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comparison profiler.xml @ 26:2ad3b027dfcd draft

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author bgruening
date Thu, 06 Feb 2014 06:40:05 -0500
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25:d2898b81b912 26:2ad3b027dfcd
1 <tool id="deeptools_profiler" name="profiler" version="1.0.4">
2 <description>
3 creates a profile plot for a score associated to genomic regions
4 </description>
5 <expand macro="requirements" />
6 <expand macro="stdio" />
7 <macros>
8 <token name="@BINARY@">profiler</token>
9 <import>deepTools_macros.xml</import>
10 </macros>
11 <command>
12 profiler
13
14 --matrixFile $matrixFile
15 --outFileName $outFileName
16
17 #if $output.showOutputSettings == "yes"
18 --plotFileFormat $output.outFileFormat
19
20 #if $output.saveData:
21 --outFileNameData '$outFileNameData'
22 #end if
23
24 #if $output.saveSortedRegions:
25 --outFileSortedRegions '$outFileSortedRegions'
26 #end if
27 #else
28 --plotFileFormat 'png'
29 #end if
30
31 #if $scaleRegions.showScaleRegionsOpt == "yes":
32 --startLabel $scaleRegions.startLabel
33 --endLabel $scaleRegions.endLabel
34 #end if
35
36 #if $advancedOpt.showAdvancedOpt == "yes":
37 #if $advancedOpt.averageType:
38 --averageType '$advancedOpt.averageType'
39 #end if
40 --plotHeight $advancedOpt.plotHeight
41 --plotWidth $advancedOpt.plotWidth
42 --plotType $advancedOpt.plotType
43
44 --regionsLabel '$advancedOpt.regionsLabel'
45
46 #if str($advancedOpt.plotTitle).strip() != "":
47 --plotTitle '$advancedOpt.plotTitle'
48 #end if
49
50 #if str($advancedOpt.colors).strip() != "":
51 --colors #echo ' '.join( ["'%s'" % $color for $color in $advancedOpt.colors.split()] )#
52 #end if
53
54 $advancedOpt.onePlotPerGroup
55
56 #if $advancedOpt.yMin:
57 --yMin $advancedOpt.yMin
58 #end if
59 #if $advancedOpt.yMax:
60 --yMax $advancedOpt.yMax
61 #end if
62
63 --xAxisLabel '$advancedOpt.xAxisLabel'
64 #if str($advancedOpt.yAxisLabel.value) != "None":
65 --yAxisLabel '$advancedOpt.yAxisLabel'
66 #end if
67
68 @kmeans_clusterin@
69
70 #end if
71 </command>
72 <inputs>
73 <param name="matrixFile" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/>
74 <conditional name="scaleRegions">
75 <param name="showScaleRegionsOpt" type="select" label="The input matrix was computed in scale-regions mode">
76 <option value="no" selected="true">no</option>
77 <option value="yes">yes</option>
78 </param>
79 <when value="no" />
80 <when value="yes">
81 <param name="startLabel" type="text" value="TSS" size="10" label="Label for the region start" help ="[only for scale-regions mode] Label shown in the plot for the start of the region. Default is TSS (transcription start site), but could be changed to anything, e.g. &quot;peak start&quot;." />
82 <param name="endLabel" type="text" value="TES" size="10" label="Label for the region end" help="[only for scale-regions mode] Label shown in the plot for the region end. Default is TES (transcription end site)."/>
83 </when>
84 </conditional>
85
86 <expand macro="input_graphic_output_settings">
87 <expand macro="input_image_file_format" />
88 </expand>
89
90 <conditional name="advancedOpt">
91 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
92 <option value="no" selected="true">no</option>
93 <option value="yes">yes</option>
94 </param>
95 <when value="no" />
96 <when value="yes">
97 <param name="averageType" type="select" label="Define the type of statistic that should be used for the profile.">
98 <option value="mean" selected="true">mean</option>
99 <option value="median">median</option>
100 <option value="min">min</option>
101 <option value="max">max</option>
102 <option value="sum">sum</option>
103 <option value="std">std</option>
104 </param>
105 <param name="plotHeight" type="integer" value="5" min="3"
106 label="Plot height"
107 help="Height in cm. The default for the plot height is 5 centimeters. The minimum value is 3 cm." />
108 <param name="plotWidth" type="integer" value="8" min="1"
109 label="Plot width"
110 help="Width in cm. The default value is 8 centimeters. The minimum value is 1 cm." />
111 <param name="plotType" type="select" label="Plot type"
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.">
113 <option value="lines" selected="true">lines</option>
114 <option value="fill">fill</option>
115 <option value="se">add standard error</option>
116 <option value="overlapped_lines">overlapped lines</option>
117 </param>
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;."/>
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
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."/>
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"/>
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"/>
127 <param name="xAxisLabel" type="text" value="gene distance (bp)" size="50" label="Description for the x-axis label" />
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
132 </when>
133 </conditional>
134 </inputs>
135 <outputs>
136 <expand macro="output_image_file_format" />
137 <expand macro="output_graphic_outputs" />
138 </outputs>
139 <help>
140
141 **What it does**
142
143 This tool plots the average enrichments over all genomic
144 regions supplied to computeMarix. It requires that computeMatrix was successfully run.
145 It is a very useful complement to the heatmapper, especially in cases when you want to
146 compare the scores for many different groups. Like heatmapper, profiler does not change the
147 values that were compute by computeMatrix, but you can choose between
148 many different ways to color and display the plots.
149
150
151 .. image:: $PATH_TO_IMAGES/visual_profiler_DmelPolII.png
152 :alt: Meta-gene profile of Rna Polymerase II
153
154
155 You can find more details on the profiler wiki page: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-profiler
156
157
158 -----
159
160 @REFERENCES@
161
162 </help>
163 </tool>