataMatrix_in' |
29 sampleMetadata_in '$sampleMetadata_in' | 35 sampleMetadata_in '$sampleMetadata_in' |
52 contrast_corcov '$contrast_corcov' | 58 contrast_corcov '$contrast_corcov' |
53 contrast_salience '$contrast_salience' | 59 contrast_salience '$contrast_salience' |
54 ]]></command> | 60 ]]></command> |
55 | 61 |
56 <inputs> | 62 <inputs> |
57 <param name="dataMatrix_in" type="data" format="tabular" label="Data matrix file" | 63 <param name="dataMatrix_in" format="tabular" label="Data matrix file" type="data" |
58 help="Features x samples (tabular data - decimal: '.'; missing: NA; mode: numerical; separator: tab character)" /> | 64 help="variables ✖ samples" /> |
59 <param name="sampleMetadata_in" type="data" format="tabular" label="Sample metadata file" | 65 <param name="sampleMetadata_in" format="tabular" label="Sample metadata file" type="data" |
60 help="Samples x metadata (tabular data - decimal: '.'; missing: NA; mode: character or numerical; separator: tab character)" /> | 66 help="sample metadata, one row per sample" /> |
61 <param name="variableMetadata_in" type="data" format="tabular" | 67 <param name="variableMetadata_in" format="tabular" label="Variable metadata file (ideally from Univariate)" |
62 label="Variable metadata file (ideally from Univariate)" | 68 type="data" help="variable metadata, one row per variable" /> |
63 help="Features x metadata (tabular data - decimal: '.'; missing: NA; mode: character or numerical; separator: tab character)" /> | |
64 <param name="facC" type="text" | 69 <param name="facC" type="text" |
65 label="Factor of interest" | 70 label="Factor of interest" |
66 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."/> | 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."/> |
67 <conditional name="signif_test"> | 72 <conditional name="signif_test"> |
68 <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."> | 73 <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."> |
147 * factor-level 2, lexically greater than level 1 | 152 * factor-level 2, lexically greater than level 1 |
148 * Wiklund_2008 correlation | 153 * Wiklund_2008 correlation |
149 * Wiklund_2008 covariance | 154 * Wiklund_2008 covariance |
150 * Galindo_Prieto_2014 VIP for predictive components, VIP[4,p] | 155 * Galindo_Prieto_2014 VIP for predictive components, VIP[4,p] |
151 * Galindo_Prieto_2014 VIP for orthogonal components, VIP[4,o] | 156 * Galindo_Prieto_2014 VIP for orthogonal components, VIP[4,o] |
152 * (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. | 157 * 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. |
153 --> | 158 --> |
154 <data name="contrast_corcov" format="tabular" label="${tool.name}_${variableMetadata_in.name}_corcov" /> | 159 <data name="contrast_corcov" format="tabular" label="${tool.name}_${variableMetadata_in.name}_corcov" /> |
155 <!-- | 160 <!-- |
156 tsv2: salience table with columns (experimental feature): | 161 tsv2: salience table with columns (experimental feature): |
157 * feature-ID | 162 * feature-ID |
422 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. | 427 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. |
423 | 428 |
424 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: | 429 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: |
425 | 430 |
426 - picking features with maximum loadings along the projection parallel to the predictor (loadp), | 431 - picking features with maximum loadings along the projection parallel to the predictor (loadp), |
427 - examining extreme values on S-PLOTs (for which covariance is linearly related to loadp), | 432 - examining extreme values on S-PLOTs |
428 - examining "variable importance in projection VIP for OPLS-DA" (Galindo-Prieto *et al.* 2014), and | 433 - examining "variable importance in projection VIP for OPLS-DA" (Galindo-Prieto *et al.* 2014), and |
429 - examining a feature's "selectivity ratio" (Rajalahti *et al.*, 2009). | 434 - examining a feature's "selectivity ratio" (Rajalahti *et al.*, 2009). |
430 | 435 |
431 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. | 436 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. |
432 | 437 |
598 Working examples | 603 Working examples |
599 ---------------- | 604 ---------------- |
600 | 605 |
601 **Input files** | 606 **Input files** |
602 | 607 |
603 +-------------------------------------------------------------------------------------------------------------------+ | 608 +-----------------------------------------------------------------------------------------------------------------------------------------------+ |
604 | Download from URL | | 609 | Download from URL | |
605 +===================================================================================================================+ | 610 +===============================================================================================================================================+ |
606 | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/input_dataMatrix.tsv | | 611 | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/input_dataMatrix.tsv | |
607 +-------------------------------------------------------------------------------------------------------------------+ | 612 +-----------------------------------------------------------------------------------------------------------------------------------------------+ |
608 | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/input_sampleMetadata.tsv | | 613 | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/input_sampleMetadata.tsv | |
609 +-------------------------------------------------------------------------------------------------------------------+ | 614 +-----------------------------------------------------------------------------------------------------------------------------------------------+ |
610 | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/input_variableMetadata.tsv | | 615 | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/input_variableMetadata.tsv | |
611 +-------------------------------------------------------------------------------------------------------------------+ | 616 +-----------------------------------------------------------------------------------------------------------------------------------------------+ |
612 | 617 |
613 **Example 1:** Include in the analysis only features identified as pair-wise significant in the Univariate test. | 618 **Example 1:** Include in the analysis only features identified as pair-wise significant in the Univariate test. |
614 | 619 |
615 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ | 620 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ |
616 | Input Parameter or Result | Value | | 621 | Input Parameter or Result | Value | |
625 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ | 630 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ |
626 | Level-name matching | use regular expressions for matching level-names | | 631 | Level-name matching | use regular expressions for matching level-names | |
627 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ | 632 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ |
628 | Number of features having extreme loadings | ALL | | 633 | Number of features having extreme loadings | ALL | |
629 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ | 634 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ |
630 | Output primary table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_corcov.tsv | | 635 | Output primary table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_corcov.tsv | |
631 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ | 636 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ |
632 | Output salience table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_salience.tsv | | 637 | Output salience table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_salience.tsv | |
633 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ | 638 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ |
634 | Output figures PDF | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_detail.pdf | | 639 | Output figures PDF | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_detail.pdf | |
635 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ | 640 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ |
636 | 641 |
637 **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. | 642 **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. |
638 | 643 |
639 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ | 644 +--------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------+ |
