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comparison w4mcorcov.xml @ 8:342570ad880c draft

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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 0c81f4f1416129dd7061042b12cd28c0b8927aab
author eschen42
date Sat, 04 Aug 2018 17:43:16 -0400
parents 066b1f409e9f
children 06c51af11531
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7:066b1f409e9f 8:342570ad880c
1 <tool id="w4mcorcov" name="OPLS-DA_Contrasts" version="0.98.11"> 1 <tool id="w4mcorcov" name="OPLS-DA_Contrasts" version="0.98.12">
2 2 <description>OPLS-DA Contrasts of Univariate Results</description>
3 <description>OPLS-DA Contrasts of Univariate Results</description> 3 <macros>
4 4 <xml name="paramPairSigFeatOnly">
5 <macros> 5 <param name="pairSigFeatOnly" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE"
6 <xml name="paramPairSigFeatOnly"> 6 label="Retain only pairwise-significant features"
7 <param 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." />
8 name="pairSigFeatOnly" 8 </xml>
9 type="boolean" 9 <xml name="cplots">
10 checked="true" 10 <param name="cplot_y" label="C-plot Y-axis" type="select" help="Choose the Y-axis for C-plots.">
11 truevalue="TRUE" 11 <option value="correlation">Plot VIP versus correlation</option>
12 falsevalue="FALSE" 12 <option value="covariance">Plot VIP versus covariance</option>
13 label="Retain only pairwise-significant features" 13 </param>
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." /> 14 <param name="cplot_p" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE"
15 </xml> 15 label="Produce predictor C-plot"
16 <xml name="cplots"> 16 help="When this option is set to 'Yes', correlation will be plotted against vip4 for predictor loadings." />
17 <param name="cplot_y" label="C-plot Y-axis" type="select" help="Choose the Y-axis for C-plots."> 17 <param name="cplot_o" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE"
18 <option value="correlation">Plot VIP versus correlation</option> 18 label="Produce orthogonal C-plot"
19 <option value="covariance">Plot VIP versus covariance</option> 19 help="When this option is set to 'Yes', correlation will be plotted against vip4 for orthogonal loadings." />
20 </param> 20 </xml>
21 <param 21 </macros>
22 name="cplot_p" 22 <requirements>
23 type="boolean" 23 <requirement type="package">r-batch</requirement>
24 checked="TRUE" 24 <requirement type="package">bioconductor-ropls</requirement>
25 truevalue="TRUE" 25 </requirements>
26 falsevalue="FALSE" 26 <command detect_errors="aggressive"><![CDATA[
27 label="Produce predictor C-plot" 27 Rscript '$__tool_directory__/w4mcorcov_wrapper.R'
28 help="When this option is set to 'Yes', correlation will be plotted against vip4 for predictor loadings." /> 28 dataMatrix_in '$dataMatrix_in'
29 <param 29 sampleMetadata_in '$sampleMetadata_in'
30 name="cplot_o" 30 variableMetadata_in '$variableMetadata_in'
31 type="boolean" 31 facC '$facC'
32 checked="TRUE" 32 #if str( $signif_test.tesC ) == "none":
33 truevalue="TRUE" 33 tesC "none"
34 falsevalue="FALSE" 34 pairSigFeatOnly "FALSE"
35 label="Produce orthogonal C-plot" 35 #else:
36 help="When this option is set to 'Yes', correlation will be plotted against vip4 for orthogonal loadings." /> 36 tesC '$signif_test.tesC'
37 </xml> 37 pairSigFeatOnly '$signif_test.pairSigFeatOnly'
38 </macros> 38 #end if
39 39 levCSV '$levCSV'
40 <requirements> 40 matchingC '$matchingC'
41 <requirement type="package">r-batch</requirement> 41 labelFeatures '$labelFeatures'
42 <requirement type="package">bioconductor-ropls</requirement> 42 #if str( $xplots.expPlot ) == "none":
43 </requirements> 43 cplot_p "FALSE"
44 44 cplot_o "FALSE"
45 <stdio> 45 cplot_y "correlation"
46 <exit_code range="1:" level="fatal" /> 46 #else if str( $xplots.expPlot ) == "cplot":
47 </stdio> 47 cplot_p '$xplots.cplot_p'
48 48 cplot_o '$xplots.cplot_o'
49 <command><![CDATA[ 49 cplot_y '$xplots.cplot_y'
50 cd $__tool_directory__; Rscript w4mcorcov_wrapper.R 50 #end if
51 dataMatrix_in "$dataMatrix_in" 51 contrast_detail '$contrast_detail'
52 sampleMetadata_in "$sampleMetadata_in" 52 contrast_corcov '$contrast_corcov'
53 variableMetadata_in "$variableMetadata_in" 53 contrast_salience '$contrast_salience'
54 facC "$facC"
55 #if str( $signif_test.tesC ) == "none":
56 tesC "none"
57 pairSigFeatOnly "FALSE"
58 #else:
59 tesC "$signif_test.tesC"
60 pairSigFeatOnly "$signif_test.pairSigFeatOnly"
61 #end if
62 levCSV '$levCSV'
63 matchingC '$matchingC'
64 labelFeatures '$labelFeatures'
65 #if str( $xplots.expPlot ) == "none":
66 cplot_p "FALSE"
67 cplot_o "FALSE"
68 cplot_y "correlation"
69 #else if str( $xplots.expPlot ) == "cplot":
70 cplot_p "$xplots.cplot_p"
71 cplot_o "$xplots.cplot_o"
