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comparison loadandplot.xml @ 76:7dcc25a1a062 draft

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Uploaded 20170620
author fabio
date Tue, 20 Jun 2017 12:57:03 -0400
parents 2bb6b44093ba
children dc2707da8ba4
comparison
equal deleted inserted replaced
75:0a17de046de0 76:7dcc25a1a062
1 <tool id="iwtomics_loadandplot" name="IWTomics Load" version="@VERSION@.0"> 1 <tool id="iwtomics_loadandplot" name="IWTomics Load" version="@VERSION@.0">
2 <description>Smooth and Plot</description> 2 <description>Smooth and Plot</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <!--<expand macro="requirements" />-->
7 7
8 <command detect_errors="exit_code"> 8 <command detect_errors="exit_code">
9 <![CDATA[ 9 <![CDATA[
10 Rscript '$__tool_directory__/loadandplot.R' outrdata='${outrdata}' outregions='${outregions}' outfeatures='${outfeatures}' outpdf='${outpdf}' 10 Rscript '$__tool_directory__/loadandplot.R' outrdata='${outrdata}' outregions='${outregions}' outfeatures='${outfeatures}' outpdf='${outpdf}'
11 11
34 smoothing="'${conditionaltype.smoothing}'" 34 smoothing="'${conditionaltype.smoothing}'"
35 start.are.0based='${zerobased}' 35 start.are.0based='${zerobased}'
36 #if $conditionaltype.smoothing == 'no': 36 #if $conditionaltype.smoothing == 'no':
37 alignment="'${conditionaltype.alignment}'" 37 alignment="'${conditionaltype.alignment}'"
38 #elif $conditionaltype.smoothing == 'locpoly': 38 #elif $conditionaltype.smoothing == 'locpoly':
39 alignment="'${conditionaltype.locpolyconditionalscale.alignment}'"
40 #if $conditionaltype.locpolyconditionalscale.alignment == 'scale':
41 scale='${conditionaltype.locpolyconditionalscale.scalegrid}'
42 #end if
43 bandwidth='${conditionaltype.locpolybandwidth}' 39 bandwidth='${conditionaltype.locpolybandwidth}'
44 degree='${conditionaltype.locpolydegree}' 40 degree='${conditionaltype.locpolydegree}'
45 fill_gaps='${conditionaltype.fillgaps}' 41 alignment="'${conditionaltype.conditionalscale.alignment}'"
46 #elif $conditionaltype.smoothing == 'kernel': 42 #elif $conditionaltype.smoothing == 'kernel':
47 alignment="'${conditionaltype.kernelconditionalscale.alignment}'"
48 #if $conditionaltype.kernelconditionalscale.alignment == 'scale':
49 scale='${conditionaltype.kernelconditionalscale.scalegrid}'
50 #end if
51 bandwidth='${conditionaltype.kernelbandwidth}' 43 bandwidth='${conditionaltype.kernelbandwidth}'
52 fill_gaps='${conditionaltype.fillgaps}' 44 alignment="'${conditionaltype.conditionalscale.alignment}'"
53 #elif $conditionaltype.smoothing == 'splines': 45 #elif $conditionaltype.smoothing == 'splines':
54 alignment="'${conditionaltype.splinesconditionalscale.alignment}'"
55 #if $conditionaltype.splinesconditionalscale.alignment == 'scale':
56 scale='${conditionaltype.splinesconditionalscale.scalegrid}'
57 #end if
58 degree='${conditionaltype.splinesdegree}' 46 degree='${conditionaltype.splinesdegree}'
59 dist_knots='${conditionaltype.splinesdistknots}' 47 dist_knots='${conditionaltype.splinesdistknots}'
60 fill_gaps='${conditionaltype.fillgaps}' 48 alignment="'${conditionaltype.conditionalscale.alignment}'"
49 #end if
50
51 #if $conditionaltype.smoothing != 'no':
52 #if $conditionaltype.conditionalscale.alignment == 'scale':
53 scale='${conditionaltype.conditionalscale.scalegrid}'
54 fill_gaps='TRUE'
55 #else
56 fill_gaps='${conditionaltype.conditionalscale.fillgaps}'
57 #end if
61 #end if 58 #end if
62 59
63 average='${plotres.average}' 60 average='${plotres.average}'
64 size='${plotres.size}' 61 size='${plotres.size}'
65 plottype="'${plotres.conditionalplottype.plottype}'" 62 plottype="'${plotres.conditionalplottype.plottype}'"
102 <option value="kernel">Gaussian Kernel</option> 99 <option value="kernel">Gaussian Kernel</option>
103 <option value="splines">B-Splines</option> 100 <option value="splines">B-Splines</option>
104 </param> 101 </param>
105 <!-- conditional choice: smoothing=no --> 102 <!-- conditional choice: smoothing=no -->
106 <when value="no"> 103 <when value="no">
107 <param name="alignment" type="select" label="Region alignment" help=""> 104 <expand macro="alignment" />
108 <option value="center">Center - Alignment on the central position</option>
109 <option value="left">Left - Alignment on the starting position</option>
110 <option value="right">Right - Alignment on the ending position</option>
111 </param>
112 </when> 105 </when>
113 <!-- conditional choice: smoothing=locpoly --> 106 <!-- conditional choice: smoothing=locpoly -->
114 <when value="locpoly"> 107 <when value="locpoly">
115 <!-- conditional region alignment -->
116 <conditional name="locpolyconditionalscale">
117 <param name="alignment" type="select" label="Region alignment" help="">
118 <option value="center">Center - Alignment on the central position</option>
119 <option value="left">Left - Alignment on the starting position</option>
120 <option value="right">Right - Alignment on the ending position</option>
121 <option value="scale">Scale - Scaling all regions to the same length</option>
122 </param>
123 <when value="scale">
124 <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." />
125 </when>
126 </conditional>
