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comparison plotProfiler.xml @ 13:d2205d523d83 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
author bgruening
date Mon, 15 Feb 2016 10:10:46 -0500
parents 9d7d837a76bf
children a3d4a84b8c47
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12:bc9f70c1cff6 13:d2205d523d83
1 <tool id="deeptools_plot_profile" name="plotProfile" version="@WRAPPER_VERSION@.0"> 1 <tool id="deeptools_plot_profile" name="plotProfile" version="@WRAPPER_VERSION@.0">
2 <description> 2 <description>
3 creates a profile plot for a score associated to genomic regions 3 creates a profile plot for score distributions across genomic regions
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <token name="@BINARY@">plotProfile</token> 6 <token name="@BINARY@">plotProfile</token>
7 <import>deepTools_macros.xml</import> 7 <import>deepTools_macros.xml</import>
8 </macros> 8 </macros>
33 --averageType '$advancedOpt.averageType' 33 --averageType '$advancedOpt.averageType'
34 #end if 34 #end if
35 --plotHeight $advancedOpt.plotHeight 35 --plotHeight $advancedOpt.plotHeight
36 --plotWidth $advancedOpt.plotWidth 36 --plotWidth $advancedOpt.plotWidth
37 --plotType $advancedOpt.plotType 37 --plotType $advancedOpt.plotType
38 --regionsLabel '$advancedOpt.regionsLabel' 38 #if $advancedOpt.samplesLabel and str($advancedOpt.samplesLabel).strip() != "":
39 --samplesLabel $advancedOpt.samplesLabel
40 #end if
41
42 #if $advancedOpt.regionsLabel and str($advancedOpt.regionsLabel).strip() != "":
43 --regionsLabel $advancedOpt.regionsLabel
44 #end if
39 45
40 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle).strip() != "": 46 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle).strip() != "":
41 --plotTitle '$advancedOpt.plotTitle' 47 --plotTitle '$advancedOpt.plotTitle'
42 #end if 48 #end if
43 49
100 </param> 106 </param>
101 <param argument="--plotHeight" type="integer" value="5" min="3" 107 <param argument="--plotHeight" type="integer" value="5" min="3"
102 label="Plot height" 108 label="Plot height"
103 help="Height in cm. The default for the plot height is 5 centimeters. The minimum value is 3 cm." /> 109 help="Height in cm. The default for the plot height is 5 centimeters. The minimum value is 3 cm." />
104 110
105 <param argument="--plotWidth" type="integer" value="8" min="1" 111 <param argument="--plotWidth" type="integer" value="11" min="1"
106 label="Plot width" 112 label="Plot width"
107 help="Width in cm. The default value is 8 centimeters. The minimum value is 1 cm." /> 113 help="Width in cm. The default value is 11 centimeters. The minimum value is 1 cm." />
108 114
109 <param argument="--plotType" type="select" label="Plot type" 115 <param argument="--plotType" type="select" label="Plot type"
110 help="The &quot;lines&quot; option will 116 help="The &quot;lines&quot; option will
111 plot the profile line based on the average type selected. The &quot;fill&quot; 117 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 118 option fills the region between zero and the profile curve. The filled in color is
118 <option value="lines" selected="true">lines</option> 124 <option value="lines" selected="true">lines</option>
119 <option value="fill">fill</option> 125 <option value="fill">fill</option>
120 <option value="se">add standard error</option> 126 <option value="se">add standard error</option>
121 <option value="overlapped_lines">overlapped lines</option> 127 <option value="overlapped_lines">overlapped lines</option>
122 </param> 128 </param>
123 <param argument="--regionsLabel" type="text" value="coverage" size="30" 129 <param argument="--samplesLabel" type="text" size="30"
130 label="Labels for the samples (each bigwig) plotted"
131 help="The default is to use the file name of the sample. The sample labels should be separated by
132 spaces and quoted if a label itself contains a space, e.g., label-1 &quot;label 2&quot;">
133 <sanitizer>
134 <valid initial="string.printable">
135 </valid>
136 </sanitizer>
137 </param>
138 <param argument="--regionsLabel" type="text" size="30"
124 label="Labels for the regions plotted in the heatmap" 139 label="Labels for the regions plotted in the heatmap"
125 help="If more than one region is being plotted a list of labels separated 140 help="If more than one region is being plotted a list of labels separated by space is required.