72 cplot_y "$xplots.cplot_y"
73 #end if
74 contrast_detail '$contrast_detail'
75 contrast_corcov '$contrast_corcov'
76 contrast_salience '$contrast_salience'
77 ]]></command> 54 ]]></command>
78 55
79 <inputs> 56 <inputs>
80 <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)" /> 57 <param name="dataMatrix_in" type="data" format="tabular" label="Data matrix file"
81 <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)" /> 58 help="Features x samples (tabular data - decimal: '.'; missing: NA; mode: numerical; separator: tab character)" />
82 <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)" /> 59 <param name="sampleMetadata_in" type="data" format="tabular" label="Sample metadata file"
83 <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."/> 60 help="Samples x metadata (tabular data - decimal: '.'; missing: NA; mode: character or numerical; separator: tab character)" />
84 <conditional name="signif_test"> 61 <param name="variableMetadata_in" type="data" format="tabular"
85 <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."> 62 label="Variable metadata file (ideally from Univariate)"
86 <option value="none">none - Display all features from variableMetadata (rather than choosing a subset based on significance in univariate testing)</option> 63 help="Features x metadata (tabular data - decimal: '.'; missing: NA; mode: character or numerical; separator: tab character)" />
87 <option value="ttest">ttest - Student's t-test (parametric test, qualitative factor with exactly 2 levels)</option> 64 <param name="facC" type="text"
88 <option value="anova">anova - Analysis of variance (parametric test, qualitative factor with more than 2 levels)</option> 65 label="Factor of interest"
89 <option value="wilcoxon">wilcoxon - Wilcoxon rank test (nonparametric test, qualitative factor with exactly 2 levels)</option> 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."/>
90 <option value="kruskal">kruskal - Kruskal-Wallis rank test (nonparametric test, qualitative factor with more than 2 levels)</option> 67 <conditional name="signif_test">
91 </param> 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.">
92 <when value="none" /> 69 <option value="none">none - Display all features from variableMetadata (rather than choosing a subset based on significance in univariate testing)</option>
93 <when value="ttest"> 70 <option value="ttest">ttest - Student's t-test (parametric test, qualitative factor with exactly 2 levels)</option>
94 <expand macro="paramPairSigFeatOnly" /> 71 <option value="anova">anova - Analysis of variance (parametric test, qualitative factor with more than 2 levels)</option>
95 </when> 72 <option value="wilcoxon">wilcoxon - Wilcoxon rank test (nonparametric test, qualitative factor with exactly 2 levels)</option>
96 <when value="anova"> 73 <option value="kruskal">kruskal - Kruskal-Wallis rank test (nonparametric test, qualitative factor with more than 2 levels)</option>
97 <expand macro="paramPairSigFeatOnly" /> 74 </param>
98 </when> 75 <when value="none" />
99 <when value="wilcoxon"> 76 <when value="ttest">
100 <expand macro="paramPairSigFeatOnly" /> 77 <expand macro="paramPairSigFeatOnly" />
101 </when> 78 </when>
102 <when value="kruskal"> 79 <when value="anova">
103 <expand macro="paramPairSigFeatOnly" /> 80 <expand macro="paramPairSigFeatOnly" />
104 </when> 81 </when>
105 </conditional> 82 <when value="wilcoxon">
106 <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."> 83 <expand macro="paramPairSigFeatOnly" />
107 <sanitizer> 84 </when>
108 <valid initial="string.letters"> 85 <when value="kruskal">
109 <add preset="string.digits"/> 86 <expand macro="paramPairSigFeatOnly" />
110 <add value="&#36;" /> <!-- $ dollar, dollar-sign --> 87 </when>
111 <add value="&#40;" /> <!-- ( left-paren --> 88 </conditional>
112 <add value="&#41;" /> <!-- ) right-paren --> 89 <param name="levCSV" type="text" value="*" label="Levels of interest"
113 <add value="&#42;" /> <!-- * splat, asterisk --> 90 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.">
114 <add value="&#43;" /> <!-- + plus --> 91 <sanitizer>
115 <add value="&#44;" /> <!-- , comma --> 92 <valid initial="string.letters">
116 <add value="&#45;" /> <!-- - dash, minus-sign --> 93 <add preset="string.digits"/>
117 <add value="&#46;" /> <!-- . dot, period --> 94 <add value="&#36;" /> <!-- $ dollar, dollar-sign -->
118 <add value="&#58;" /> <!-- : colon --> 95 <add value="&#40;" /> <!-- ( left-paren -->
119 <add value="&#59;" /> <!-- ; semi, semicolon --> 96 <add value="&#41;" /> <!-- ) right-paren -->
120 <add value="&#63;" /> <!-- ? what, question mark --> 97 <add value="&#42;" /> <!-- * splat, asterisk -->
121 <add value="&#91;" /> <!-- [ l-squib, left-squre-bracket --> 98 <add value="&#43;" /> <!-- + plus -->
