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comparison iwtomics-1.0/testandplot.xml @ 82:8e397b62df4c draft

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Uploaded 20171006
author fabio
date Fri, 06 Oct 2017 11:03:56 -0400
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81:6610fd91c760 82:8e397b62df4c
1 <tool id="iwtomics_testandplot" name="IWTomics Test" version="@VERSION@.0">
2 <description>and Plot</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7
8 <command detect_errors="exit_code">
9 <![CDATA[
10 Rscript '$__tool_directory__/testandplot.R' adjustedpvaluematrix='${adjustedpvaluematrix}' iwtomicsrespdf='${iwtomicsrespdf}' iwtomicssumpdf='${iwtomicssumpdf}' iwtomicsrdata='${iwtomicsrdata}' iwtomicstests='${iwtomicstests}' iwtomicsselectedfeatures='${iwtomicsselectedfeatures}'
11 regionids='${regionids}'
12 featureids='${featureids}'
13 rdatafile='${rdata}'
14
15 #set region1 = ','.join( [ str( $r.region0 ) for $r in $regionssection.regions ] )
16 #set region2 = ','.join( [ str( $r.region1 ) for $r in $regionssection.regions ] )
17 region1='c(${region1})'
18 region2='c(${region2})'
19
20 features_subset='c(${featureslist})'
21
22 statistics="'${conditionalstatistics.statistics}'"
23 #if $conditionalstatistics.statistics == "quantile":
24 #set probabilities = ','.join( [ str( $p.qprob ) for $p in $conditionalstatistics.quantilesection.qprobabilities ] )
25 testprobs='c(${probabilities})'
26 #end if
27
28 B='${permutations}'
29
30 testalpha='${plotres.alpha}'
31 average='${plotres.average}'
32 size='${plotres.size}'
33 plottype="'${plotres.conditionalplottype.plottype}'"
34 #if $plotres.conditionalplottype.plottype == "boxplot":
35 #set probs = ','.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )
36 #if $probs != "":
37 probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})'
38 #else:
39 probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})'
40 #end if
41 #end if
42
43 groupby="'${plotsum.conditionalgroupby.groupby}'"
44 #if $plotsum.conditionalgroupby.groupby == "test":
45 summaryalpha='${plotsum.conditionalgroupby.testalphaplot}'
46 only_significant='${plotsum.conditionalgroupby.testonlysig}'
47 #elif $plotsum.conditionalgroupby.groupby == "feature":
48 summaryalpha='${plotsum.conditionalgroupby.featurealphaplot}'
49 only_significant='${plotsum.conditionalgroupby.featureonlysig}'
50 #end if
51 ]]>
52 </command>
53
54 <inputs>
55 <!-- RData -->
56 <param format="rdata" name="rdata" type="data" label="Select IWTomicsData object" help="File created by 'IWTomics Load Smooth and Plot'." />
57 <!-- region IDs -->
58 <param format="tabular" name="regionids" type="data" label="Select region dataset IDs" help="File created by 'IWTomics Load Smooth and Plot'." />
59 <!-- feature IDs -->
60 <param format="tabular" name="featureids" type="data" label="Select feature IDs" help="File created by 'IWTomics Load Smooth and Plot'." />
61
62 <!-- repeat region ids -->
63 <section name="regionssection" title="Select regions for Interval-Wise Testing" expanded="True" help="IDs of the region datasets to be tested.">
64 <repeat name="regions" title="Two-sample test" min="1">
65 <param name="region0" type="data_column" data_ref="regionids" numerical="False" label="Region 1" multiple="False" use_header_names="True" />
66 <param name="region1" type="data_column" data_ref="regionids" numerical="False" label="Region 2" multiple="False" use_header_names="True" />
67 </repeat>
68 </section>
69
70 <!-- feature ids list -->
71 <param name="featureslist" type="data_column" data_ref="featureids" numerical="False" label="Select features" multiple="True" use_header_names="True" help="IDs of the features to be tested." />
72
73 <!-- conditional statistics -->
74 <conditional name="conditionalstatistics">
75 <!-- statistics -->
76 <param name="statistics" type="select" label="Test statistics">
77 <option value="mean">Mean difference</option>
78 <option value="median">Median difference</option>
79 <option value="variance">Variance ratio</option>
80 <option value="quantile">Quantile difference(s)</option>
81 </param>
82 <!-- conditional choice: statistics=quantile -->
83 <when value="quantile">
84 <section name="quantilesection" title="Probabilities" expanded="True" help="Probabilities corresponding to the quantiles in test statistics.">
85 <repeat name="qprobabilities" title="Probabilities" min="1">
86 <param name="qprob" size="4" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
87 </repeat>
88 </section>
89 </when>
90 </conditional>
91
92 <!-- permutations -->
93 <param name="permutations" type="integer" value="1000" min="1" label="Number of permutations" />
94
95 <!-- plot IWTomics results -->
96 <section name="plotres" title="Plot IWTomics test results" expanded="True">
97 <!-- alpha -->
98 <param name="alpha" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
99 <expand macro="plot-params" />
100 </section>
101
102 <!-- summary plot -->
103 <expand macro="plot-sum" />
104 </inputs>
105
106 <outputs>
