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comparison profiler.xml @ 30:5231f398d784 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
author bgruening
date Tue, 20 Oct 2015 14:43:12 -0400
parents 3a2aab18a217
children
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29:3a2aab18a217 30:5231f398d784
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>
11 <![CDATA[
12 profiler 12 profiler
13 13
14 --matrixFile $matrixFile 14 --matrixFile $matrixFile
15 --outFileName $outFileName 15 --outFileName $outFileName
16 16
27 #else 27 #else
28 --plotFileFormat 'png' 28 --plotFileFormat 'png'
29 #end if 29 #end if
30 30
31 #if $scaleRegions.showScaleRegionsOpt == "yes": 31 #if $scaleRegions.showScaleRegionsOpt == "yes":
32 --startLabel $scaleRegions.startLabel 32 --startLabel '$scaleRegions.startLabel'
33 --endLabel $scaleRegions.endLabel 33 --endLabel '$scaleRegions.endLabel'
34 #end if 34 #end if
35 35
36 #if $advancedOpt.showAdvancedOpt == "yes": 36 #if $advancedOpt.showAdvancedOpt == "yes":
37 #if $advancedOpt.averageType: 37 #if $advancedOpt.averageType:
38 --averageType '$advancedOpt.averageType' 38 --averageType '$advancedOpt.averageType'
41 --plotWidth $advancedOpt.plotWidth 41 --plotWidth $advancedOpt.plotWidth
42 --plotType $advancedOpt.plotType 42 --plotType $advancedOpt.plotType
43 43
44 --regionsLabel '$advancedOpt.regionsLabel' 44 --regionsLabel '$advancedOpt.regionsLabel'
45 45
46 #if str($advancedOpt.plotTitle).strip() != "": 46 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle).strip() != "":
47 --plotTitle '$advancedOpt.plotTitle' 47 --plotTitle '$advancedOpt.plotTitle'
48 #end if 48 #end if
49 49
50 #if str($advancedOpt.colors).strip() != "": 50 #if str($advancedOpt.colors).strip() != "":
51 --colors #echo ' '.join( ["'%s'" % $color for $color in $advancedOpt.colors.split()] )# 51 --colors #echo ' '.join( ["'%s'" % $color for $color in $advancedOpt.colors.split()] )#
63 --xAxisLabel '$advancedOpt.xAxisLabel' 63 --xAxisLabel '$advancedOpt.xAxisLabel'
64 #if str($advancedOpt.yAxisLabel.value) != "None": 64 #if str($advancedOpt.yAxisLabel.value) != "None":
65 --yAxisLabel '$advancedOpt.yAxisLabel' 65 --yAxisLabel '$advancedOpt.yAxisLabel'
66 #end if 66 #end if
67 67
68 @kmeans_clusterin@ 68 @KMEANS_CLUSTERING@
69 69
70 #end if 70 #end if
71 ]]>
71 </command> 72 </command>
72 <inputs> 73 <inputs>
73 <param name="matrixFile" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/> 74 <param name="matrixFile" format="deeptools_compute_matrix_archive" type="data" label="Matrix file from the computeMatrix tool"/>
74 <conditional name="scaleRegions"> 75 <conditional name="scaleRegions">
75 <param name="showScaleRegionsOpt" type="select" label="The input matrix was computed in scale-regions mode"> 76 <param name="showScaleRegionsOpt" type="select" label="The input matrix was computed in scale-regions mode">
76 <option value="no" selected="true">no</option> 77 <option value="no" selected="true">no</option>
77 <option value="yes">yes</option> 78 <option value="yes">yes</option>
78 </param> 79 </param>
79 <when value="no" /> 80 <when value="no" />
80 <when value="yes"> 81 <when value="yes">
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;." /> 82 <param name="startLabel" type="text" value="TSS" size="10"
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)."/> 83 label="Label for the region start"
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;." />
87 <param name="endLabel" type="text" value="TES" size="10"
88 label="Label for the region end"
89 help="[only for scale-regions mode] Label shown in the plot for the region end. Default is TES (transcription end site)."/>
83 </when> 90 </when>
84 </conditional> 91 </conditional>
85 92
86 <expand macro="input_graphic_output_settings"> 93 <expand macro="input_graphic_output_settings">
87 <expand macro="input_image_file_format" /> 94 <expand macro="input_image_file_format" />
107 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." />
108 <param name="plotWidth" type="integer" value="8" min="1" 115 <param name="plotWidth" type="integer" value="8" min="1"
109 label="Plot width" 116 label="Plot width"
110 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." />