122 <add value="&#92;" /> <!-- \ whack, backslash --> 99 <add value="&#44;" /> <!-- , comma -->
123 <add value="&#93;" /> <!-- ] r-squib, right-squre-bracket --> 100 <add value="&#45;" /> <!-- - dash, minus-sign -->
124 <add value="&#94;" /> <!-- ^ hat, caret --> 101 <add value="&#46;" /> <!-- . dot, period -->
125 <add value="&#123;" /> <!-- { l-cube, left-curly-bracket --> 102 <add value="&#58;" /> <!-- : colon -->
126 <add value="&#124;" /> <!-- | pipe --> 103 <add value="&#59;" /> <!-- ; semi, semicolon -->
127 <add value="&#125;" /> <!-- } r-cube, right-curly-bracket --> 104 <add value="&#63;" /> <!-- ? what, question mark -->
128 <!-- 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. --> 105 <add value="&#91;" /> <!-- [ l-squib, left-squre-bracket -->
129 </valid> 106 <add value="&#92;" /> <!-- \ whack, backslash -->
130 </sanitizer> 107 <add value="&#93;" /> <!-- ] r-squib, right-squre-bracket -->
131 </param> 108 <add value="&#94;" /> <!-- ^ hat, caret -->
132 <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.)"> 109 <add value="&#123;" /> <!-- { l-cube, left-curly-bracket -->
133 <option value="none">do no generic matching (default)</option> 110 <add value="&#124;" /> <!-- | pipe -->
134 <option value="wildcard" selected="true">use wild-cards for matching level-names</option> 111 <add value="&#125;" /> <!-- } r-cube, right-curly-bracket -->
135 <option value="regex">use regular expressions for matching level-names</option> 112 <!-- 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. -->
136 </param> 113 </valid>
137 <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."/> 114 </sanitizer>
138 <conditional name="xplots"> 115 </param>
139 <param name="expPlot" label="Extra plots to include" type="select" help="Choosing 'none' hides further choices."> 116 <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.)">
140 <option value="none">none - Do not include additonal extra plots.</option> 117 <option value="none">do no generic matching (default)</option>
141 <option value="cplot">cplot - Include C-plots (predictor-loading vs. 'vip4p' and orthogonal-loading versus 'vip4o')</option> 118 <option value="wildcard" selected="true">use wild-cards for matching level-names</option>
142 </param> 119 <option value="regex">use regular expressions for matching level-names</option>
143 <when value="none" /> 120 </param>
144 <when value="cplot"> 121 <param name="labelFeatures" type="text" value="3"
145 <expand macro="cplots" /> 122 label="How many features having extreme loadings should be labelled on cov-vs.-cor plot"
146 </when> 123 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."/>
147 </conditional> 124 <conditional name="xplots">
148 </inputs> 125 <param name="expPlot" label="Extra plots to include" type="select" help="Choosing 'none' hides further choices.">
149 126 <option value="none">Do not include additonal extra plots.</option>
150 <outputs> 127 <option value="cplot">Include C-plots (predictor-loading vs. 'vip4p' and orthogonal-loading versus 'vip4o')</option>
128 </param>
129 <when value="none" />
130 <when value="cplot">
131 <expand macro="cplots" />
132 </when>
133 </conditional>
134 </inputs>
135 <outputs>
151 <!-- 136 <!--
152 pdf1: summaries of each contrasts, clearly labelled by level=pair name 137 pdf1: summaries of each contrasts, clearly labelled by level=pair name
153 * first PCA score-plot 138 * first PCA score-plot
154 * then PLS score-plot 139 * then PLS score-plot
155 * then PLS S-PLOT; color in red features with VIP > 1; color in grey any non-pairwise-significant features, if these are included 140 * then PLS S-PLOT; color in red features with VIP > 1; color in grey any non-pairwise-significant features, if these are included
156 --> 141 -->
157 <data name="contrast_detail" label="${tool.name}_${variableMetadata_in.name}_detail" format="pdf" /> 142 <data name="contrast_detail" format="pdf" label="${tool.name}_${variableMetadata_in.name}_detail" />
158 <!-- 143 <!--
159 tsv1: cor and cov table with columns: 144 tsv1: cor and cov table with columns:
160 * feature-ID 145 * feature-ID
161 * factor-level 1 146 * factor-level 1
162 * factor-level 2, lexically greater than level 1 147 * factor-level 2, lexically greater than level 1
164 * Wiklund_2008 covariance 149 * Wiklund_2008 covariance
165 * Galindo_Prieto_2014 VIP for predictive components, VIP[4,p] 150 * Galindo_Prieto_2014 VIP for predictive components, VIP[4,p]
166 * Galindo_Prieto_2014 VIP for orthogonal components, VIP[4,o] 151 * Galindo_Prieto_2014 VIP for orthogonal components, VIP[4,o]
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. 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.
