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comparison profiler.xml @ 18:5ea8782d650c draft

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author bgruening
date Mon, 03 Feb 2014 13:44:35 -0500
parents b4c5dd45778a
children 8c452f37c896
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17:ef65d6b68ccc 18:5ea8782d650c
1 <tool id="deeptools_profiler" name="profiler" version="1.0.2"> 1 <tool id="deeptools_profiler" name="profiler" version="1.0.3">
2 <description> 2 <description>
3 creates a profile plot for a score associated to genomic regions 3 creates a profile plot for a score associated to genomic regions
4 </description> 4 </description>
5 <expand macro="requirements" /> 5 <expand macro="requirements" />
6 <expand macro="stdio" /> 6 <expand macro="stdio" />
7 <macros> 7 <macros>
8 <token name="@BINARY@">profiler</token>
8 <import>deepTools_macros.xml</import> 9 <import>deepTools_macros.xml</import>
9 </macros> 10 </macros>
10 <command> 11 <command>
11 profiler 12 profiler
12 13
40 --plotWidth $advancedOpt.plotWidth 41 --plotWidth $advancedOpt.plotWidth
41 --plotType $advancedOpt.plotType 42 --plotType $advancedOpt.plotType
42 43
43 --regionsLabel '$advancedOpt.regionsLabel' 44 --regionsLabel '$advancedOpt.regionsLabel'
44 45
45 #if str($advancedOpt.plotTitle.value) != "None": 46 #if str($advancedOpt.plotTitle).strip() != "":
46 --plotTitle '$advancedOpt.plotTitle' 47 --plotTitle '$advancedOpt.plotTitle'
48 #end if
49
50 #if str($advancedOpt.colors).strip() != "":
51 --colors #echo ' '.join( ["'%s'" % $color for $color in $advancedOpt.colors.split()] )#
47 #end if 52 #end if
48 53
49 $advancedOpt.onePlotPerGroup 54 $advancedOpt.onePlotPerGroup
50 55
51 #if $advancedOpt.yMin: 56 #if $advancedOpt.yMin:
57 62
58 --xAxisLabel '$advancedOpt.xAxisLabel' 63 --xAxisLabel '$advancedOpt.xAxisLabel'
59 #if str($advancedOpt.yAxisLabel.value) != "None": 64 #if str($advancedOpt.yAxisLabel.value) != "None":
60 --yAxisLabel '$advancedOpt.yAxisLabel' 65 --yAxisLabel '$advancedOpt.yAxisLabel'
61 #end if 66 #end if
67
68 @kmeans_clusterin@
69
62 #end if 70 #end if
63 </command> 71 </command>
64 <inputs> 72 <inputs>
65 <param name="matrixFile" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/> 73 <param name="matrixFile" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/>
66 <conditional name="scaleRegions"> 74 <conditional name="scaleRegions">
99 help="Height in cm. The default for the plot height is 5 centimeters. The minimum value is 3 cm." /> 107 help="Height in cm. The default for the plot height is 5 centimeters. The minimum value is 3 cm." />
100 <param name="plotWidth" type="integer" value="8" min="1" 108 <param name="plotWidth" type="integer" value="8" min="1"
101 label="Plot width" 109 label="Plot width"
102 help="Width in cm. The default value is 8 centimeters. The minimum value is 1 cm." /> 110 help="Width in cm. The default value is 8 centimeters. The minimum value is 1 cm." />
103 <param name="plotType" type="select" label="Plot type" 111 <param name="plotType" type="select" label="Plot type"
104 help="For the summary plot (profile) only. The &quot;lines&quot; option will plot the profile line based on the average type selected. The &quot;fill&quot; option fills the region between zero and the profile curve. The fill in color is semi transparent to distinguish different profiles. The &quot;std&quot; option colors the region between the profile and the standard deviation of the data. As in the case of fill, a semi-transparent color is used. The option &quot;overlapped_lines&quot; plots each region values, one on top of the other; this option only works if &quot;one plot per proup&quot; is set."> 112 help="For the summary plot (profile) only. The &quot;lines&quot; option will plot the profile line based on the average type selected. The &quot;fill&quot; option fills the region between zero and the profile curve. The fill in color is semi transparent to distinguish different profiles. The &quot;add standard error&quot; option colors the region between the profile and the standard error of the data. As in the case of fill, a semi-transparent color is used. The option &quot;overlapped_lines&quot; plots each region values, one on top of the other; this option only works if &quot;one plot per proup&quot; is set.">
