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comparison plotProfiler.xml @ 0:506970788461 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
author bgruening
date Wed, 16 Dec 2015 16:43:08 -0500
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1 <tool id="deeptools_plot_profile" name="plotProfile" version="@WRAPPER_VERSION@.0">
2 <description>
3 creates a profile plot for a score associated to genomic regions
4 </description>
5 <macros>
6 <token name="@BINARY@">plotProfile</token>
7 <import>deepTools_macros.xml</import>
8 </macros>
9 <expand macro="requirements" />
10 <command>
11 <![CDATA[
12 @BINARY@
13 --matrixFile "$matrixFile"
14 --outFileName "$outFileName"
15
16 #if $output.showOutputSettings == "yes"
17 --plotFileFormat $output.outFileFormat
18
19 #if $output.saveData:
20 --outFileNameData "$outFileNameData"
21 #end if
22
23 #if $output.saveSortedRegions:
24 --outFileSortedRegions '$outFileSortedRegions'
25 #end if
26 #else
27 --plotFileFormat 'png'
28 #end if
29
30 #if $scaleRegions.showScaleRegionsOpt == "yes":
31 --startLabel '$scaleRegions.startLabel'
32 --endLabel '$scaleRegions.endLabel'
33 #end if
34
35 #if $advancedOpt.showAdvancedOpt == "yes":
36 #if $advancedOpt.averageType:
37 --averageType '$advancedOpt.averageType'
38 #end if
39 --plotHeight $advancedOpt.plotHeight
40 --plotWidth $advancedOpt.plotWidth
41 --plotType $advancedOpt.plotType
42 --regionsLabel '$advancedOpt.regionsLabel'
43
44 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle).strip() != "":
45 --plotTitle '$advancedOpt.plotTitle'
46 #end if
47
48 #if str($advancedOpt.colors).strip() != "":
49 --colors #echo ' '.join( ["'%s'" % $color for $color in $advancedOpt.colors.split()] )#
50 #end if
51
52 $advancedOpt.onePlotPerGroup
53
54 #if $advancedOpt.yMin:
55 --yMin $advancedOpt.yMin
56 #end if
57 #if $advancedOpt.yMax:
58 --yMax $advancedOpt.yMax
59 #end if
60
61 @KMEANS_CLUSTERING@
62
63 #end if
64 ]]>
65 </command>
66 <inputs>
67 <param argument="--matrixFile" format="deeptools_compute_matrix_archive" type="data" label="Matrix file from the computeMatrix tool"/>
68 <conditional name="scaleRegions">
69 <param name="showScaleRegionsOpt" type="select" label="The input matrix was computed in scale-regions mode">
70 <option value="no" selected="true">no</option>
71 <option value="yes">yes</option>
72 </param>
73 <when value="no" />
74 <when value="yes">
75 <param argument="--startLabel" type="text" value="TSS" size="10"
76 label="Label for the region start"
77 help ="[only for scale-regions mode] Label shown in the plot
78 for the start of the region. Default is TSS (transcription start site),
79 but could be changed to anything, e.g. &quot;peak start&quot;." />
80 <param argument="--endLabel" type="text" value="TES" size="10"
81 label="Label for the region end"
82 help="Label shown in the plot for the region end. Default is TES (transcription end site)."/>
83 </when>
84 </conditional>
85
86 <expand macro="input_graphic_output_settings">
87 <expand macro="input_image_file_format" />
88 </expand>
89
90 <conditional name="advancedOpt">
91 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
92 <option value="no" selected="true">no</option>
93 <option value="yes">yes</option>
94 </param>
95 <when value="no" />
96 <when value="yes">
97 <param name="averageType" type="select" label="Define the type of statistic that should be used for the profile.">
98 <option value="mean" selected="true">mean</option>
99 <option value="median">median</option>
100 <option value="min">min</option>
101 <option value="max">max</option>
102 <option value="sum">sum</option>
103 <option value="std">std</option>
104 </param>
105 <param argument="--plotHeight" type="integer" value="5" min="3"
106 label="Plot height"
107 help="Height in cm. The default for the plot height is 5 centimeters. The minimum value is 3 cm." />
108
109 <param argument="--plotWidth" type="integer" value="8" min="1"
110 label="Plot width"
111 help="Width in cm. The default value is 8 centimeters. The minimum value is 1 cm." />
112
113 <param argument="--plotType" type="select" label="Plot type"
114 help="For the summary plot (profile) only. The &quot;lines&quot; option will
115 plot the profile line based on the average type selected. The &quot;fill&quot;
116 option fills the region between zero and the profile curve. The fill in color is
117 semi transparent to distinguish different profiles. The &quot;add standard error&quot;
118 option colors the region between the profile and the standard error of the data.