640 | Input Parameter or Result | Value | | 645 | Input Parameter or Result | Value | |
641 +============================================+========================================================================================================================================+ | 646 +============================================+============================================================================================================================================+ |
642 | Factor of interest | k10 | | 647 | Factor of interest | k10 | |
643 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ | 648 +--------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------+ |
644 | Univariate Significance-Test | kruskal | | 649 | Univariate Significance-Test | kruskal | |
645 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ | 650 +--------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------+ |
646 | Retain only pairwise-significant features | No | | 651 | Retain only pairwise-significant features | No | |
647 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ | 652 +--------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------+ |
648 | Levels of interest | ``*`` | | 653 | Levels of interest | ``*`` | |
649 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ | 654 +--------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------+ |
650 | Level-name matching | use wild cards for matching level-names | | 655 | Level-name matching | use wild cards for matching level-names | |
651 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ | 656 +--------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------+ |
652 | Number of features having extreme loadings | 5 | | 657 | Number of features having extreme loadings | 5 | |
653 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ | 658 +--------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------+ |
654 | Output primary table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_corcov_all.tsv | | 659 | Output primary table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_corcov_all.tsv | |
655 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ | 660 +--------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------+ |
656 | Output salience table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_salience_all.tsv | | 661 | Output salience table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_salience_all.tsv | |
657 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ | 662 +--------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------+ |
658 | Output figures PDF | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_detail_all.pdf | | 663 | Output figures PDF | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_detail_all.pdf | |
659 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ | 664 +--------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------+ |
660 | 665 |
661 **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. | 666 **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. |
662 | 667 |
663 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ | 668 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ |
664 | Input Parameter or Result | Value | | 669 | Input Parameter or Result | Value | |
665 +============================================+========================================================================================================================================+ | 670 +============================================+==============================================================================================================================================+ |
666 | Factor of interest | k10 | | 671 | Factor of interest | k10 | |
667 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ | 672 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ |
668 | Univariate Significance-Test | none | | 673 | Univariate Significance-Test | none | |
669 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ | 674 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ |
670 | Levels of interest | k[12],k[3-4] | | 675 | Levels of interest | k[12],k[3-4] | |
671 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ | 676 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ |
672 | Level-name matching | use regular expressions for matching level-names | | 677 | Level-name matching | use regular expressions for matching level-names | |
673 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ | 678 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ |
674 | Number of features having extreme loadings | 0 | | 679 | Number of features having extreme loadings | 0 | |
675 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ | 680 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ |
676 | Output primary table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_corcov_global.tsv | | 681 | Output primary table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_corcov_global.tsv | |
677 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ | 682 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ |
678 | Output salience table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_salience_global.tsv | | 683 | Output salience table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_salience_global.tsv | |
679 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ | 684 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ |
680 | Output figures PDF | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_detail_global.pdf | | 685 | Output figures PDF | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_detail_global.pdf | |
681 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ | 686 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ |
682 | 687 |
683 **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". | 688 **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". |
684 | 689 |
685 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ | 690 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ |
686 | Input Parameter or Result | Value | | 691 | Input Parameter or Result | Value | |
687 +============================================+========================================================================================================================================+ | 692 +============================================+==============================================================================================================================================+ |
688 | Factor of interest | lohi | | 693 | Factor of interest | lohi | |
689 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ | 694 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ |
690 | Univariate Significance-Test | none | | 695 | Univariate Significance-Test | none | |
691 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ | 696 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ |
692 | Levels of interest | low,high | | 697 | Levels of interest | low,high | |
693 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ | 698 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ |
694 | Level-name matching | use regular expressions for matching level-names | | 699 | Level-name matching | use regular expressions for matching level-names | |
695 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ | 700 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ |
696 | Number of features having extreme loadings | 3 | | 701 | Number of features having extreme loadings | 3 | |
697 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ | 702 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ |
698 | Output primary table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_corcov_lohi.tsv | | 703 | Output primary table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_corcov_lohi.tsv | |
699 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ | 704 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ |
700 | Output salience table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_salience_lohi.tsv | | 705 | Output salience table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_salience_lohi.tsv | |
701 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ | 706 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ |
702 | Output figures PDF | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_detail_lohi.pdf | | 707 | Output figures PDF | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_detail_lohi.pdf | |
703 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ | 708 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ |
704 | 709 |
705 | 710 |
706 Trademarks | 711 Trademarks |
707 ---------- | 712 ---------- |
708 | 713 |