Mercurial > repos > iuc > iwtomics_testandplot

comparison macros.xml @ 0:800c7e974e3b draft

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planemo upload for repository https://github.com/fabio-cumbo/IWTomics4Galaxy commit 90c984bb9f803e1531fe4cb670e876809d48d205
author iuc
date Fri, 04 Aug 2017 17:51:00 -0400
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children 926cdd3158ae
comparison
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-1:000000000000 0:800c7e974e3b
1 <macros>
2 <token name="@VERSION@">1.0.0</token>
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package" version="@VERSION@">bioconductor-iwtomics</requirement>
6 </requirements>
7 </xml>
8
9 <xml name="alignment-s">
10 <conditional name="conditionalscale">
11 <param name="alignment" type="select" label="Region alignment" help="">
12 <option value="center">Center - Alignment on the central position</option>
13 <option value="left">Left - Alignment on the starting position</option>
14 <option value="right">Right - Alignment on the ending position</option>
15 <option value="scale">Scale - Scaling all regions to the same length</option>
16 </param>
17 <when value="center">
18 <!-- fill gaps -->
19 <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
20 </when>
21 <when value="left">
22 <!-- fill gaps -->
23 <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
24 </when>
25 <when value="right">
26 <!-- fill gaps -->
27 <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
28 </when>
29 <when value="scale">
30 <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." />
31 </when>
32 </conditional>
33 </xml>
34
35 <xml name="alignment">
36 <param name="alignment" type="select" label="Region alignment" help="">
37 <option value="center">Center - Alignment on the central position</option>
38 <option value="left">Left - Alignment on the starting position</option>
39 <option value="right">Right - Alignment on the ending position</option>
40 </param>
41 </xml>
42
43 <xml name="citations">
44 <citations>
45 <citation type="doi">10.1080/10485252.2017.1306627</citation>
46 <citation type="bibtex">
47 @MANUAL{
48 iwtomics,
49 author = {Cremona, M.A. and Pini, A. and Chiaromonte, F. and Vantini, S.},
50 title = {IWTomics: Interval-Wise Testing for Omics Data},
51 note = {R package version 1.0.0},
52 year = {2017}
53 }
54 </citation>
55 </citations>
56 </xml>
57
58 <xml name="plot-params">
59 <!-- average -->
60 <param name="average" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot the mean curves" />
61 <!-- average -->
62 <param name="size" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot sample size in each position" />
63 <!-- conditional plot type -->
64 <conditional name="conditionalplottype">
65 <!-- plot type -->
66 <param name="plottype" type="select" label="Plot type">
67 <option value="boxplot">Pointwise quantile curves (boxplot)</option>
68 <option value="curves">Curves (aligned)</option>
69 </param>
70 <!-- conditional choice: plottype=boxplot -->
71 <when value="boxplot">
72 <section name="probabilitiessection" title="Probabilities" expanded="True" help="Probabilities corresponding to the quantile curves to be drawn.">
73 <param name="prob0" size="3" type="float" value="0.25" min="0.0" max="1.0" label="Probability" />
74 <param name="prob1" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
75 <param name="prob2" size="3" type="float" value="0.75" min="0.0" max="1.0" label="Probability" />
76 <repeat name="probabilities" title="Probabilities">
77 <param name="prob" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
78 </repeat>
79 </section>
80 </when>
81 </conditional>
82 </xml>
83
84 <xml name="plot-sum">
85 <section name="plotsum" title="Summary plot" expanded="True">
86 <!-- conditional group by -->
87 <conditional name="conditionalgroupby">
88 <!-- group by -->
89 <param name="groupby" type="select" label="Group by" help="How tests should be grouped.">
90 <option value="none">No plot</option>
91 <option value="test">Group by test</option>
92 <option value="feature">Group by feature</option>
93 </param>
94 <when value="test">
95 <param name="testalphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
96 <param name="testonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
97 </when>
98 <when value="feature">
99 <param name="featurealphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
100 <param name="featureonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
101 </when>
102 </conditional>
103 </section>
104 </xml>
105 </macros>