119 As in the case of fill, a semi-transparent color is used.
120 The option &quot;overlapped_lines&quot; plots each region values, one on top of
121 the other; this option only works if &quot;one plot per proup&quot; is set.">
122 <option value="lines" selected="true">lines</option>
123 <option value="fill">fill</option>
124 <option value="se">add standard error</option>
125 <option value="overlapped_lines">overlapped lines</option>
126 </param>
127 <param argument="--regionsLabel" type="text" value="genes" size="30"
128 label="Labels for the regions plotted in the heatmap"
129 help="If more than one region is being plotted a list of labels separated
130 by comma and limited by quotes, is required. For example, &quot;label1, label2&quot;."/>
131
132 <expand macro="plotTitle" />
133 <param argument="--colors" type="text" value="" size="40"
134 label="List of colors to use for the plotted lines"
135 help="Color names and html hex strings (e.g. #eeff22) are accepted.
136 The color names should be given separated by spaces. (--colors red blue green)">
137 <validator type="expression"
138 message="Only numbers, digits, '#' and spaces are allowed.">all(c in ' #abcdefghijklmnopqrstuvwxyz0123456789' for c in value)</validator>
139 </param>
140
141 <param argument="--onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue=""
142 label="Do one plot per group"
143 help="When the region file contains groups separated by &quot;#&quot;, the default is
144 to plot the averages for the distinct plots in one plot. If this option is set, each group
145 will get its own plot, stacked on top of each other." />
146
147
148 <param argument="--yMin" type="float" value="" size="3" optional="true"
149 label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values"/>
150 <param argument="--yMax" type="float" value="" size="3" optional="true"
151 label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" />
152
153 <expand macro="kmeans_clustering" />
154
155 </when>
156 </conditional>
157 </inputs>
158 <outputs>
159 <expand macro="output_image_file_format" />
160 <expand macro="output_graphic_outputs" />
161 </outputs>
162 <tests>
163 <test>
164 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
165 <output name="outFileName" file="profiler_result1.png" ftype="png" compare="sim_size" delta="100" />
166 </test>
167 <test>
168 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
169 <param name="showAdvancedOpt" value="yes" />
170 <param name="showScaleRegionsOpt" value="yes" />
171 <output name="outFileName" file="profiler_result2.png" ftype="png" compare="sim_size" delta="100" />
172 </test>
173 </tests>
174 <help>
175 <![CDATA[
176
177 **What it does**
178
179 This tool plots the average enrichments over all genomic
180 regions supplied to computeMarix. It requires that computeMatrix was successfully run.
181 It is a very useful complement to the heatmapper, especially in cases when you want to
182 compare the scores for many different groups. Like heatmapper, profiler does not change the
183 values that were compute by computeMatrix, but you can choose between
184 many different ways to color and display the plots.
185
186
187 .. image:: $PATH_TO_IMAGES/visual_profiler_DmelPolII.png
188 :alt: Meta-gene profile of Rna Polymerase II
189
190
191 You can find more details on the profiler wiki page: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-profiler
192
193
194 -----
195
196 @REFERENCES@
197 ]]>
198 </help>
199 <expand macro="citations" />
200 </tool>