105 <option value="lines" selected="true">lines</option> 113 <option value="lines" selected="true">lines</option>
106 <option value="fill">fill</option> 114 <option value="fill">fill</option>
107 <option value="std">std</option> 115 <option value="se">add standard error</option>
108 <option value="overlapped_lines">overlapped lines</option> 116 <option value="overlapped_lines">overlapped lines</option>
109 </param> 117 </param>
110 <param name="regionsLabel" type="text" value="genes" size="30" label="Labels for the regions plotted in the heatmap" help="If more than one region is being plotted a list of labels separated by comma and limited by quotes, is required. For example, &quot;label1, label2&quot;."/> 118 <param name="regionsLabel" type="text" value="genes" size="30" label="Labels for the regions plotted in the heatmap" help="If more than one region is being plotted a list of labels separated by comma and limited by quotes, is required. For example, &quot;label1, label2&quot;."/>
111 <param name="plotTitle" type="text" value="" size="30" label="Title of the plot" help="Title of the plot, to be printed on top of the generated image. Leave blank for no title." /> 119 <param name="plotTitle" type="text" value="" size="30" label="Title of the plot" help="Title of the plot, to be printed on top of the generated image. Leave blank for no title." />
120 <param name="colors" type="text" value="" size="40" label="List of colors to use for the plotted lines" help="Color names and html hex strings (e.g. #eeff22) are accepted. The color names should be given separated by spaces. (--colors red blue green)">
121 <validator type="expression" message="Only numbers, digits, '#' and spaces are allowed.">all(c in ' #abcdefghijklmnopqrstuvwxyz0123456789' for c in value)</validator>
122 </param>
123
112 <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue="" label="Do one plot per group" help="When the region file contains groups separated by &quot;#&quot;, the default is to plot the averages for the distinct plots in one plot. If this option is set, each group will get its own plot, stacked on top of each other."/> 124 <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue="" label="Do one plot per group" help="When the region file contains groups separated by &quot;#&quot;, the default is to plot the averages for the distinct plots in one plot. If this option is set, each group will get its own plot, stacked on top of each other."/>
113 <param name="yMin" type="float" value="" size="3" label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values" optional="true"/> 125 <param name="yMin" type="float" value="" size="3" label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values" optional="true"/>
114 <param name="yMax" type="float" value="" size="3" label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" optional="true"/> 126 <param name="yMax" type="float" value="" size="3" label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" optional="true"/>
115 <param name="xAxisLabel" type="text" value="gene distance (bp)" size="50" label="Description for the x-axis label" /> 127 <param name="xAxisLabel" type="text" value="gene distance (bp)" size="50" label="Description for the x-axis label" />
116 <param name="yAxisLabel" type="text" value="" size="50" label="Description for the y-axis label for the top panel" /> 128 <param name="yAxisLabel" type="text" value="" size="50" label="Description for the y-axis label for the top panel" />
129
130 <expand macro="kmeans_clustering" />
131
117 </when> 132 </when>
118 </conditional> 133 </conditional>
119 </inputs> 134 </inputs>
120 <outputs> 135 <outputs>
121 <expand macro="output_image_file_format" /> 136 <expand macro="output_image_file_format" />
135 150
136 .. image:: $PATH_TO_IMAGES/visual_profiler_DmelPolII.png 151 .. image:: $PATH_TO_IMAGES/visual_profiler_DmelPolII.png
137 :alt: Meta-gene profile of Rna Polymerase II 152 :alt: Meta-gene profile of Rna Polymerase II
138 153
139 154
155 You can find more details in the `profiler wiki`_.
156
157 .. _profiler wiki: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-profiler
158
159
140 ----- 160 -----
141
142 .. class:: infomark
143 161
144 @REFERENCES@ 162 @REFERENCES@
145 163
146 </help> 164 </help>
147 </tool> 165 </tool>