annotate macros.xml @ 90:436406a68157 draft

Deleted selected files
author fabio
date Wed, 21 Feb 2018 11:08:11 -0500
parents e089b19da14c
children 2a83c5aafade
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
83
f81d72e482cf Uploaded
fabio
parents:
diff changeset
1 <macros>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
2 <token name="@VERSION@">1.0.0</token>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
3 <xml name="requirements">
f81d72e482cf Uploaded
fabio
parents:
diff changeset
4 <requirements>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
5 <requirement type="package" version="3.3.1">r-base</requirement>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
6 <requirement type="package" version="@VERSION@">bioconductor-iwtomics</requirement>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
7 </requirements>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
8 </xml>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
9
f81d72e482cf Uploaded
fabio
parents:
diff changeset
10 <xml name="alignment-s">
f81d72e482cf Uploaded
fabio
parents:
diff changeset
11 <conditional name="conditionalscale">
f81d72e482cf Uploaded
fabio
parents:
diff changeset
12 <param name="alignment" type="select" label="Region alignment" help="">
f81d72e482cf Uploaded
fabio
parents:
diff changeset
13 <option value="center">Center - Alignment on the central position</option>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
14 <option value="left">Left - Alignment on the starting position</option>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
15 <option value="right">Right - Alignment on the ending position</option>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
16 <option value="scale">Scale - Scaling all regions to the same length</option>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
17 </param>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
18 <when value="center">
f81d72e482cf Uploaded
fabio
parents:
diff changeset
19 <!-- fill gaps -->
f81d72e482cf Uploaded
fabio
parents:
diff changeset
20 <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
f81d72e482cf Uploaded
fabio
parents:
diff changeset
21 </when>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
22 <when value="left">
f81d72e482cf Uploaded
fabio
parents:
diff changeset
23 <!-- fill gaps -->
f81d72e482cf Uploaded
fabio
parents:
diff changeset
24 <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
f81d72e482cf Uploaded
fabio
parents:
diff changeset
25 </when>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
26 <when value="right">
f81d72e482cf Uploaded
fabio
parents:
diff changeset
27 <!-- fill gaps -->
f81d72e482cf Uploaded
fabio
parents:
diff changeset
28 <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
f81d72e482cf Uploaded
fabio
parents:
diff changeset
29 </when>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
30 <when value="scale">
f81d72e482cf Uploaded
fabio
parents:
diff changeset
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." />
f81d72e482cf Uploaded
fabio
parents:
diff changeset
32 </when>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
33 </conditional>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
34 </xml>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
35
f81d72e482cf Uploaded
fabio
parents:
diff changeset
36 <xml name="alignment">
f81d72e482cf Uploaded
fabio
parents:
diff changeset
37 <param name="alignment" type="select" label="Region alignment" help="">
f81d72e482cf Uploaded
fabio
parents:
diff changeset
38 <option value="center">Center - Alignment on the central position</option>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
39 <option value="left">Left - Alignment on the starting position</option>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
40 <option value="right">Right - Alignment on the ending position</option>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
41 </param>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
42 </xml>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
43
f81d72e482cf Uploaded
fabio
parents:
diff changeset
44 <xml name="citations">
f81d72e482cf Uploaded
fabio
parents:
diff changeset
45 <citations>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
46 <citation type="doi">10.1080/10485252.2017.1306627</citation>
89
e089b19da14c Uploaded 20180221
fabio
parents: 83
diff changeset
47 <citation type="doi">10.1093/bioinformatics/bty090</citation>
83
f81d72e482cf Uploaded
fabio
parents:
diff changeset
48 </citations>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
49 </xml>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
50
f81d72e482cf Uploaded
