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comparison profiler.xml @ 65:9bee2c86eeb1 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
author iuc
date Mon, 25 May 2015 05:16:10 -0400
parents f3140d17939e
children 1dbd76a58d8b
comparison
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64:627004611e98 65:9bee2c86eeb1
1 <tool id="deeptools_profiler" name="profiler" version="@WRAPPER_VERSION@.0"> 1 <tool id="deeptools_profiler" name="profiler" version="@WRAPPER_VERSION@.0">
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" />
6 <expand macro="stdio" />
7 <macros> 5 <macros>
8 <token name="@BINARY@">profiler</token> 6 <token name="@BINARY@">profiler</token>
9 <import>deepTools_macros.xml</import> 7 <import>deepTools_macros.xml</import>
10 </macros> 8 </macros>
9 <expand macro="requirements" />
11 <command> 10 <command>
12 <![CDATA[ 11 <![CDATA[
13 profiler 12 profiler
14 13
15 --matrixFile $matrixFile 14 --matrixFile $matrixFile
42 --plotWidth $advancedOpt.plotWidth 41 --plotWidth $advancedOpt.plotWidth
43 --plotType $advancedOpt.plotType 42 --plotType $advancedOpt.plotType
44 43
45 --regionsLabel '$advancedOpt.regionsLabel' 44 --regionsLabel '$advancedOpt.regionsLabel'
46 45
47 #if str($advancedOpt.plotTitle).strip() != "": 46 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle).strip() != "":
48 --plotTitle '$advancedOpt.plotTitle' 47 --plotTitle '$advancedOpt.plotTitle'
49 #end if 48 #end if
50 49
51 #if str($advancedOpt.colors).strip() != "": 50 #if str($advancedOpt.colors).strip() != "":
52 --colors #echo ' '.join( ["'%s'" % $color for $color in $advancedOpt.colors.split()] )# 51 --colors #echo ' '.join( ["'%s'" % $color for $color in $advancedOpt.colors.split()] )#
80 </param> 79 </param>
81 <when value="no" /> 80 <when value="no" />
82 <when value="yes"> 81 <when value="yes">
83 <param name="startLabel" type="text" value="TSS" size="10" 82 <param name="startLabel" type="text" value="TSS" size="10"
84 label="Label for the region start" 83 label="Label for the region start"
85 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;." /> 84 help ="[only for scale-regions mode] Label shown in the plot
85 for the start of the region. Default is TSS (transcription start site),
86 but could be changed to anything, e.g. &quot;peak start&quot;." />
86 <param name="endLabel" type="text" value="TES" size="10" 87 <param name="endLabel" type="text" value="TES" size="10"
87 label="Label for the region end" 88 label="Label for the region end"
88 help="[only for scale-regions mode] Label shown in the plot for the region end. Default is TES (transcription end site)."/> 89 help="[only for scale-regions mode] Label shown in the plot for the region end. Default is TES (transcription end site)."/>
89 </when> 90 </when>
90 </conditional> 91 </conditional>
113 help="Height in cm. The default for the plot height is 5 centimeters. The minimum value is 3 cm." /> 114 help="Height in cm. The default for the plot height is 5 centimeters. The minimum value is 3 cm." />
114 <param name="plotWidth" type="integer" value="8" min="1" 115 <param name="plotWidth" type="integer" value="8" min="1"
115 label="Plot width" 116 label="Plot width"
116 help="Width in cm. The default value is 8 centimeters. The minimum value is 1 cm." /> 117 help="Width in cm. The default value is 8 centimeters. The minimum value is 1 cm." />
117 <param name="plotType" type="select" label="Plot type" 118 <param name="plotType" type="select" label="Plot type"
118 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."> 119 help="For the summary plot (profile) only. The &quot;lines&quot; option will
120 plot the profile line based on the average type selected. The &quot;fill&quot;
121 option fills the region between zero and the profile curve. The fill in color is
122 semi transparent to distinguish different profiles. The &quot;add standard error&quot;
123 option colors the region between the profile and the standard error of the data.
