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comparison plotwithscale.xml @ 83:f81d72e482cf draft

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author fabio
date Fri, 06 Oct 2017 11:06:44 -0400
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82:8e397b62df4c 83:f81d72e482cf
1 <tool id="iwtomics_plotwithscale" name="IWTomics Plot with Threshold" version="@VERSION@.0">
2 <description>on Test Scale</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 '$__tool_directory__/plotwithscale.R' adjustedpvalue='${adjustedpvalue}' iwtomicsrespdf='${iwtomicsrespdf}' iwtomicssumpdf='${iwtomicssumpdf}'
11 iwtomicsrdata='${rdata}'
12 iwtomicstests='${testids}'
13 iwtomicsselectedfeatures='${featureids}'
14
15 #set test_subset = '|'.join( [ str( $e.test ) for $e in $scalesection.thresholdontestscale ] )
16 test_subset='${test_subset}'
17 #set feature_subset = '|'.join( [ str( $e.feature ) for $e in $scalesection.thresholdontestscale ] )
18 feature_subset='${feature_subset}'
19 #set scale_subset = ','.join( [ str( $e.scale ) for $e in $scalesection.thresholdontestscale ] )
20 scale_subset='c(${scale_subset})'
21
22 testalpha='${plotres.alpha}'
23 average='${plotres.average}'
24 size='${plotres.size}'
25 plottype="'${plotres.conditionalplottype.plottype}'"
26 #if $plotres.conditionalplottype.plottype == 'boxplot':
27 #set probs = ','.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )
28 #if $probs != "":
29 probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})'
30 #else:
31 probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})'
32 #end if
33 #end if
34
35 groupby="'${plotsum.conditionalgroupby.groupby}'"
36 #if $plotsum.conditionalgroupby.groupby == "test":
37 summaryalpha='${plotsum.conditionalgroupby.testalphaplot}'
38 only_significant='${plotsum.conditionalgroupby.testonlysig}'
39 #elif $plotsum.conditionalgroupby.groupby == "feature":
40 summaryalpha='${plotsum.conditionalgroupby.featurealphaplot}'
41 only_significant='${plotsum.conditionalgroupby.featureonlysig}'
42 #end if
43 ]]>
44 </command>
45
46 <inputs>
47 <!-- RData -->
48 <param format="rdata" name="rdata" type="data" label="Select IWTomicsData object with test results" help="File created by 'IWTomics Test and Plot'." />
49 <!-- test IDs -->
50 <param format="tabular" name="testids" type="data" label="Select test IDs" help="File created by 'IWTomics Test and Plot'." />
51 <!-- feature IDs -->
52 <param format="tabular" name="featureids" type="data" label="Select feature IDs" help="File created by 'IWTomics Test and Plot'." />
53
54 <!-- repeat threshold on test scale -->
55 <section name="scalesection" title="Select scale for Interval-Wise Testing and plot" expanded="True" help="Maximum interval length for the p-value adjustment. If 0 the maximum possible scale is used.">
56 <repeat name="thresholdontestscale" title="Threshold on test scale" min="1">
57 <param name="test" type="data_column" data_ref="testids" numerical="False" label="Test ID" multiple="True" use_header_names="True" />
58 <param name="feature" type="data_column" data_ref="featureids" numerical="False" label="Feature ID" multiple="True" use_header_names="True" />
59 <param name="scale" type="integer" value="0" min="0" label="Scale" />
60 </repeat>
61 </section>
62
63 <!-- plot IWTomics results -->
64 <section name="plotres" title="Plot IWTomics test results" expanded="True">
65 <!-- alpha -->
66 <param name="alpha" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
67 <expand macro="plot-params" />
68 </section>
69
70 <!-- summary plot -->
71 <expand macro="plot-sum" />
72 </inputs>
73
74 <outputs>
75 <data format="txt" name="adjustedpvalue" label="${tool.name} on ${on_string}: Adjusted p-value" from_work_dir="iwtomics.plotwithscale.adjustedpvalue.txt" />
76 <data format="pdf" name="iwtomicsrespdf" label="${tool.name} on ${on_string}: Plotted Test Results" from_work_dir="iwtomics.plotwithscale.iwtomicstestresults.pdf" />
77 <data format="pdf" name="iwtomicssumpdf" label="${tool.name} on ${on_string}: Summary Plot" from_work_dir="iwtomics.plotwithscale.summaryplot.pdf" />
78 </outputs>
79
80 <tests>
81 <test>
82 <param name="rdata" value="output_testandplot/iwtomics.testandplot.RData" ftype="rdata" />
83 <param name="testids" value="output_testandplot/iwtomics.testandplot.tests.txt" ftype="tabular" />
84 <param name="featureids" value="output_testandplot/iwtomics.testandplot.selectedfeatures.txt" ftype="tabular" />
85 <repeat name="thresholdontestscale">
86 <param name="test" value="1" />
87 <param name="feature" value="1" />
88 <param name="scale" value="10" />
89 </repeat>
90 <repeat name="thresholdontestscale">
91 <param name="test" value="1,2,3" />
92 <param name="feature" value="2" />
93 <param name="scale" value="20" />
94 </repeat>
95 <param name="alpha" value="0.05" />
96 <param name="average" value="TRUE" />
97 <param name="size" value="TRUE" />
98 <param name="plottype" value="boxplot" />
99 <param name="prob0" value="0.25" />
100 <param name="prob1" value="0.5" />
101 <param name="prob2" value="0.75" />
102 <param name="groupby" value="feature" />
103 <param name="featurealphaplot" value="0.05" />
104 <param name="featureonlysig" value="TRUE" />
105 <output name="adjustedpvalue" file="output_plotwithscale/iwtomics.plotwithscale.adjustedpvalue.txt" compare="sim_size" />
106 <output name="iwtomicsrespdf" file="output_plotwithscale/iwtomics.plotwithscale.iwtomicstestresults.pdf" compare="sim_size" />
107 <output name="iwtomicssumpdf" file="output_plotwithscale/iwtomics.plotwithscale.summaryplot.pdf" compare="sim_size" />
108 </test>
109 </tests>
110
111 <help><![CDATA[
112 This tool allows to select the scale for the Interval-Wise Testing results. In particular, it returns the p-value curves
113 for the different tests performed at the selected scale, and it creates a graphical representation of the
114 Interval-Wise Testing results and a summary plot (optional) at the selected scale.
115
116 -----
117
118 **Input files**
119
120 RData file with the IWTomicsData object with test results, tabular files with test IDs and feature IDs.
121 These files are created by the tool *IWTomics Test and Plot*.
122
123 -----
124
125 **Output**
126
127 The tool returns:
128
129 1. TXT file with an adjusted p-value curve for every test performed at the selected scale;
130 2. PDF file with the plotted test results;
131 3. PDF file with the summary plot.
132
133 -----
134
135 .. class:: infomark
136
137 **Notes**
138
139 This Galaxy tool has been developed by Fabio Cumbo (Third University of Rome, Italy) and Marzia A. Cremona (The Pennsylvania State University, USA).
140
141 It implements a simplified version of the function *IWTomicsTest*, *plotTest* and *plotSummary* for *IWTomicsData* objects.
142 The complete version can be found in the *R/Bioconductor* package *IWTomics* (see vignette_).
143
144 .. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf
145 ]]></help>
146
147 <expand macro="citations" />
148
149 </tool>