126 by commas is required. For example, &quot;label1, label2&quot;."/> 141 If a label itself contains a space, then quotes are needed.
142 For example, label_1, &quot;label 2&quot;" />
127 143
128 <expand macro="plotTitle" /> 144 <expand macro="plotTitle" />
129 <param argument="--colors" type="text" value="" size="40" 145 <param argument="--colors" type="text" value="" size="40"
130 label="List of colors to use for the plotted lines" 146 label="List of colors to use for the plotted lines"
131 help="Color names and html hex strings (e.g. #eeff22) are accepted. 147 help="Color names and html hex strings (e.g. #eeff22) are accepted.
133 <validator type="expression" 149 <validator type="expression"
134 message="Only numbers, digits, '#' and spaces are allowed.">all(c in ' #abcdefghijklmnopqrstuvwxyz0123456789' for c in value)</validator> 150 message="Only numbers, digits, '#' and spaces are allowed.">all(c in ' #abcdefghijklmnopqrstuvwxyz0123456789' for c in value)</validator>
135 </param> 151 </param>
136 152
137 <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue="" 153 <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue=""
138 label="Do one plot per group" 154 label="Make one plot per group of regions"
139 help="When clustering is applied to the data or multiple BED files were used, 155 help="The default is to make one plot per bigWig file, i.e., all samples next to each other. Choosing this option will make one plot per group of regions. " />
140 plot the groups next to each other. The default is to plot the samples next to each other." />
141 156
142 157
143 <param argument="--yMin" type="float" value="" size="3" optional="true" 158 <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"/> 159 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" 160 <param argument="--yMax" type="float" value="" size="3" optional="true"
167 </test> 182 </test>
168 </tests> 183 </tests>
169 <help> 184 <help>
170 <![CDATA[ 185 <![CDATA[
171 186
172 **What it does** 187 What it does
188 -------------
173 189
174 This tool plots the average enrichments over all genomic 190 This tool plots the average enrichments over all genomic
175 regions supplied to computeMarix. It requires that computeMatrix was successfully run. 191 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 192 It is a very useful complement to ``plotHeatmap``, especially in cases where you want to
177 compare the scores for many different groups. Like heatmapper, profiler does not change the 193 compare the scores for many different groups. Like ``plotHeatmap``, ``plotProfile`` does not change the
178 values that were compute by computeMatrix, but you can modify the color and other display properties of the plots. 194 values that were computed by ``computeMatrix``, but you can modify the color and other display properties of the plots.
179 195
180 196 Output
181 .. image:: $PATH_TO_IMAGES/visual_profiler_DmelPolII.png 197 -------------
182 :alt: Meta-gene profile of Rna Polymerase II 198
183 199 .. image:: $PATH_TO_IMAGES/plotProfiler_examples.png
184 200 :width: 600
185 You can find more details on the profiler doc page: https://deeptools.readthedocs.org/en/master/content/tools/plotProfile.html 201 :height: 858
186 202
203 =======
204
205 In addition to the image, ``plotProfile`` can also generate the values underlying the profile.
206
207 See the following table for the **optional output** options:
208
209 +-----------------------------------+--------------------+-----------------+-----------------+
210 | **optional output type** | **computeMatrix** | **plotHeatmap** | **plotProfile** |
211 +-----------------------------------+--------------------+-----------------+-----------------+
212 | values underlying the heatmap | yes | yes | no |
213 +-----------------------------------+--------------------+-----------------+-----------------+
214 | values underlying the profile | no | no | yes |
215 +-----------------------------------+--------------------+-----------------+-----------------+
216 | sorted and/or filtered regions | yes | yes | yes |
217 +-----------------------------------+--------------------+-----------------+-----------------+
187 218
188 ----- 219 -----
189 220
190 @REFERENCES@ 221 @REFERENCES@
191 ]]> 222 ]]>