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comparison heatmapper.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_heatmapper" name="heatmapper" version="@WRAPPER_VERSION@.0"> 1 <tool id="deeptools_heatmapper" name="heatmapper" version="@WRAPPER_VERSION@.0">
2 <description>creates a heatmap for a score associated to genomic regions</description> 2 <description>creates a heatmap for a score associated to genomic regions</description>
3 <expand macro="requirements"/>
4 <expand macro="stdio" />
5 <macros> 3 <macros>
6 <token name="@BINARY@">heatmapper</token> 4 <token name="@BINARY@">heatmapper</token>
7 <import>deepTools_macros.xml</import> 5 <import>deepTools_macros.xml</import>
8 </macros> 6 </macros>
7 <expand macro="requirements"/>
9 <command> 8 <command>
10 <![CDATA[ 9 <![CDATA[
11 heatmapper 10 heatmapper
12 11
13 --matrixFile $matrixFile 12 --matrixFile $matrixFile
74 --startLabel '$advancedOpt.startLabel' 73 --startLabel '$advancedOpt.startLabel'
75 --endLabel '$advancedOpt.endLabel' 74 --endLabel '$advancedOpt.endLabel'
76 --refPointLabel '$advancedOpt.referencePointLabel' 75 --refPointLabel '$advancedOpt.referencePointLabel'
77 --regionsLabel '$advancedOpt.regionsLabel' 76 --regionsLabel '$advancedOpt.regionsLabel'
78 77
79 #if str($advancedOpt.plotTitle.value) != "None": 78 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
80 --plotTitle '$advancedOpt.plotTitle' 79 --plotTitle '$advancedOpt.plotTitle'
81 #end if 80 #end if
82 81
83 $advancedOpt.onePlotPerGroup 82 $advancedOpt.onePlotPerGroup
84 83
175 <sanitizer> 174 <sanitizer>
176 <valid initial="string.printable"> 175 <valid initial="string.printable">
177 </valid> 176 </valid>
178 </sanitizer> 177 </sanitizer>
179 </param> 178 </param>
180 <param name="plotTitle" type="text" value="" size="30" 179 <expand macro="plotTitle" />
181 label="Title of the plot" help="Title of the plot, to be printed on top of the generated image. Leave blank for no title. (--plotTitle)" />
182 <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue="" 180 <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue=""
183 label="Do one plot per group" 181 label="Do one plot per group"
184 help="When computeMatrix was used on more than one group of genes, the average plots for all the groups will be drawn in one panel by default. If this option is set, each group will get its own plot, stacked on top of each other."/> 182 help="When computeMatrix was used on more than one group of genes, the average plots for all the groups will be drawn in one panel by default. If this option is set, each group will get its own plot, stacked on top of each other."/>
185 183
186 <expand macro="kmeans_clustering" /> 184 <expand macro="kmeans_clustering" />
192 <expand macro="output_graphic_outputs" /> 190 <expand macro="output_graphic_outputs" />
193 <expand macro="output_save_matrix_values" /> 191 <expand macro="output_save_matrix_values" />
194 </outputs> 192 </outputs>
195 <tests> 193 <tests>
196 <test> 194 <test>
197 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="bgzip" /> 195 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_matrix" />
198 <output name="outFileName" file="heatmapper_result1.png" ftype="png" compare="sim_size" delta="100" /> 196 <output name="outFileName" file="heatmapper_result1.png" ftype="png" compare="sim_size" delta="100" />
199 </test> 197 </test>
200 </tests> 198 </tests>
201 <help> 199 <help>
202 <![CDATA[ 200 <![CDATA[