Mercurial > repos > bgruening > deeptools_plot_heatmap

comparison plotHeatmap.xml @ 23:751adcc1ce82 draft

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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d
author bgruening
date Tue, 19 Feb 2019 10:08:15 -0500
parents 46992aa30bd6
children 42cb23d80271
comparison
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22:46992aa30bd6 23:751adcc1ce82
40 40
41 #if $advancedOpt.averageTypeSummaryPlot: 41 #if $advancedOpt.averageTypeSummaryPlot:
42 --averageTypeSummaryPlot '$advancedOpt.averageTypeSummaryPlot' 42 --averageTypeSummaryPlot '$advancedOpt.averageTypeSummaryPlot'
43 #end if 43 #end if
44 44
45 --plotType '$advancedOpt.plotType'
46
45 #if str($advancedOpt.missingDataColor.value) != "None": 47 #if str($advancedOpt.missingDataColor.value) != "None":
46 --missingDataColor '$advancedOpt.missingDataColor' 48 --missingDataColor '$advancedOpt.missingDataColor'
47 #end if 49 #end if
48 50
49 #set colorMap = [] 51 #set colorMap = []
95 #end if 97 #end if
96 98
97 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "": 99 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
98 --plotTitle '$advancedOpt.plotTitle' 100 --plotTitle '$advancedOpt.plotTitle'
99 #end if 101 #end if
102
103 --legendLocation '$advancedOpt.legendLocation'
100 104
101 --labelRotation '$advancedOpt.labelRotation' 105 --labelRotation '$advancedOpt.labelRotation'
102 106
103 $advancedOpt.perGroup 107 $advancedOpt.perGroup
104 108
134 <option value="min">min</option> 138 <option value="min">min</option>
135 <option value="max">max</option> 139 <option value="max">max</option>
136 <option value="sum">sum</option> 140 <option value="sum">sum</option>
137 <option value="std">std</option> 141 <option value="std">std</option>
138 </param> 142 </param>
139 143 <param argument="--plotType" type="select" label="Type of summary plot">
144 <option value="lines">plot the profile line based on the statistic selected above.</option>
145 <option value="fill">fills the region between zero and the profile.</option>
146 <option value="se">color the region between the profile and the standard error.</option>
147 <option value="std">color the region between the profile and the standard deviation.</option>
148 </param>
140 <param argument="--missingDataColor" type="text" value="black" optional="true" label="Missing data color" 149 <param argument="--missingDataColor" type="text" value="black" optional="true" label="Missing data color"
141 help="If 'Represent missing data as zero' is not set, such cases will be colored in black by default. 150 help="If 'Represent missing data as zero' is not set, such cases will be colored in black by default.
142 By using this parameter a different color can be set. A value between 0 and 1 will be used for a gray scale (black is 0). 151 By using this parameter a different color can be set. A value between 0 and 1 will be used for a gray scale (black is 0).
143 Also color names can be used, see a list here: http://packages.python.org/ete2/reference/reference_svgcolors.html. 152 Also color names can be used, see a list here: http://packages.python.org/ete2/reference/reference_svgcolors.html.
144 Alternatively colors can be specified using the #rrggbb notation." /> 153 Alternatively colors can be specified using the #rrggbb notation." />
204 help="If more than one region is being plotted a list of labels separated by space is required. 213 help="If more than one region is being plotted a list of labels separated by space is required.
205 If a label itself contains a space, then quotes are needed. 214 If a label itself contains a space, then quotes are needed.
206 For example, label_1 &quot;label 2&quot;" /> 215 For example, label_1 &quot;label 2&quot;" />
207 216
208 <expand macro="plotTitle" /> 217 <expand macro="plotTitle" />
218 <expand macro="legendLocation" />
209 <expand macro="labelRotation" /> 219 <expand macro="labelRotation" />
210 <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue="" 220 <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue=""
211 label="Make one plot per group of regions" 221 label="Make one plot per group of regions"
212 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."/> 222 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."/>
213 223