111 <param name="plotType" type="select" label="Plot type" 118 <param name="plotType" type="select" label="Plot type"
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."> 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.">
113 <option value="lines" selected="true">lines</option> 127 <option value="lines" selected="true">lines</option>
114 <option value="fill">fill</option> 128 <option value="fill">fill</option>
115 <option value="se">add standard error</option> 129 <option value="se">add standard error</option>
116 <option value="overlapped_lines">overlapped lines</option> 130 <option value="overlapped_lines">overlapped lines</option>
117 </param> 131 </param>
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;."/> 132 <param name="regionsLabel" type="text" value="genes" size="30"
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." /> 133 label="Labels for the regions plotted in the heatmap"
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)"> 134 help="If more than one region is being plotted a list of labels separated
121 <validator type="expression" message="Only numbers, digits, '#' and spaces are allowed.">all(c in ' #abcdefghijklmnopqrstuvwxyz0123456789' for c in value)</validator> 135 by comma and limited by quotes, is required. For example, &quot;label1, label2&quot;."/>
136
137 <expand macro="plotTitle" />
138 <param name="colors" type="text" value="" size="40"
139 label="List of colors to use for the plotted lines"
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)">
142 <validator type="expression"
143 message="Only numbers, digits, '#' and spaces are allowed.">all(c in ' #abcdefghijklmnopqrstuvwxyz0123456789' for c in value)</validator>
122 </param> 144 </param>
123 145
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."/> 146 <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue=""
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"/> 147 label="Do one plot per group"
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"/> 148 help="When the region file contains groups separated by &quot;#&quot;, the default is
127 <param name="xAxisLabel" type="text" value="gene distance (bp)" size="50" label="Description for the x-axis label" /> 149 to plot the averages for the distinct plots in one plot. If this option is set, each group
128 <param name="yAxisLabel" type="text" value="" size="50" label="Description for the y-axis label for the top panel" /> 150 will get its own plot, stacked on top of each other."/>
151 <param name="yMin" type="float" value="" size="3" optional="true"
152 label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values"/>
153 <param name="yMax" type="float" value="" size="3" optional="true"
154 label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" />
155 <param name="xAxisLabel" type="text" value="gene distance (bp)" size="50"
156 label="Description for the x-axis label" />
157 <param name="yAxisLabel" type="text" value="" size="50"
158 label="Description for the y-axis label for the top panel" />
129 159
130 <expand macro="kmeans_clustering" /> 160 <expand macro="kmeans_clustering" />
131 161
132 </when> 162 </when>
133 </conditional> 163 </conditional>
134 </inputs> 164 </inputs>
135 <outputs> 165 <outputs>
136 <expand macro="output_image_file_format" /> 166 <expand macro="output_image_file_format" />
137 <expand macro="output_graphic_outputs" /> 167 <expand macro="output_graphic_outputs" />
138 </outputs> 168 </outputs>
169 <tests>
170 <test>
171 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
172 <output name="outFileName" file="profiler_result1.png" ftype="png" compare="sim_size" delta="100" />
173 </test>
174 </tests>
139 <help> 175 <help>
176 <![CDATA[
140 177
141 **What it does** 178 **What it does**
142 179
143 This tool plots the average enrichments over all genomic 180 This tool plots the average enrichments over all genomic
144 regions supplied to computeMarix. It requires that computeMatrix was successfully run. 181 regions supplied to computeMarix. It requires that computeMatrix was successfully run.
156 193
157 194
158 ----- 195 -----
159 196
160 @REFERENCES@ 197 @REFERENCES@
161 198 ]]>
162 </help> 199 </help>
163 <expand macro="citations" /> 200 <expand macro="citations" />
164 </tool> 201 </tool>