annotate testandplot.xml @ 60:c2cae0d8176e draft

Uploaded 20170608
author fabio
date Thu, 08 Jun 2017 17:11:01 -0400
parents 7a806a3aeda1
children bd5ba4648ac0
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
58
7a806a3aeda1 Uploaded 20170608
fabio
parents: 56
diff changeset
1 <tool id="iwtomics_testandplot" name="IWTomics Test" version="@VERSION@.0">
18
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
2 <description>and Plot</description>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
3 <macros>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
4 <import>macros.xml</import>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
5 </macros>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
6 <expand macro="requirements" />
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
7 <stdio>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
8 <exit_code range="-1" source="both" level="fatal" description="Missing IWTomics package. Please be sure to have it installed before using this tool." />
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
9 <exit_code range="10" source="both" level="fatal" description="Wrong region ids." />
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
10 <exit_code range="20" source="both" level="fatal" description="Wrong feature ids." />
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
11 <exit_code range="30" source="both" level="fatal" description="Same test repeated multiple times." />
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
12 <exit_code range="40" source="both" level="fatal" description="Testing error." />
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
13 <regex match="Error" source="both" level="fatal" description="An error has occurred. Please try again." />
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
14 </stdio>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
15
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
16 <command>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
17 <![CDATA[
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
18 Rscript $__tool_directory__/testandplot.R adjustedpvaluematrix="${adjustedpvaluematrix}" iwtomicsrespdf="${iwtomicsrespdf}" iwtomicssumpdf="${iwtomicssumpdf}" iwtomicsrdata="${iwtomicsrdata}" iwtomicstests="${iwtomicstests}" iwtomicsselectedfeatures="${iwtomicsselectedfeatures}"
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
19 regionids="${regionids}"
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
20 featureids="${featureids}"
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
21 rdatafile="${rdata}"
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
22
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
23 #set region1 = '","'.join( [ str( $r.region0 ) for $r in $regionssection.regions ] )
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
24 #set region2 = '","'.join( [ str( $r.region1 ) for $r in $regionssection.regions ] )
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
25 region1="c(${region1})"
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
26 region2="c(${region2})"
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
27
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
28 features_subset="c(${featureslist})"
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
29
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
30 statistics="'${conditionalstatistics.statistics}'"
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
31 #if $conditionalstatistics.statistics == "quantile":
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
32 #set probabilities = '","'.join( [ str( $p.qprob ) for $p in $conditionalstatistics.quantilesection.qprobabilities ] )
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
33 testprobs="c(${probabilities})"
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
34 #end if
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
35
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
36 B="${permutations}"
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
37
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
38 testalpha="${plotres.alpha}"
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
39 average="${plotres.average}"
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
40 size="${plotres.size}"
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
41 plottype="'${plotres.conditionalplottype.plottype}'"
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
42 #if $plotres.conditionalplottype.plottype == 'boxplot':
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
43 #set probs = '","'.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
44 #if $probs != "":
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
45 probs="c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})"
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
46 #else:
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
47 probs="c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})"
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
48 #end if
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
49 #end if
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
50
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
51 groupby="'${plotsum.conditionalgroupby.groupby}'"
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
52 #if $plotsum.conditionalgroupby.groupby == "test":
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
53 summaryalpha="${plotsum.conditionalgroupby.testalphaplot}"
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
54 only_significant="${plotsum.conditionalgroupby.testonlysig}"
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
55 #elif $plotsum.conditionalgroupby.groupby == "feature":
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
56 summaryalpha="${plotsum.conditionalgroupby.featurealphaplot}"
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
57 only_significant="${plotsum.conditionalgroupby.featureonlysig}"
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
58 #end if
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
59
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
60 >& /dev/null
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
61 ]]>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
62 <!--
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
63 to print the stack add the following line at the end of the command and enable the corresponding entry in output
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
64 2> "${stackerr}"
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
65 -->
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
66 </command>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
67
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
68 <inputs>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
69 <!-- RData -->
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
70 <param format="rdata" name="rdata" type="data" label="Select IWTomicsData object" help="File created by 'IWTomics Load Smooth and Plot'." />
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
71 <!-- region IDs -->
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
72 <param format="tabular" name="regionids" type="data" label="Select region dataset IDs" help="File created by 'IWTomics Load Smooth and Plot'." />
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
73 <!-- feature IDs -->
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
74 <param format="tabular" name="featureids" type="data" label="Select feature IDs" help="File created by 'IWTomics Load Smooth and Plot'." />
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
75
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
76 <!-- repeat region ids -->
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
77 <section name="regionssection" title="Select regions for Interval-Wise Testing" expanded="True" help="IDs of the region datasets to be tested.">
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
78 <repeat name="regions" title="Two-sample test" min="1">
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
79 <param name="region0" type="data_column" data_ref="regionids" numerical="False" label="Region 1" multiple="False" use_header_names="True" />
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
80 <param name="region1" type="data_column" data_ref="regionids" numerical="False" label="Region 2" multiple="False" use_header_names="True" />
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
81 </repeat>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
82 </section>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
83
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
84 <!-- feature ids list -->
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
85 <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." />
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
86
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
87 <!-- conditional statistics -->
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
88 <conditional name="conditionalstatistics">
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
89 <!-- statistics -->
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
90 <param name="statistics" type="select" label="Test statistics">
