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comparison profiler.xml @ 0:d957e25e18a3 draft

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author bgruening
date Thu, 14 Nov 2013 16:39:18 -0500
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1 <tool id="deeptools_profiler" name="profiler" version="1.0">
2 <description>
3 creates a profile plot for a score associated to genomic regions
4 </description>
5 <expand macro="requirements" />
6 <macros>
7 <import>deepTools_macros.xml</import>
8 </macros>
9 <command>
10 profiler
11
12 --matrixFile $matrixFile
13
14 #if $output.showOutputSettings == "yes"
15 #set newoutFileName = str($outFileName)+"."+str($output.outFileFormat)
16 --outFileName $newoutFileName
17
18 #if $output.saveData:
19 --outFileNameData '$outFileNameData'
20 #end if
21
22 #if $output.saveMatrix:
23 --outFileNameMatrix '$outFileNameMatrix'
24 #end if
25
26 #if $output.saveSortedRegions:
27 --outFileSortedRegions '$outFileSortedRegions'
28 #end if
29 #else
30 #set newoutFileName = str($outFileName)+".png"
31 --outFileName $newoutFileName
32 #end if
33
34 #if $scaleRegions.showScaleRegionsOpt == "yes":
35 --startLabel $scaleRegions.startLabel
36 --endLabel $scaleRegions.endLabel
37 #end if
38
39 #if $advancedOpt.showAdvancedOpt == "yes":
40 #if $advancedOpt.averageType:
41 --averageType '$advancedOpt.averageType'
42 #end if
43 --plotHeight $advancedOpt.plotHeight
44 --plotWidth $advancedOpt.plotWidth
45 --plotType $advancedOpt.plotType
46
47 --regionsLabel '$advancedOpt.regionsLabel'
48
49 #if str($advancedOpt.plotTitle.value) != "None":
50 --plotTitle '$advancedOpt.plotTitle'
51 #end if
52
53 $advancedOpt.onePlotPerGroup
54
55 #if $advancedOpt.yMin:
56 --yMin $advancedOpt.yMin
57 #end if
58 #if $advancedOpt.yMax:
59 --yMax $advancedOpt.yMax
60 #end if
61
62 --xAxisLabel '$advancedOpt.xAxisLabel'
63 #if str($advancedOpt.yAxisLabel.value) != "None":
64 --yAxisLabel '$advancedOpt.yAxisLabel'
65 #end if
66 #end if
67 ; mv $newoutFileName $outFileName
68 </command>
69 <inputs>
70 <param name="matrixFile" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/>
71 <conditional name="scaleRegions">
72 <param name="showScaleRegionsOpt" type="select" label="The input matrix was computed in scale-regions mode">
73 <option value="no" selected="true">no</option>
74 <option value="yes">yes</option>
75 </param>
76 <when value="no" />
77 <when value="yes">
78 <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;." />
79 <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)."/>
80 </when>
81 </conditional>
82
83 <expand macro="graphic_output_settings" />
84
85 <conditional name="advancedOpt">
86 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
87 <option value="no" selected="true">no</option>
88 <option value="yes">yes</option>
89 </param>
90 <when value="no" />
91 <when value="yes">
92 <param name="averageType" type="select" label="Define the type of statistic that should be used for the profile.">
93 <option value="mean" selected="true">mean</option>
94 <option value="median">median</option>
95 <option value="min">min</option>
96 <option value="max">max</option>
97 <option value="sum">sum</option>
98 <option value="std">std</option>
99 </param>
100 <param name="plotHeight" type="integer" value="5" min="3"
101 label="Plot height"
102 help="Height in cm. The default for the plot height is 5 centimeters. The minimum value is 3 cm." />
103 <param name="plotWidth" type="integer" value="8" min="1"
104 label="Plot width"
105 help="Width in cm. The default value is 8 centimeters. The minimum value is 1 cm." />
106 <param name="plotType" type="select" label="Plot type"
107 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.">
108 <option value="lines" selected="true">lines</option>
109 <option value="fill">fill</option>
110 <option value="std">std</option>
111 <option value="overlapped_lines">overlapped lines</option>
112 </param>
113
114 <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;."/>
115 <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." />
116 <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."/>
117 <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"/>
118 <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"/>
119 <param name="xAxisLabel" type="text" value="gene distance (bp)" size="50" label="Description for the x-axis label" />
120 <param name="yAxisLabel" type="text" value="" size="50" label="Description for the y-axis label for the top panel" />
121 </when>
122 </conditional>
123 </inputs>
124 <outputs>
125 <data format="png" name="outFileName" label="${tool.name} image">
126 <change_format>
127 <when input="output.outFileFormat" value="pdf" format="pdf" />
128 <when input="output.outFileFormat" value="svg" format="svg" />
129 <when input="output.outFileFormat" value="eps" format="eps" />
130 <when input="output.outFileFormat" value="emf" format="emf" />
131 </change_format>
132 </data>
133 <data format="tabular" name="outFileNameData" label="${tool.name} raw plot data">
134 <filter>(output['showOutputSettings'] == 'yes' and output['saveData'] == True)</filter>
135 </data>
136 <data format="tabular" name="outFileNameMatrix" label="${tool.name} matrix of heatmap values">
137 <filter>(output['showOutputSettings'] == 'yes' and output['saveMatrix'] == True)</filter>
138 </data>
139 <data format="bed" name="outFileSortedRegions" label="${tool.name} sorted/filtered regions">
140 <filter>(output['showOutputSettings'] == 'yes' and output['saveSortedRegions'] == True)</filter>
141 </data>
142 </outputs>
143 <help>
144
145 **What it does**
146
147 This tool plots the average enrichments over all genomic
148 regions supplied to computeMarix. It is a very useful complement to the
149 heatmapper, especially in cases when you want to compare the scores for
150 many different groups. Like heatmapper, profiler does not change the
151 values that were compute by computeMatrix, but you can choose between
152 many different ways to color and display the plots.
153
154
155 .. image:: $PATH_TO_IMAGES/visual_profiler_DmelPolII.png
156 :alt: Meta-gene profile of Rna Polymerase II
157
158
159 -----
160
161 .. class:: infomark
162
163 @REFERENCES@
164
165 </help>
166 </tool>