127
128 <param name="locpolybandwidth" type="integer" value="5" min="2" label="Bandwidth for smoothing" help="" /> 108 <param name="locpolybandwidth" type="integer" value="5" min="2" label="Bandwidth for smoothing" help="" />
129 <param name="locpolydegree" type="integer" value="3" min="0" label="Degree of local polynomial" help="" /> 109 <param name="locpolydegree" type="integer" value="3" min="0" label="Degree of local polynomial" help="" />
130 110 <!-- conditional region alignment -->
131 <!-- fill gaps --> 111 <expand macro="alignment-s" />
132 <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
133 </when> 112 </when>
134 <!-- conditional choice: smoothing=kernel --> 113 <!-- conditional choice: smoothing=kernel -->
135 <when value="kernel"> 114 <when value="kernel">
115 <param name="kernelbandwidth" type="integer" value="5" min="2" label="Bandwidth for smoothing" help="" />
136 <!-- conditional region alignment --> 116 <!-- conditional region alignment -->
137 <conditional name="kernelconditionalscale"> 117 <expand macro="alignment-s" />
138 <param name="alignment" type="select" label="Region alignment" help="">
139 <option value="center">Center - Alignment on the central position</option>
140 <option value="left">Left - Alignment on the starting position</option>
141 <option value="right">Right - Alignment on the ending position</option>
142 <option value="scale">Scale - Scaling all regions to the same length</option>
143 </param>
144 <when value="scale">
145 <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." />
146 </when>
147 </conditional>
148
149 <param name="kernelbandwidth" type="integer" value="5" min="2" label="Bandwidth for smoothing" help="" />
150
151 <!-- fill gaps -->
152 <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
153 </when> 118 </when>
154 <!-- conditional choice: smoothing=splines --> 119 <!-- conditional choice: smoothing=splines -->
155 <when value="splines"> 120 <when value="splines">
156 <!-- conditional region alignment -->
157 <conditional name="splinesconditionalscale">
158 <param name="alignment" type="select" label="Region alignment" help="">
159 <option value="center">Center - Alignment on the central position</option>
160 <option value="left">Left - Alignment on the starting position</option>
161 <option value="right">Right - Alignment on the ending position</option>
162 <option value="scale">Scale - Scaling all regions to the same length</option>
163 </param>
164 <when value="scale">
165 <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." />
166 </when>
167 </conditional>
168
169 <param name="splinesdegree" type="integer" value="3" min="0" label="Degree of B-splines" help="" /> 121 <param name="splinesdegree" type="integer" value="3" min="0" label="Degree of B-splines" help="" />
170 <param name="splinesdistknots" type="integer" value="10" min="2" label="Distance between nodes (approximate)" help="" /> 122 <param name="splinesdistknots" type="integer" value="10" min="2" label="Distance between nodes (approximate)" help="" />
171 123 <!-- conditional region alignment -->
172 <!-- fill gaps --> 124 <expand macro="alignment-s" />
173 <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
174 </when> 125 </when>
175 </conditional> 126 </conditional>
176 127
177 <!-- plot IWTomics results --> 128 <!-- plot IWTomics results -->
178 <section name="plotres" title="Plot data" expanded="True"> 129 <section name="plotres" title="Plot data" expanded="True">
179 <!-- average --> 130 <expand macro="plot-params" />
180 <param name="average" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot the mean curves" help="" />
181 <!-- sample size in each position -->
182 <param name="size" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot sample size in each position" help="" />
183 <!-- conditional plot type -->
184 <conditional name="conditionalplottype">
185 <!-- plot type -->
186 <param name="plottype" type="select" label="Plot type" help="">
187 <option value="boxplot">Pointwise quantile curves (boxplot)</option>
188 <option value="curves">Curves (aligned)</option>
189 </param>
190 <!-- conditional choice: plottype=boxplot -->
191 <when value="boxplot">
192 <section name="probabilitiessection" title="Probabilities" expanded="True" help="Probabilities corresponding to the quantile curves to be drawn.">
193 <param name="prob0" size="3" type="float" value="0.25" min="0.0" max="1.0" label="Probability" />
194 <param name="prob1" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
195 <param name="prob2" size="3" type="float" value="0.75" min="0.0" max="1.0" label="Probability" />
196 <repeat name="probabilities" title="Probabilities">
197 <param name="prob" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
198 </repeat>
199 </section>
200 </when>
201 </conditional>
202 </section> 131 </section>
203 </inputs> 132 </inputs>
204 133
205 <outputs> 134 <outputs>
206 <data format="rdata" name="outrdata" label="${tool.name} on ${on_string}: IWTomicsData Object" from_work_dir="iwtomics.loadandplot.RData" /> 135 <data format="rdata" name="outrdata" label="${tool.name} on ${on_string}: IWTomicsData Object" from_work_dir="iwtomics.loadandplot.RData" />