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comparison plotProfiler.xml @ 7:a6d65190c7e5 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69
author bgruening
date Wed, 23 Dec 2015 07:35:12 -0500
parents e6dbb616211e
children 4339a4d28e97
comparison
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6:e6dbb616211e 7:a6d65190c7e5
13 --matrixFile "$matrixFile" 13 --matrixFile "$matrixFile"
14 --outFileName "$outFileName" 14 --outFileName "$outFileName"
15 15
16 #if $output.showOutputSettings == "yes" 16 #if $output.showOutputSettings == "yes"
17 --plotFileFormat $output.outFileFormat 17 --plotFileFormat $output.outFileFormat
18
19 #if $output.saveData:
20 --outFileNameData "$outFileNameData"
21 #end if
22 18
23 #if $output.saveSortedRegions: 19 #if $output.saveSortedRegions:
24 --outFileSortedRegions '$outFileSortedRegions' 20 --outFileSortedRegions '$outFileSortedRegions'
25 #end if 21 #end if
26 #else 22 #else
47 43
48 #if str($advancedOpt.colors).strip() != "": 44 #if str($advancedOpt.colors).strip() != "":
49 --colors #echo ' '.join( ["'%s'" % $color for $color in $advancedOpt.colors.split()] )# 45 --colors #echo ' '.join( ["'%s'" % $color for $color in $advancedOpt.colors.split()] )#
50 #end if 46 #end if
51 47
52 $advancedOpt.onePlotPerGroup 48 $advancedOpt.perGroup
53 49
54 #if $advancedOpt.yMin: 50 #if $advancedOpt.yMin:
55 --yMin $advancedOpt.yMin 51 --yMin $advancedOpt.yMin
56 #end if 52 #end if
57 #if $advancedOpt.yMax: 53 #if $advancedOpt.yMax:
122 <option value="lines" selected="true">lines</option> 118 <option value="lines" selected="true">lines</option>
123 <option value="fill">fill</option> 119 <option value="fill">fill</option>
124 <option value="se">add standard error</option> 120 <option value="se">add standard error</option>
125 <option value="overlapped_lines">overlapped lines</option> 121 <option value="overlapped_lines">overlapped lines</option>
126 </param> 122 </param>
127 <param argument="--regionsLabel" type="text" value="genes" size="30" 123 <param argument="--regionsLabel" type="text" value="coverage" size="30"
128 label="Labels for the regions plotted in the heatmap" 124 label="Labels for the regions plotted in the heatmap"
129 help="If more than one region is being plotted a list of labels separated 125 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;."/> 126 by comma and limited by quotes, is required. For example, &quot;label1, label2&quot;."/>
131 127
132 <expand macro="plotTitle" /> 128 <expand macro="plotTitle" />
136 The color names should be given separated by spaces. (--colors red blue green)"> 132 The color names should be given separated by spaces. (--colors red blue green)">
137 <validator type="expression" 133 <validator type="expression"
138 message="Only numbers, digits, '#' and spaces are allowed.">all(c in ' #abcdefghijklmnopqrstuvwxyz0123456789' for c in value)</validator> 134 message="Only numbers, digits, '#' and spaces are allowed.">all(c in ' #abcdefghijklmnopqrstuvwxyz0123456789' for c in value)</validator>
139 </param> 135 </param>
140 136
141 <param argument="--onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue="" 137 <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue=""
142 label="Do one plot per group" 138 label="Do one plot per group"
143 help="When the region file contains groups separated by &quot;#&quot;, the default is 139 help="When clustering is applied to the data, or the region file contains groups separated by &quot;#&quot;,
144 to plot the averages for the distinct plots in one plot. If this option is set, each group 140 plot the groups next to each other. The default is to plot the samples next to each other.
145 will get its own plot, stacked on top of each other." /> 141 If this option is set, each group (or cluster) will get its own plot, with different samples
142 stacked on top of each other." />
146 143
147 144
148 <param argument="--yMin" type="float" value="" size="3" optional="true" 145 <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"/> 146 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" 147 <param argument="--yMax" type="float" value="" size="3" optional="true"
186 183
187 .. image:: $PATH_TO_IMAGES/visual_profiler_DmelPolII.png 184 .. image:: $PATH_TO_IMAGES/visual_profiler_DmelPolII.png
188 :alt: Meta-gene profile of Rna Polymerase II 185 :alt: Meta-gene profile of Rna Polymerase II
189 186
190 187
191 You can find more details on the profiler wiki page: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-profiler 188 You can find more details on the profiler doc page: https://deeptools.readthedocs.org/en/release-1.6/content/tools/plotProfile.html
192 189
193 190
194 ----- 191 -----
195 192
196 @REFERENCES@ 193 @REFERENCES@