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
91 <option value="mean">Mean difference</option>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
92 <option value="median">Median difference</option>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
93 <option value="variance">Variance ratio</option>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
94 <option value="quantile">Quantile difference(s)</option>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
95 </param>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
96 <!-- conditional choice: statistics=quantile -->
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
97 <when value="quantile">
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
98 <section name="quantilesection" title="Probabilities" expanded="True" help="Probabilities corresponding to the quantiles in test statistics.">
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
99 <repeat name="qprobabilities" title="Probabilities" min="1">
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
100 <param name="qprob" size="4" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
101 </repeat>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
102 </section>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
103 </when>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
104 </conditional>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
105
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
106 <!-- permutations -->
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
107 <param name="permutations" type="integer" value="1000" min="1" label="Number of permutations" />
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
108
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
109 <!-- plot IWTomics results -->
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
110 <section name="plotres" title="Plot IWTomics test results" expanded="True">
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
111 <!-- alpha -->
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
112 <param name="alpha" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
113 <!-- average -->
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
114 <param name="average" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot the mean curves" />
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
115 <!-- average -->
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
116 <param name="size" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot sample size in each position" />
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
117 <!-- conditional plot type -->
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
118 <conditional name="conditionalplottype">
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
119 <!-- plot type -->
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
120 <param name="plottype" type="select" label="Plot type">
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
121 <option value="boxplot">Pointwise quantile curves (boxplot)</option>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
122 <option value="curves">Curves (aligned)</option>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
123 </param>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
124 <!-- conditional choice: plottype=boxplot -->
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
125 <when value="boxplot">
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
126 <section name="probabilitiessection" title="Probabilities" expanded="True" help="Probabilities corresponding to the quantile curves to be drawn.">
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
127 <param name="prob0" size="3" type="float" value="0.25" min="0.0" max="1.0" label="Probability" />
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
128 <param name="prob1" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
129 <param name="prob2" size="3" type="float" value="0.75" min="0.0" max="1.0" label="Probability" />
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
130 <repeat name="probabilities" title="Probabilities">
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
131 <param name="prob" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
132 </repeat>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
133 </section>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
134 </when>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
135 </conditional>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
136 </section>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
137
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
138 <!-- summary plot -->
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
139 <section name="plotsum" title="Summary plot" expanded="True">
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
140 <!-- conditional group by -->
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
141 <conditional name="conditionalgroupby">
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
142 <!-- group by -->
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
143 <param name="groupby" type="select" label="Group by" help="How tests should be grouped.">
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
144 <option value="none">No plot</option>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
145 <option value="test">Group by test</option>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
146 <option value="feature">Group by feature</option>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
147 </param>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
148 <when value="test">
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
149 <param name="testalphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
150 <param name="testonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
151 </when>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
152 <when value="feature">
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
153 <param name="featurealphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
154 <param name="featureonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
155 </when>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
156 </conditional>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
157 </section>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
158 </inputs>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
159
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
160 <outputs>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
161 <!--<data format="txt" name="stackerr" label="iwtomics.testandplot.stackerr.txt" from_work_dir="iwtomics.testandplot.stackerr.txt" />-->
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
162 <data format="txt" name="adjustedpvaluematrix" label="${tool.name} on ${on_string}: Adjusted p-value Matrix" from_work_dir="iwtomics.testandplot.adjustedpvalue.matrix.txt" />
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
163 <data format="pdf" name="iwtomicsrespdf" label="${tool.name} on ${on_string}: Plotted Test Results" from_work_dir="iwtomics.testandplot.iwtomicstestresults.pdf" />
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
164 <data format="pdf" name="iwtomicssumpdf" label="${tool.name} on ${on_string}: Summary Plot" from_work_dir="iwtomics.testandplot.summaryplot.pdf" />
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
165 <data format="rdata" name="iwtomicsrdata" label="${tool.name} on ${on_string}: IWTomicsData Object with Test Results" from_work_dir="iwtomics.testandplot.RData" />
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
166 <data format="tabular" name="iwtomicstests" label="${tool.name} on ${on_string}: Test IDs" from_work_dir="iwtomics.testandplot.tests.txt" />
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
167 <data format="tabular" name="iwtomicsselectedfeatures" label="${tool.name} on ${on_string}: Feature IDs" from_work_dir="iwtomics.testandplot.selectedfeatures.txt" />
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
168 </outputs>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
169
56
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
170 <tests>
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
171 <test>
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
172 <param name="rdata" value="output_loadandplot/iwtomics.loadandplot.RData" ftype="rdata" />
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
173 <param name="regionids" value="output_loadandplot/iwtomics.loadandplot.regions.txt" ftype="tabular" />
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
174 <param name="featureids" value="output_loadandplot/iwtomics.loadandplot.features.txt" ftype="tabular" />
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
175 <repeat name="regions">
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
176 <param name="region0" value="2" />
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
177 <param name="region1" value="1" />
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
178 </repeat>
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
179 <repeat name="regions">
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
180 <param name="region0" value="3" />
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