107 <data format="txt" name="adjustedpvaluematrix" label="${tool.name} on ${on_string}: Adjusted p-value Matrix" from_work_dir="iwtomics.testandplot.adjustedpvalue.matrix.txt" />
108 <data format="pdf" name="iwtomicsrespdf" label="${tool.name} on ${on_string}: Plotted Test Results" from_work_dir="iwtomics.testandplot.iwtomicstestresults.pdf" />
109 <data format="pdf" name="iwtomicssumpdf" label="${tool.name} on ${on_string}: Summary Plot" from_work_dir="iwtomics.testandplot.summaryplot.pdf" />
110 <data format="rdata" name="iwtomicsrdata" label="${tool.name} on ${on_string}: IWTomicsData Object with Test Results" from_work_dir="iwtomics.testandplot.RData" />
111 <data format="tabular" name="iwtomicstests" label="${tool.name} on ${on_string}: Test IDs" from_work_dir="iwtomics.testandplot.tests.txt" />
112 <data format="tabular" name="iwtomicsselectedfeatures" label="${tool.name} on ${on_string}: Feature IDs" from_work_dir="iwtomics.testandplot.selectedfeatures.txt" />
113 </outputs>
114
115 <tests>
116 <test>
117 <param name="rdata" value="output_loadandplot/iwtomics.loadandplot.RData" ftype="rdata" />
118 <param name="regionids" value="output_loadandplot/iwtomics.loadandplot.regions.txt" ftype="tabular" />
119 <param name="featureids" value="output_loadandplot/iwtomics.loadandplot.features.txt" ftype="tabular" />
120 <repeat name="regions">
121 <param name="region0" value="2" />
122 <param name="region1" value="1" />
123 </repeat>
124 <repeat name="regions">
125 <param name="region0" value="3" />
126 <param name="region1" value="1" />
127 </repeat>
128 <repeat name="regions">
129 <param name="region0" value="4" />
130 <param name="region1" value="1" />
131 </repeat>
132 <param name="featureslist" value="1,2" />
133 <param name="statistics" value="mean" />
134 <param name="permutations" value="1000" />
135 <param name="alpha" value="0.05" />
136 <param name="average" value="TRUE" />
137 <param name="size" value="TRUE" />
138 <param name="plottype" value="boxplot" />
139 <param name="prob0" value="0.25" />
140 <param name="prob1" value="0.5" />
141 <param name="prob2" value="0.75" />
142 <param name="groupby" value="feature" />
143 <param name="featurealphaplot" value="0.05" />
144 <param name="featureonlysig" value="TRUE" />
145 <output name="adjustedpvaluematrix" file="output_testandplot/iwtomics.testandplot.adjustedpvalue.matrix.txt" compare="sim_size" />
146 <output name="iwtomicsrespdf" file="output_testandplot/iwtomics.testandplot.iwtomicstestresults.pdf" compare="sim_size" />
147 <output name="iwtomicssumpdf" file="output_testandplot/iwtomics.testandplot.summaryplot.pdf" compare="sim_size" />
148 <output name="iwtomicsrdata" file="output_testandplot/iwtomics.testandplot.RData" compare="sim_size" />
149 <output name="iwtomicstests" file="output_testandplot/iwtomics.testandplot.tests.txt" />
150 <output name="iwtomicsselectedfeatures" file="output_testandplot/iwtomics.testandplot.selectedfeatures.txt" />
151 </test>
152 </tests>
153
154 <help><![CDATA[
155 This tool statistically evaluates differences in genomic features between groups of regions along the genome.
156 In particular, it implements the Interval-Wise Testing for omics data, an extended version of the Interval-Wise
157 Testing for functional data presented in Pini and Vantini (2017). It allows to perform multiple two sample permutation
158 tests between pairs of region datasets, on several features. It returns the adjusted p-value curves for every test
159 and all possible scales. Moreover, it creates a graphical representation of the Interval-Wise Testing results
160 and a summary plot (optional) with p-values at the maximum scale. The tool *IWTomics Plot with Threshold on Test Scale*
161 permits to select the scale to be used in the plots.
162
163 -----
164
165 **Input files**
166
167 RData file with the IWTomicsData object, tabular files with region dataset IDs and feature IDs.
168 These files are created by the tool *IWTomics Load Smooth and Plot*.
169
170 -----
171
172 **Output**
173
174 The tool returns:
175
176 1. TXT file with an adjusted p-value matrix for every test performed. Each matrix contains a p-value curve (row) for every scale considered in the test;
177 2. PDF file with the plotted test results;
178 3. PDF file with the summary plot;
179 4. RData with the IWTomicsData object with the test results;
180 5. Test identifiers;
181 6. Feature identifiers.
182
183 4-6 can be used as input of the tool *IWTomics Plot with Threshold on Test Scale*
184
185 -----
186
187 .. class:: infomark
188
189 **Notes**
190
191 This Galaxy tool has been developed by Fabio Cumbo (Third University of Rome, Italy) and Marzia A. Cremona (The Pennsylvania State University, USA).
192
193 It implements a simplified version of the function *IWTomicsTest*, *plotTest* and *plotSummary* for *IWTomicsData* objects.
194 The complete version can be found in the *R/Bioconductor* package *IWTomics* (see vignette_).
195
196 .. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf
197 ]]></help>
198
199 <expand macro="citations" />
200
201 </tool>