|
83
|
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>
|
|
89
|
47 <citation type="doi">10.1093/bioinformatics/bty090</citation>
|
|
83
|
48 </citations>
|
|
|
49 </xml>
|
|
|
50
|
|
|
51 <xml name="plot-params">
|
|
|
52 <!-- average -->
|
|
|
53 <param name="average" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot the mean curves" />
|
|
|
54 <!-- average -->
|
|
|
55 <param name="size" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot sample size in each position" />
|
|
|
56 <!-- conditional plot type -->
|
|
|
57 <conditional name="conditionalplottype">
|
|
|
58 <!-- plot type -->
|
|
|
59 <param name="plottype" type="select" label="Plot type">
|
|
|
60 <option value="boxplot">Pointwise quantile curves (boxplot)</option>
|
|
|
61 <option value="curves">Curves (aligned)</option>
|
|
|
62 </param>
|
|
|
63 <!-- conditional choice: plottype=boxplot -->
|
|
|
64 <when value="boxplot">
|
|
|
65 <section name="probabilitiessection" title="Probabilities" expanded="True" help="Probabilities corresponding to the quantile curves to be drawn.">
|
|
|
66 <param name="prob0" size="3" type="float" value="0.25" min="0.0" max="1.0" label="Probability" />
|
|
|
67 <param name="prob1" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
|
|
|
68 <param name="prob2" size="3" type="float" value="0.75" min="0.0" max="1.0" label="Probability" />
|
|
|
69 <repeat name="probabilities" title="Probabilities">
|
|
|
70 <param name="prob" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
|
|
|
71 </repeat>
|
|
|
72 </section>
|
|
|
73 </when>
|
|
|
74 </conditional>
|
|
|
75 </xml>
|
|
|
76
|
|
|
77 <xml name="plot-sum">
|
|
|
78 <section name="plotsum" title="Summary plot" expanded="True">
|
|
|
79 <!-- conditional group by -->
|
|
|
80 <conditional name="conditionalgroupby">
|
|
|
81 <!-- group by -->
|
|
|
82 <param name="groupby" type="select" label="Group by" help="How tests should be grouped.">
|
|
|
83 <option value="none">No plot</option>
|
|
|
84 <option value="test">Group by test</option>
|
|
|
85 <option value="feature">Group by feature</option>
|
|
|
86 </param>
|
|
|
87 <when value="test">
|
|
|
88 <param name="testalphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
|
|
|
89 <param name="testonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
|
|
|
90 </when>
|
|
|
91 <when value="feature">
|
|
|
92 <param name="featurealphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
|
|
|
93 <param name="featureonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
|
|
|
94 </when>
|
|
|
95 </conditional>
|
|
|
96 </section>
|
|
|
97 </xml>
|
|
|
98 </macros> |