168 --> 153 -->
169 <data name="contrast_corcov" label="${tool.name}_${variableMetadata_in.name}_corcov" format="tabular" /> 154 <data name="contrast_corcov" format="tabular" label="${tool.name}_${variableMetadata_in.name}_corcov" />
170 <!-- 155 <!--
171 tsv2: salience table with columns (experimental feature): 156 tsv2: salience table with columns (experimental feature):
172 * feature-ID 157 * feature-ID
173 * Salient level, i.e., for the feature, the class-level having the greatest median intensity 158 * Salient level, i.e., for the feature, the class-level having the greatest median intensity
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 159 * 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
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. 160 * 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.
176 --> 161 -->
177 <data name="contrast_salience" label="${tool.name}_${variableMetadata_in.name}_salience" format="tabular" /> 162 <data name="contrast_salience" format="tabular" label="${tool.name}_${variableMetadata_in.name}_salience" />
178 </outputs> 163 </outputs>
179
180 <tests> 164 <tests>
181 <!-- test #1 --> 165 <!-- test #1 -->
182 <test> 166 <test>
183 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/> 167 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
184 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/> 168 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
723 ---------- 707 ----------
724 708
725 OPLS-DA, SIMCA, and S-PLOT are registered trademarks of the Umetrics company. http://umetrics.com/about-us/trademarks 709 OPLS-DA, SIMCA, and S-PLOT are registered trademarks of the Umetrics company. http://umetrics.com/about-us/trademarks
726 710
727 711
728 Release notes
729 -------------
730
731 0.98.11
732
733 - bug fix: Readdress issue 2 - features now are pareto-scaled *and centered* per Wikland *op cit.*.
734
735 0.98.10
736
737 - new feature: C-plots of VIP versus correlation or relative covariance.
738 - bug fix: Handle issue 2 - features now are only pareto-scaled per Wikland *op cit.*.
739
740 0.98.9
741
742 - bug fix: Handle issue 1 - handle features removed by ropls because variance is less than 2.2e-16.
743
744 0.98.8
745
746 - 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
747
748 0.98.7
749
750 - bug fix: Handle case of a treatment level with only one sample.
751
752 0.98.6
753
754 - bug fix: Set 'crossvalI' param (of R function 'ropls::opls') to the number of samples when the there are fewer than seven samples.
755
756 0.98.5
757
758 - bug fix: Fit feature-labels within clipping region of cor-vs.cov plot
759 - new feature: optionally (and by default) suppress labels for features with extreme orthogonal loadings
760
761 0.98.3
762
763 - Add support for two-level factors
764 - Add adjusted mz and rt to output tables
765 - Allow explicitly setting the number of features with extreme loadings to be labelled on the correlation vs. covariance plot
766 - Add loadings to corcov table
767
768 0.98.2
769
770 - first release
771
772
773 ]]></help> 712 ]]></help>
774 <citations> 713 <citations>
775 <!-- this tool --> 714 <!-- this tool -->
776 <citation type="doi">10.5281/zenodo.1034784</citation> 715 <citation type="doi">10.5281/zenodo.1034784</citation>
777 <!-- Galindo_Prieto_2014 Variable influence on projection (VIP) for OPLS --> 716 <!-- Galindo_Prieto_2014 Variable influence on projection (VIP) for OPLS -->