124 As in the case of fill, a semi-transparent color is used.
125 The option &quot;overlapped_lines&quot; plots each region values, one on top of
126 the other; this option only works if &quot;one plot per proup&quot; is set.">
119 <option value="lines" selected="true">lines</option> 127 <option value="lines" selected="true">lines</option>
120 <option value="fill">fill</option> 128 <option value="fill">fill</option>
121 <option value="se">add standard error</option> 129 <option value="se">add standard error</option>
122 <option value="overlapped_lines">overlapped lines</option> 130 <option value="overlapped_lines">overlapped lines</option>
123 </param> 131 </param>
124 <param name="regionsLabel" type="text" value="genes" size="30" 132 <param name="regionsLabel" type="text" value="genes" size="30"
125 label="Labels for the regions plotted in the heatmap" 133 label="Labels for the regions plotted in the heatmap"
126 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;."/> 134 help="If more than one region is being plotted a list of labels separated
127 <param name="plotTitle" type="text" value="" size="30" 135 by comma and limited by quotes, is required. For example, &quot;label1, label2&quot;."/>
128 label="Title of the plot" 136
129 help="Title of the plot, to be printed on top of the generated image. Leave blank for no title." /> 137 <expand macro="plotTitle" />
130 <param name="colors" type="text" value="" size="40" 138 <param name="colors" type="text" value="" size="40"
131 label="List of colors to use for the plotted lines" 139 label="List of colors to use for the plotted lines"
132 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)"> 140 help="Color names and html hex strings (e.g. #eeff22) are accepted.
141 The color names should be given separated by spaces. (--colors red blue green)">
133 <validator type="expression" 142 <validator type="expression"
134 message="Only numbers, digits, '#' and spaces are allowed.">all(c in ' #abcdefghijklmnopqrstuvwxyz0123456789' for c in value)</validator> 143 message="Only numbers, digits, '#' and spaces are allowed.">all(c in ' #abcdefghijklmnopqrstuvwxyz0123456789' for c in value)</validator>
135 </param> 144 </param>
136 145
137 <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue="" 146 <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue=""
138 label="Do one plot per group" 147 label="Do one plot per group"
139 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."/> 148 help="When the region file contains groups separated by &quot;#&quot;, the default is
149 to plot the averages for the distinct plots in one plot. If this option is set, each group
150 will get its own plot, stacked on top of each other."/>
140 <param name="yMin" type="float" value="" size="3" optional="true" 151 <param name="yMin" type="float" value="" size="3" optional="true"
141 label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values"/> 152 label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values"/>
142 <param name="yMax" type="float" value="" size="3" optional="true" 153 <param name="yMax" type="float" value="" size="3" optional="true"
143 label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" /> 154 label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" />
144 <param name="xAxisLabel" type="text" value="gene distance (bp)" size="50" 155 <param name="xAxisLabel" type="text" value="gene distance (bp)" size="50"
153 </inputs> 164 </inputs>
154 <outputs> 165 <outputs>
155 <expand macro="output_image_file_format" /> 166 <expand macro="output_image_file_format" />
156 <expand macro="output_graphic_outputs" /> 167 <expand macro="output_graphic_outputs" />
157 </outputs> 168 </outputs>
169 <tests>
170 <test>
171 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_matrix" />
172 <output name="outFileName" file="profiler_result1.png" ftype="png" compare="sim_size" delta="100" />
173 </test>
174 </tests>
158 <help> 175 <help>
159 <![CDATA[ 176 <![CDATA[
177
160 **What it does** 178 **What it does**
161 179
162 This tool plots the average enrichments over all genomic 180 This tool plots the average enrichments over all genomic
163 regions supplied to computeMarix. It requires that computeMatrix was successfully run. 181 regions supplied to computeMarix. It requires that computeMatrix was successfully run.
164 It is a very useful complement to the heatmapper, especially in cases when you want to 182 It is a very useful complement to the heatmapper, especially in cases when you want to