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comparison profiler.xml @ 10:135f3bae5c56 draft

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Uploaded
author bgruening
date Sat, 14 Dec 2013 03:29:29 -0500
parents d957e25e18a3
children baf4283e2d7f
comparison
equal deleted inserted replaced
9:c53a73b8eef9 10:135f3bae5c56
1 <tool id="deeptools_profiler" name="profiler" version="1.0"> 1 <tool id="deeptools_profiler" name="profiler" version="1.0.2">
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 <macros> 7 <macros>
7 <import>deepTools_macros.xml</import> 8 <import>deepTools_macros.xml</import>
8 </macros> 9 </macros>
9 <command> 10 <command>
10 profiler 11 profiler
11 12
12 --matrixFile $matrixFile 13 --matrixFile $matrixFile
14 --outFileName $outFileName
13 15
14 #if $output.showOutputSettings == "yes" 16 #if $output.showOutputSettings == "yes"
15 #set newoutFileName = str($outFileName)+"."+str($output.outFileFormat) 17 --plotFileFormat $output.outFileFormat
16 --outFileName $newoutFileName
17 18
18 #if $output.saveData: 19 #if $output.saveData:
19 --outFileNameData '$outFileNameData' 20 --outFileNameData '$outFileNameData'
20 #end if 21 #end if
21 22
25 26
26 #if $output.saveSortedRegions: 27 #if $output.saveSortedRegions:
27 --outFileSortedRegions '$outFileSortedRegions' 28 --outFileSortedRegions '$outFileSortedRegions'
28 #end if 29 #end if
29 #else 30 #else
30 #set newoutFileName = str($outFileName)+".png" 31 --plotFileFormat 'png'
31 --outFileName $newoutFileName
32 #end if 32 #end if
33 33
34 #if $scaleRegions.showScaleRegionsOpt == "yes": 34 #if $scaleRegions.showScaleRegionsOpt == "yes":
35 --startLabel $scaleRegions.startLabel 35 --startLabel $scaleRegions.startLabel
36 --endLabel $scaleRegions.endLabel 36 --endLabel $scaleRegions.endLabel
62 --xAxisLabel '$advancedOpt.xAxisLabel' 62 --xAxisLabel '$advancedOpt.xAxisLabel'
63 #if str($advancedOpt.yAxisLabel.value) != "None": 63 #if str($advancedOpt.yAxisLabel.value) != "None":
64 --yAxisLabel '$advancedOpt.yAxisLabel' 64 --yAxisLabel '$advancedOpt.yAxisLabel'
65 #end if 65 #end if
66 #end if 66 #end if
67 ; mv $newoutFileName $outFileName
68 </command> 67 </command>
69 <inputs> 68 <inputs>
70 <param name="matrixFile" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/> 69 <param name="matrixFile" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/>
71 <conditional name="scaleRegions"> 70 <conditional name="scaleRegions">
72 <param name="showScaleRegionsOpt" type="select" label="The input matrix was computed in scale-regions mode"> 71 <param name="showScaleRegionsOpt" type="select" label="The input matrix was computed in scale-regions mode">
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;." /> 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;." />
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)."/> 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)."/>
80 </when> 79 </when>
81 </conditional> 80 </conditional>
82 81
83 <expand macro="graphic_output_settings" /> 82 <expand macro="graphic_output_settings">
83 <expand macro="image_file_format" />
84 <expand>
84 85
85 <conditional name="advancedOpt"> 86 <conditional name="advancedOpt">
86 <param name="showAdvancedOpt" type="select" label="Show advanced options" > 87 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
87 <option value="no" selected="true">no</option> 88 <option value="no" selected="true">no</option>
88 <option value="yes">yes</option> 89 <option value="yes">yes</option>
108 <option value="lines" selected="true">lines</option> 109 <option value="lines" selected="true">lines</option>
109 <option value="fill">fill</option> 110 <option value="fill">fill</option>
110 <option value="std">std</option> 111 <option value="std">std</option>
111 <option value="overlapped_lines">overlapped lines</option> 112 <option value="overlapped_lines">overlapped lines</option>
112 </param> 113 </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;."/> 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." /> 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."/> 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"/> 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"/> 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"/>
120 <param name="yAxisLabel" type="text" value="" size="50" label="Description for the y-axis label for the top panel" /> 120 <param name="yAxisLabel" type="text" value="" size="50" label="Description for the y-axis label for the top panel" />
121 </when> 121 </when>
122 </conditional> 122 </conditional>
123 </inputs> 123 </inputs>
124 <outputs> 124 <outputs>
125 <data format="png" name="outFileName" label="${tool.name} image"> 125 <expand macro="output_graphic_outputs" />
126 <change_format> 126 </outputs>
127 <when input="output.outFileFormat" value="pdf" format="pdf" /> 127 <help>
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>
144 128
145 **What it does** 129 **What it does**
146 130
147 This tool plots the average enrichments over all genomic 131 This tool plots the average enrichments over all genomic
148 regions supplied to computeMarix. It is a very useful complement to the 132 regions supplied to computeMarix. It is a very useful complement to the