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comparison computeMatrix.xml @ 66:1dbd76a58d8b draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
author galaxyp
date Sat, 30 May 2015 13:55:46 -0400
parents 9bee2c86eeb1
children
comparison
equal deleted inserted replaced
65:9bee2c86eeb1 66:1dbd76a58d8b
61 --averageTypeBins '$advancedOpt.averageTypeBins' 61 --averageTypeBins '$advancedOpt.averageTypeBins'
62 $advancedOpt.missingDataAsZero 62 $advancedOpt.missingDataAsZero
63 $advancedOpt.skipZeros 63 $advancedOpt.skipZeros
64 --binSize $advancedOpt.binSize 64 --binSize $advancedOpt.binSize
65 65
66 #if $advancedOpt.minThreshold: 66 #if $advancedOpt.minThreshold is not None and str($advancedOpt.minThreshold) != '':
67 --minThreshold $advancedOpt.minThreshold 67 --minThreshold $advancedOpt.minThreshold
68 #end if 68 #end if
69 #if $advancedOpt.maxThreshold: 69 #if $advancedOpt.maxThreshold is not None and str($advancedOpt.maxThreshold) != '':
70 --maxThreshold $advancedOpt.maxThreshold 70 --maxThreshold $advancedOpt.maxThreshold
71 #end if 71 #end if
72 #if $advancedOpt.scale: 72 #if $advancedOpt.scale is not None and str($advancedOpt.scale) != '':
73 --scale $advancedOpt.scale 73 --scale $advancedOpt.scale
74 #end if 74 #end if
75 75
76 #end if 76 #end if
77 ]]> 77 ]]>
221 help="If set, all values are multiplied by this number. (--scale)"/> 221 help="If set, all values are multiplied by this number. (--scale)"/>
222 </when> 222 </when>
223 </conditional> 223 </conditional>
224 </inputs> 224 </inputs>
225 <outputs> 225 <outputs>
226 <data format="deeptools_matrix" name="outFileName" label="${tool.name} on ${on_string}: Matrix" /> 226 <data format="deeptools_compute_matrix_archive" name="outFileName" label="${tool.name} on ${on_string}: Matrix" />
227 <expand macro="output_graphic_outputs" /> 227 <expand macro="output_graphic_outputs" />
228 <expand macro="output_save_matrix_values" /> 228 <expand macro="output_save_matrix_values" />
229 </outputs> 229 </outputs>
230 <!-- 230 <!--
231 computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1 231 computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1
240 <param name="sortUsing" value="sum" /> 240 <param name="sortUsing" value="sum" />
241 <param name="averageTypeBins" value="sum" /> 241 <param name="averageTypeBins" value="sum" />
242 <param name="missingDataAsZero" value="True" /> 242 <param name="missingDataAsZero" value="True" />
243 <param name="beforeRegionStartLength" value="10" /> 243 <param name="beforeRegionStartLength" value="10" />
244 <param name="afterRegionStartLength" value="10" /> 244 <param name="afterRegionStartLength" value="10" />
245 <output name="outFileName" file="computeMatrix_result1.gz" ftype="deeptools_matrix" compare="sim_size" /> 245 <output name="outFileName" file="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />
246 </test> 246 </test>
247 <test> 247 <test>
248 <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" /> 248 <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" />
249 <param name="scoreFile" value="computeMatrix2.bw" ftype="bigwig" /> 249 <param name="scoreFile" value="computeMatrix2.bw" ftype="bigwig" />
250 <param name="showAdvancedOpt" value="yes" /> 250 <param name="showAdvancedOpt" value="yes" />
251 <param name="mode_select" value="reference-point" /> 251 <param name="mode_select" value="reference-point" />
252 <param name="binSize" value="10" /> 252 <param name="binSize" value="10" />
253 <param name="beforeRegionStartLength" value="10" /> 253 <param name="beforeRegionStartLength" value="10" />
254 <param name="afterRegionStartLength" value="10" /> 254 <param name="afterRegionStartLength" value="10" />
255 <output name="outFileName" file="computeMatrix_result2.gz" ftype="deeptools_matrix" compare="sim_size" /> 255 <output name="outFileName" file="computeMatrix_result2.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />
256 </test> 256 </test>
257 </tests> 257 </tests>
258 <help> 258 <help>
259 <![CDATA[ 259 <![CDATA[
260 **What it does** 260 **What it does**