annotate profiler.xml @ 26:2ad3b027dfcd draft

Uploaded
author bgruening
date Thu, 06 Feb 2014 06:40:05 -0500
parents
children bf1b1dcdd67b
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
26
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
1 <tool id="deeptools_profiler" name="profiler" version="1.0.4">
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
2 <description>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
3 creates a profile plot for a score associated to genomic regions
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
4 </description>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
5 <expand macro="requirements" />
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
6 <expand macro="stdio" />
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
7 <macros>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
8 <token name="@BINARY@">profiler</token>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
9 <import>deepTools_macros.xml</import>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
10 </macros>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
11 <command>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
12 profiler
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
13
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
14 --matrixFile $matrixFile
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
15 --outFileName $outFileName
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
16
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
17 #if $output.showOutputSettings == "yes"
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
18 --plotFileFormat $output.outFileFormat
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
19
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
20 #if $output.saveData:
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
21 --outFileNameData '$outFileNameData'
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
22 #end if
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
23
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
24 #if $output.saveSortedRegions:
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
25 --outFileSortedRegions '$outFileSortedRegions'
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
26 #end if
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
27 #else
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
28 --plotFileFormat 'png'
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
29 #end if
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
30
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
31 #if $scaleRegions.showScaleRegionsOpt == "yes":
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
32 --startLabel $scaleRegions.startLabel
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
33 --endLabel $scaleRegions.endLabel
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
34 #end if
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
35
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
36 #if $advancedOpt.showAdvancedOpt == "yes":
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
37 #if $advancedOpt.averageType:
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
38 --averageType '$advancedOpt.averageType'
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
39 #end if
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
40 --plotHeight $advancedOpt.plotHeight
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
41 --plotWidth $advancedOpt.plotWidth
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
42 --plotType $advancedOpt.plotType
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
43
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
44 --regionsLabel '$advancedOpt.regionsLabel'
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
45
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
46 #if str($advancedOpt.plotTitle).strip() != "":
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
47 --plotTitle '$advancedOpt.plotTitle'
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
48 #end if
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
49
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
50 #if str($advancedOpt.colors).strip() != "":
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
51 --colors #echo ' '.join( ["'%s'" % $color for $color in $advancedOpt.colors.split()] )#
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
52 #end if
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
53
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
54 $advancedOpt.onePlotPerGroup
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
55
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
56 #if $advancedOpt.yMin:
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
57 --yMin $advancedOpt.yMin
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
58 #end if
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
59 #if $advancedOpt.yMax:
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
60 --yMax $advancedOpt.yMax
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
61 #end if
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
62
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
63 --xAxisLabel '$advancedOpt.xAxisLabel'
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
64 #if str($advancedOpt.yAxisLabel.value) != "None":
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
65 --yAxisLabel '$advancedOpt.yAxisLabel'
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
66 #end if
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
67
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
68 @kmeans_clusterin@
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
69
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
70 #end if
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
71 </command>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
72 <inputs>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
73 <param name="matrixFile" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
74 <conditional name="scaleRegions">
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
75 <param name="showScaleRegionsOpt" type="select" label="The input matrix was computed in scale-regions mode">
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
76 <option value="no" selected="true">no</option>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
77 <option value="yes">yes</option>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
78 </param>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
79 <when value="no" />
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
80 <when value="yes">
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
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;." />
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
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)."/>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
83 </when>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
84 </conditional>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
85
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
86 <expand macro="input_graphic_output_settings">
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
87 <expand macro="input_image_file_format" />
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
88 </expand>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
89
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
90 <conditional name="advancedOpt">
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
91 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
92 <option value="no" selected="true">no</option>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
93 <option value="yes">yes</option>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
94 </param>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
95 <when value="no" />
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
96 <when value="yes">
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
97 <param name="averageType" type="select" label="Define the type of statistic that should be used for the profile.">
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
98 <option value="mean" selected="true">mean</option>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
99 <option value="median">median</option>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
100 <option value="min">min</option>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
101 <option value="max">max</option>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
102 <option value="sum">sum</option>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
103 <option value="std">std</option>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
104 </param>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
105 <param name="plotHeight" type="integer" value="5" min="3"
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
106 label="Plot height"
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
107 help="Height in cm. The default for the plot height is 5 centimeters. The minimum value is 3 cm." />
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
108 <param name="plotWidth" type="integer" value="8" min="1"
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
109 label="Plot width"
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
110 help="Width in cm. The default value is 8 centimeters. The minimum value is 1 cm." />
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
111 <param name="plotType" type="select" label="Plot type"
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
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.">
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
113 <option value="lines" selected="true">lines</option>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
114 <option value="fill">fill</option>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
115 <option value="se">add standard error</option>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
116 <option value="overlapped_lines">overlapped lines</option>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
117 </param>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
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;."/>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
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." />
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
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)">
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
121 <validator type="expression" message="Only numbers, digits, '#' and spaces are allowed.">all(c in ' #abcdefghijklmnopqrstuvwxyz0123456789' for c in value)</validator>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
122 </param>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
123
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
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."/>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
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"/>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
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"/>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
127 <param name="xAxisLabel" type="text" value="gene distance (bp)" size="50" label="Description for the x-axis label" />
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
128 <param name="yAxisLabel" type="text" value="" size="50" label="Description for the y-axis label for the top panel" />
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
129
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
130 <expand macro="kmeans_clustering" />
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
131
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
132 </when>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
133 </conditional>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
134 </inputs>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
135 <outputs>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
136 <expand macro="output_image_file_format" />
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
137 <expand macro="output_graphic_outputs" />
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
138 </outputs>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
139 <help>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
140
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
141 **What it does**
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
142
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
143 This tool plots the average enrichments over all genomic
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
144 regions supplied to computeMarix. It requires that computeMatrix was successfully run.
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
145 It is a very useful complement to the heatmapper, especially in cases when you want to
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
146 compare the scores for many different groups. Like heatmapper, profiler does not change the
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
147 values that were compute by computeMatrix, but you can choose between
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
148 many different ways to color and display the plots.
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
149
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
150
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
151 .. image:: $PATH_TO_IMAGES/visual_profiler_DmelPolII.png
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
152 :alt: Meta-gene profile of Rna Polymerase II
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
153
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
154
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
155 You can find more details on the profiler wiki page: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-profiler
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
156
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
157
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
158 -----
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
159
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
160 @REFERENCES@
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
161
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
162 </help>
2ad3b027dfcd Uploaded
bgruening
parents:
diff changeset
163 </tool>