181 <param name="region1" value="1" />
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
182 </repeat>
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
183 <repeat name="regions">
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
184 <param name="region0" value="4" />
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
185 <param name="region1" value="1" />
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
186 </repeat>
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
187 <param name="featureslist" value="1,2" />
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
188 <param name="statistics" value="mean" />
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
189 <param name="permutations" value="1000" />
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
190 <param name="alpha" value="0.05" />
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
191 <param name="average" value="TRUE" />
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
192 <param name="size" value="TRUE" />
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
193 <param name="plottype" value="boxplot" />
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
194 <param name="prob0" value="0.25" />
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
195 <param name="prob1" value="0.5" />
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
196 <param name="prob2" value="0.75" />
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
197 <param name="groupby" value="feature" />
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
198 <param name="featurealphaplot" value="0.05" />
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
199 <param name="featureonlysig" value="TRUE" />
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
200 <output name="adjustedpvaluematrix" file="output_testandplot/iwtomics.testandplot.adjustedpvalue.matrix.txt" compare="sim_size" />
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
201 <output name="iwtomicsrespdf" file="output_testandplot/iwtomics.testandplot.iwtomicstestresults.pdf" compare="sim_size" />
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
202 <output name="iwtomicssumpdf" file="output_testandplot/iwtomics.testandplot.summaryplot.pdf" compare="sim_size" />
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
203 <output name="iwtomicsrdata" file="output_testandplot/iwtomics.testandplot.RData" compare="sim_size" />
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
204 <output name="iwtomicstests" file="output_testandplot/iwtomics.testandplot.tests.txt" />
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
205 <output name="iwtomicsselectedfeatures" file="output_testandplot/iwtomics.testandplot.selectedfeatures.txt" />
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
206 </test>
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
207 </tests>
9ceb3ffcd817 Uploaded 20170608
fabio
parents: 54
diff changeset
208
18
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
209 <help>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
210 This tool statistically evaluates differences in genomic features between groups of regions along the genome.
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
211 In particular, it implements the Interval-Wise Testing for omics data, an extended version of the Interval-Wise
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
212 Testing for functional data presented in Pini and Vantini (2017). It allows to perform multiple two sample permutation
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
213 tests between pairs of region datasets, on several features. It returns the adjusted p-value curves for every test
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
214 and all possible scales. Moreover, it creates a graphical representation of the Interval-Wise Testing results
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
215 and a summary plot (optional) with p-values at the maximum scale. The tool *IWTomics Plot with Threshold on Test Scale*
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
216 permits to select the scale to be used in the plots.
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
217
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
218 -----
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
219
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
220 **Input files**
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
221
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
222 RData file with the IWTomicsData object, tabular files with region dataset IDs and feature IDs.
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
223 These files are created by the tool *IWTomics Load Smooth and Plot*.
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
224
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
225 -----
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
226
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
227 **Output**
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
228
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
229 The tool returns:
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
230
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
231 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;
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
232 2. PDF file with the plotted test results;
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
233 3. PDF file with the summary plot;
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
234 4. RData with the IWTomicsData object with the test results;
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
235 5. Test identifiers;
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
236 6. Feature identifiers.
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
237
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
238 4-6 can be used as input of the tool *IWTomics Plot with Threshold on Test Scale*
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
239
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
240 -----
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
241
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
242 .. class:: infomark
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
243
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
244 **Notes**
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
245
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
246 This Galaxy tool has been developed by Fabio Cumbo (Third University of Rome, Italy) and Marzia A. Cremona (The Pennsylvania State University, USA).
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
247
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
248 It implements a simplified version of the function *IWTomicsTest*, *plotTest* and *plotSummary* for *IWTomicsData* objects.
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
249 The complete version can be found in the *R/Bioconductor* package *IWTomics* (see vignette_).
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
250
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
251 .. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
252 </help>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
253
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
254 <citations>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
255 <citation type="bibtex">
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
256 @ARTICLE{
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
257 iwt-functional-data,
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
258 author = {A Pini and S. Vantini},
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
259 title = {Interval-Wise Testing for functional data},
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
260 journal = {Journal of Nonparametric Statistics},
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
261 year = {2017},
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
262 volume = {29},
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
263 number = {2},
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
264 pages = {407-424}
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
265 }
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
266 </citation>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
267 <citation type="bibtex">
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
268 @MANUAL{
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
269 iwtomics,
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
270 author = {Cremona, Marzia A and Pini, Alessia and Chiaromonte, Francesca and Vantini, Simone},
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
271 title = {IWTomics: Interval-Wise Testing for Omics Data},
54
d49031ef33d5 Uploaded 20170531
fabio
parents: 18
diff changeset
272 note = {R package version 1.0.0},
18
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
273 year = {2017}
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
274 }
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
275 </citation>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
276 </citations>
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
277
565118df598a Uploaded 20170531
fabio
parents:
diff changeset
278 </tool>