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comparison plotProfiler.xml @ 0:e4ad262c1321 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
author bgruening
date Mon, 25 Jan 2016 20:27:28 -0500
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-1:000000000000 0:e4ad262c1321
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 $output.saveSortedRegions:
20 --outFileSortedRegions '$outFileSortedRegions'
21 #end if
22 #else
23 --plotFileFormat 'png'
24 #end if
25
26 #if $scaleRegions.showScaleRegionsOpt == "yes":
27 --startLabel '$scaleRegions.startLabel'
28 --endLabel '$scaleRegions.endLabel'
29 #end if
30
31 #if $advancedOpt.showAdvancedOpt == "yes":
32 #if $advancedOpt.averageType:
33 --averageType '$advancedOpt.averageType'
34 #end if
35 --plotHeight $advancedOpt.plotHeight
36 --plotWidth $advancedOpt.plotWidth
37 --plotType $advancedOpt.plotType
38 --regionsLabel '$advancedOpt.regionsLabel'
39
40 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle).strip() != "":
41 --plotTitle '$advancedOpt.plotTitle'
42 #end if
43
44 #if str($advancedOpt.colors).strip() != "":
45 --colors #echo ' '.join( ["'%s'" % $color for $color in $advancedOpt.colors.split()] )#
46 #end if
47
48 $advancedOpt.perGroup
49
50 #if $advancedOpt.yMin:
51 --yMin $advancedOpt.yMin
52 #end if
53 #if $advancedOpt.yMax:
54 --yMax $advancedOpt.yMax
55 #end if
56
57 @KMEANS_CLUSTERING@
58
59 #end if
60 ]]>
61 </command>
62 <inputs>
63 <param argument="--matrixFile" format="deeptools_compute_matrix_archive" type="data" label="Matrix file from the computeMatrix tool"/>
64 <conditional name="scaleRegions">
65 <param name="showScaleRegionsOpt" type="select" label="The input matrix was computed in scale-regions mode">
66 <option value="no" selected="true">no</option>
67 <option value="yes">yes</option>
68 </param>
69 <when value="no" />
70 <when value="yes">
71 <param argument="--startLabel" type="text" value="TSS" size="10"
72 label="Label for the region start"
73 help ="Label shown in the plot
74 for the start of the region. Default is TSS (transcription start site),
75 but could be changed to anything, e.g. &quot;peak start&quot;." />
76 <param argument="--endLabel" type="text" value="TES" size="10"
77 label="Label for the region end"
78 help="Label shown in the plot for the region end. Default is TES (transcription end site)."/>
79 </when>
80 </conditional>
81
82 <expand macro="input_graphic_output_settings">
83 <expand macro="input_image_file_format" />
84 </expand>
85
86 <conditional name="advancedOpt">
87 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
88 <option value="no" selected="true">no</option>
89 <option value="yes">yes</option>
90 </param>
91 <when value="no" />
92 <when value="yes">
93 <param name="averageType" type="select" label="Define the type of statistic that should be used for the profile.">
94 <option value="mean" selected="true">mean</option>
95 <option value="median">median</option>
96 <option value="min">min</option>
97 <option value="max">max</option>
98 <option value="sum">sum</option>
99 <option value="std">std</option>
100 </param>
101 <param argument="--plotHeight" type="integer" value="5" min="3"
102 label="Plot height"
103 help="Height in cm. The default for the plot height is 5 centimeters. The minimum value is 3 cm." />
104
105 <param argument="--plotWidth" type="integer" value="8" min="1"
106 label="Plot width"
107 help="Width in cm. The default value is 8 centimeters. The minimum value is 1 cm." />
108
109 <param argument="--plotType" type="select" label="Plot type"
110 help="The &quot;lines&quot; option will
111 plot the profile line based on the average type selected. The &quot;fill&quot;
112 option fills the region between zero and the profile curve. The filled in color is
113 semi-transparent. The &quot;add standard error&quot;
114 option colors the region between the profile and the standard error of the data.
115 As in the case of fill, a semi-transparent color is used.
116 The option &quot;overlapped_lines&quot; plots each region's value, one on top of
117 the other.">
118 <option value="lines" selected="true">lines</option>
119 <option value="fill">fill</option>
120 <option value="se">add standard error</option>
121 <option value="overlapped_lines">overlapped lines</option>
122 </param>
123 <param argument="--regionsLabel" type="text" value="coverage" size="30"
124 label="Labels for the regions plotted in the heatmap"
125 help="If more than one region is being plotted a list of labels separated
126 by commas is required. For example, &quot;label1, label2&quot;."/>
127
128 <expand macro="plotTitle" />
129 <param argument="--colors" type="text" value="" size="40"
130 label="List of colors to use for the plotted lines"
131 help="Color names and html hex strings (e.g. #eeff22) are accepted.
132 The color names should be separated by spaces. (--colors red blue green)">
133 <validator type="expression"
134 message="Only numbers, digits, '#' and spaces are allowed.">all(c in ' #abcdefghijklmnopqrstuvwxyz0123456789' for c in value)</validator>
135 </param>
136
137 <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue=""
138 label="Do one plot per group"
139 help="When clustering is applied to the data or multiple BED files were used,
140 plot the groups next to each other. The default is to plot the samples next to each other." />
141
142
143 <param argument="--yMin" type="float" value="" size="3" optional="true"
144 label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values"/>
145 <param argument="--yMax" type="float" value="" size="3" optional="true"
146 label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" />
147
148 <expand macro="kmeans_clustering" />
149
150 </when>
151 </conditional>
152 </inputs>
153 <outputs>
154 <expand macro="output_image_file_format" />
155 <expand macro="output_graphic_outputs" />
156 </outputs>
157 <tests>
158 <test>
159 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
160 <output name="outFileName" file="profiler_result1.png" ftype="png" compare="sim_size" delta="4000" />
161 </test>
162 <test>
163 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
164 <param name="showAdvancedOpt" value="yes" />
165 <param name="showScaleRegionsOpt" value="yes" />
166 <output name="outFileName" file="profiler_result2.png" ftype="png" compare="sim_size" delta="4000" />
167 </test>
168 </tests>
169 <help>
170 <![CDATA[
171
172 **What it does**
173
174 This tool plots the average enrichments over all genomic
175 regions supplied to computeMarix. It requires that computeMatrix was successfully run.
176 It is a very useful complement to the heatmapper, especially in cases where you want to
177 compare the scores for many different groups. Like heatmapper, profiler does not change the
178 values that were compute by computeMatrix, but you can modify the color and other display properties of the plots.
179
180
181 .. image:: $PATH_TO_IMAGES/visual_profiler_DmelPolII.png
182 :alt: Meta-gene profile of Rna Polymerase II
183
184
185 You can find more details on the profiler doc page: https://deeptools.readthedocs.org/en/master/content/tools/plotProfile.html
186
187
188 -----
189
190 @REFERENCES@
191 ]]>
192 </help>
193 <expand macro="citations" />
194 </tool>