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comparison profiler.xml @ 39:c6f1a059bc7d

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author bgruening
date Fri, 02 Aug 2013 12:18:55 -0400
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children 6a2a7374450b
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38:1a78aa9ea234 39:c6f1a059bc7d
1 <tool id="dt_profiler" name="profiler" version="1.0">
2 <description>
3 creates a profile plot for a score associated to genomic regions
4 </description>
5
6 <command>
7 profiler
8 --matrixFile $matrixFile
9
10 #if $output.showOutputSettings == "yes"
11 #set newoutFileName=str($outFileName)+"."+str($output.outFileFormat)
12 --outFileName $newoutFilename
13 #if $output.outFileNameData:
14 --outFileNameData '$output.outFileNameData'
15 #end if
16
17 #if $output.outFileNameMatrix:
18 --outFileNameMatrix '$output.outFileNameMatrix'
19 #end if
20
21 #if $output.outFileSortedRegions:
22 --outFileSortedRegions '$output.outFileSortedRegions'
23 #end if
24 #else
25 #set newoutFileName=str($outFileName)+".png"
26 --outFileName $newoutFileName
27 #end if
28
29 #if $scaleRegions.showScaleRegionsOpt == "yes":
30 --startLabel $scaleRegions.startLabel
31 --endLabel $scaleRegions.endLabel
32 --refPointLabel $scaleRegions.refPointLabel
33 #end if
34
35 #if $advancedOpt.showAdvancedOpt == "yes"
36 #if $advancedOpt.averageType:
37 --averageType '$advancedOpt.averageType'
38 #end if
39 --plotHeight $advancedOpt.plotHeight
40 --plotWidth $advancedOpt.plotWidth
41 --plotType $advancedOpt.plotType
42
43 --regionsLabel '$advancedOpt.regionsLabel'
44
45 #if str($advancedOpt.plotTitle.value) != "None":
46 --plotTitle '$advancedOpt.plotTitle'
47 #end if
48
49 $advancedOpt.onePlotPerGroup
50
51 #if $advancedOpt.yMin:
52 --yMin $advancedOpt.yMin
53 #end if
54 #if $advancedOpt.yMax:
55 --yMax $advancedOpt.yMax
56 #end if
57
58 --xAxisLabel '$advancedOpt.xAxisLabel'
59 #if str($advancedOpt.yAxisLabel.value) != "None":
60 --yAxisLabel '$advancedOpt.yAxisLabel'
61 #end if
62 #end if
63 ; mv $newoutFileName $outFileName
64 </command>
65
66 <inputs>
67
68 <param name="matrixFile" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/>
69
70 <conditional name="scaleRegions">
71 <param name="showScaleRegionsOpt" type="select" label="The input matrix was computed in scale-regions mode">
72 <option value="no" selected="true">no</option>
73 <option value="yes">yes</option>
74 </param>
75 <when value="no" />
76 <when value="yes">
77 <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;." />
78 <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)."/>
79
80 <param name="refPointLabel" type="text" value="TSS" size="10" label="Reference point label" help ="[only for scale-regions mode] Label shown in the plot for the reference-point. Default is the same as the reference point selected (e.g. TSS), but could be anything, e.g. &quot;peak start&quot; etc." />
81 </when>
82 </conditional>
83
84 <conditional name="output" >
85 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
86 <option value="no" selected="true">no</option>
87 <option value="yes">yes</option>
88 </param>
89 <when value="no" />
90 <when value="yes">
91 <param name="outFileFormat" type="select" label="Image file format">
92 <option value="png" selected="true">png</option>
93 <option value="pdf">pdf</option>
94 <option value="svg">svg</option>
95 <option value="eps">eps</option>
96 <option value="emf">emf</option>
97 </param>
98 <param name="saveData" type="boolean" label="Save the data underlying data for the average profile"/>
99 <param name="saveMatrix" type="boolean" label="Save the the matrix of values underlying the heatmap"/>
100 <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
101 </when>
102 </conditional>
103
104 <conditional name="advancedOpt">
105 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
106 <option value="no" selected="true">no</option>
107 <option value="yes">yes</option>
108 </param>
109 <when value="no" />
110 <when value="yes">
111 <param name="averageType" type="select" label="Define the type of statistic that should be used for the profile.">
112 <option value="mean" selected="true">mean</option>
113 <option value="median">median</option>
114 <option value="min">min</option>
115 <option value="max">max</option>
116 <option value="sum">sum</option>
117 <option value="std">std</option>
118 </param>
119
120 <param name="plotHeight" type="integer" value="5" min="3"
121 label="Plot height"
122 help="Height in cm. The default for the plot height is 5 centimeters. The minimum value is 3 cm." />
123 <param name="plotWidth" type="integer" value="8" min="1"
124 label="Plot width"
125 help="Width in cm. The default value is 8 centimeters. The minimum value is 1 cm." />
126
127 <param name="plotType" type="select" label="Plot type"
128 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.">
129 <option value="lines" selected="true">lines</option>
130 <option value="fill">fill</option>
131 <option value="std">std</option>
132 <option value="overlapped_lines">overlapped lines</option>
133 </param>
134
135 <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;."/>
136
137 <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." />
138
139 <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."/>
140
141 <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"/>
142 <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"/>
143
144 <param name="xAxisLabel" type="text" value="gene distance (bp)" size="50" label="Description for the x-axis label" />
145 <param name="yAxisLabel" type="text" value="" size="50" label="Description for the y-axis label for the top panel" />
146
147 </when>
148 </conditional>
149
150 </inputs>
151 <outputs>
152 <data format="png" name="outFileName" label="${tool.name} image">
153 <change_format>
154 <when input="output.outFileFormat" value="pdf" format="pdf" />
155 <when input="output.outFileFormat" value="svg" format="svg" />
156 <when input="output.outFileFormat" value="eps" format="eps" />
157 <when input="output.outFileFormat" value="emf" format="emf" />
158 </change_format>
159 </data>
160 <data format="tabular" name="outFileNameData" label="${tool.name} raw plot data">
161 <filter>(output['showOutputSettings'] == 'yes' and output['saveData'] == True)</filter>
162 </data>
163 <data format="tabular" name="outFileNameMatrix" label="${tool.name} matrix of heatmap values">
164 <filter>(output['showOutputSettings'] == 'yes' and output['saveMatrix'] == True)</filter>
165 </data>
166 <data format="bed" name="outFileSortedRegions" label="${tool.name} sorted/filtered regions">
167 <filter>(output['showOutputSettings'] == 'yes' and output['saveSortedRegions'] == True)</filter>
168 </data>
169 </outputs>
170 <help>
171
172 **What it does**
173
174 This tool creates a profile plot for a score associated to genomic regions.
175 Typically, these regions are genes, but any other regions defined in a BED or
176 GFF format will work. A preprocessed matrix generated by the tool
177 computeMatrix is required.
178
179 -----
180
181 .. class:: infomark
182
183 Please acknowledge that this tool **is still in development** and we will be very happy to receive feedback from the users. If you run into any trouble please sent an email to `Fidel Ramirez`_.
184
185 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
186
187
188 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
189 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
190 .. _Fidel Ramirez: ramirez@ie-freiburg.mpg.de
191
192 </help>
193
194 </tool>