fabio
parents:
diff changeset
51 <xml name="plot-params">
f81d72e482cf Uploaded
fabio
parents:
diff changeset
52 <!-- average -->
f81d72e482cf Uploaded
fabio
parents:
diff changeset
53 <param name="average" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot the mean curves" />
f81d72e482cf Uploaded
fabio
parents:
diff changeset
54 <!-- average -->
f81d72e482cf Uploaded
fabio
parents:
diff changeset
55 <param name="size" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot sample size in each position" />
f81d72e482cf Uploaded
fabio
parents:
diff changeset
56 <!-- conditional plot type -->
f81d72e482cf Uploaded
fabio
parents:
diff changeset
57 <conditional name="conditionalplottype">
f81d72e482cf Uploaded
fabio
parents:
diff changeset
58 <!-- plot type -->
f81d72e482cf Uploaded
fabio
parents:
diff changeset
59 <param name="plottype" type="select" label="Plot type">
f81d72e482cf Uploaded
fabio
parents:
diff changeset
60 <option value="boxplot">Pointwise quantile curves (boxplot)</option>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
61 <option value="curves">Curves (aligned)</option>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
62 </param>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
63 <!-- conditional choice: plottype=boxplot -->
f81d72e482cf Uploaded
fabio
parents:
diff changeset
64 <when value="boxplot">
f81d72e482cf Uploaded
fabio
parents:
diff changeset
65 <section name="probabilitiessection" title="Probabilities" expanded="True" help="Probabilities corresponding to the quantile curves to be drawn.">
f81d72e482cf Uploaded
fabio
parents:
diff changeset
66 <param name="prob0" size="3" type="float" value="0.25" min="0.0" max="1.0" label="Probability" />
f81d72e482cf Uploaded
fabio
parents:
diff changeset
67 <param name="prob1" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
f81d72e482cf Uploaded
fabio
parents:
diff changeset
68 <param name="prob2" size="3" type="float" value="0.75" min="0.0" max="1.0" label="Probability" />
f81d72e482cf Uploaded
fabio
parents:
diff changeset
69 <repeat name="probabilities" title="Probabilities">
f81d72e482cf Uploaded
fabio
parents:
diff changeset
70 <param name="prob" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
f81d72e482cf Uploaded
fabio
parents:
diff changeset
71 </repeat>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
72 </section>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
73 </when>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
74 </conditional>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
75 </xml>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
76
f81d72e482cf Uploaded
fabio
parents:
diff changeset
77 <xml name="plot-sum">
f81d72e482cf Uploaded
fabio
parents:
diff changeset
78 <section name="plotsum" title="Summary plot" expanded="True">
f81d72e482cf Uploaded
fabio
parents:
diff changeset
79 <!-- conditional group by -->
f81d72e482cf Uploaded
fabio
parents:
diff changeset
80 <conditional name="conditionalgroupby">
f81d72e482cf Uploaded
fabio
parents:
diff changeset
81 <!-- group by -->
f81d72e482cf Uploaded
fabio
parents:
diff changeset
82 <param name="groupby" type="select" label="Group by" help="How tests should be grouped.">
f81d72e482cf Uploaded
fabio
parents:
diff changeset
83 <option value="none">No plot</option>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
84 <option value="test">Group by test</option>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
85 <option value="feature">Group by feature</option>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
86 </param>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
87 <when value="test">
f81d72e482cf Uploaded
fabio
parents:
diff changeset
88 <param name="testalphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
f81d72e482cf Uploaded
fabio
parents:
diff changeset
89 <param name="testonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
f81d72e482cf Uploaded
fabio
parents:
diff changeset
90 </when>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
91 <when value="feature">
f81d72e482cf Uploaded
fabio
parents:
diff changeset
92 <param name="featurealphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
f81d72e482cf Uploaded
fabio
parents:
diff changeset
93 <param name="featureonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
f81d72e482cf Uploaded
fabio
parents:
diff changeset
94 </when>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
95 </conditional>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
96 </section>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
97 </xml>
f81d72e482cf Uploaded
fabio
parents:
diff changeset
98 </macros>