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comparison iwtomics-1.0/macros.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 <macros>
2 <token name="@VERSION@">1.0.0</token>
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package" version="3.3.1">r-base</requirement>
6 <requirement type="package" version="@VERSION@">bioconductor-iwtomics</requirement>
7 </requirements>
8 </xml>
9
10 <xml name="alignment-s">
11 <conditional name="conditionalscale">
12 <param name="alignment" type="select" label="Region alignment" help="">
13 <option value="center">Center - Alignment on the central position</option>
14 <option value="left">Left - Alignment on the starting position</option>
15 <option value="right">Right - Alignment on the ending position</option>
16 <option value="scale">Scale - Scaling all regions to the same length</option>
17 </param>
18 <when value="center">
19 <!-- fill gaps -->
20 <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
21 </when>
22 <when value="left">
23 <!-- fill gaps -->
24 <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
25 </when>
26 <when value="right">
27 <!-- fill gaps -->
28 <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
29 </when>
30 <when value="scale">
31 <param name="scalegrid" type="integer" value="0" min="0" label="Number of grid points" help="Number of equally-spaced grid points over which the smoothed curves are evaluated." />
32 </when>
33 </conditional>
34 </xml>
35
36 <xml name="alignment">
37 <param name="alignment" type="select" label="Region alignment" help="">
38 <option value="center">Center - Alignment on the central position</option>
39 <option value="left">Left - Alignment on the starting position</option>
40 <option value="right">Right - Alignment on the ending position</option>
41 </param>
42 </xml>
43
44 <xml name="citations">
45 <citations>
46 <citation type="doi">10.1080/10485252.2017.1306627</citation>
47 <citation type="bibtex">
48 @MANUAL{
49 iwtomics,
50 author = {Cremona, M.A. and Pini, A. and Chiaromonte, F. and Vantini, S.},
51 title = {IWTomics: Interval-Wise Testing for Omics Data},
52 note = {R package version 1.0.0},
53 year = {2017}
54 }
55 </citation>
56 </citations>
57 </xml>
58
59 <xml name="plot-params">
60 <!-- average -->
61 <param name="average" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot the mean curves" />
62 <!-- average -->
63 <param name="size" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot sample size in each position" />
64 <!-- conditional plot type -->
65 <conditional name="conditionalplottype">
66 <!-- plot type -->
67 <param name="plottype" type="select" label="Plot type">
68 <option value="boxplot">Pointwise quantile curves (boxplot)</option>
69 <option value="curves">Curves (aligned)</option>
70 </param>
71 <!-- conditional choice: plottype=boxplot -->
72 <when value="boxplot">
73 <section name="probabilitiessection" title="Probabilities" expanded="True" help="Probabilities corresponding to the quantile curves to be drawn.">
74 <param name="prob0" size="3" type="float" value="0.25" min="0.0" max="1.0" label="Probability" />
75 <param name="prob1" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
76 <param name="prob2" size="3" type="float" value="0.75" min="0.0" max="1.0" label="Probability" />
77 <repeat name="probabilities" title="Probabilities">
78 <param name="prob" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
79 </repeat>
80 </section>
81 </when>
82 </conditional>
83 </xml>
84
85 <xml name="plot-sum">
86 <section name="plotsum" title="Summary plot" expanded="True">
87 <!-- conditional group by -->
88 <conditional name="conditionalgroupby">
89 <!-- group by -->
90 <param name="groupby" type="select" label="Group by" help="How tests should be grouped.">
91 <option value="none">No plot</option>
92 <option value="test">Group by test</option>
93 <option value="feature">Group by feature</option>
94 </param>
95 <when value="test">
96 <param name="testalphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
97 <param name="testonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
98 </when>
99 <when value="feature">
100 <param name="featurealphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
101 <param name="featureonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
102 </when>
103 </conditional>
104 </section>
105 </xml>
106 </macros>