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comparison computeMatrix.xml @ 52:411c871f4cfd

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Uploaded
author bgruening
date Sat, 03 Aug 2013 09:48:44 -0400
parents 6a2a7374450b
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51:6a2a7374450b 52:411c871f4cfd
42 --sortRegions '$advancedOpt.sortRegions' 42 --sortRegions '$advancedOpt.sortRegions'
43 --sortUsing '$advancedOpt.sortUsing' 43 --sortUsing '$advancedOpt.sortUsing'
44 --averageTypeBins '$advancedOpt.averageTypeBins' 44 --averageTypeBins '$advancedOpt.averageTypeBins'
45 $advancedOpt.missingDataAsZero 45 $advancedOpt.missingDataAsZero
46 $advancedOpt.skipZeros 46 $advancedOpt.skipZeros
47 $advancedOpt.binSize
47 48
48 #if $advancedOpt.minThreshold: 49 #if $advancedOpt.minThreshold:
49 --minThreshold $advancedOpt.minThreshold 50 --minThreshold $advancedOpt.minThreshold
50 #end if 51 #end if
51 #if $advancedOpt.maxThreshold: 52 #if $advancedOpt.maxThreshold:
122 <when value="yes"> 123 <when value="yes">
123 124
124 <param name="binSize" type="integer" value="100" min="1" optional="true" label="Length, in base pairs, of the non-overlapping bin for averaging the score over the regions length" /> 125 <param name="binSize" type="integer" value="100" min="1" optional="true" label="Length, in base pairs, of the non-overlapping bin for averaging the score over the regions length" />
125 126
126 <param name="sortRegions" type="select" label="Sort regions" 127 <param name="sortRegions" type="select" label="Sort regions"
127 help="Whether the output file should present the regions sorted."> 128 help="Whether the output file should present the regions sorted.">
128 <option value="no" selected="true">no ordering</option> 129 <option value="no" selected="true">no ordering</option>
129 <option value="descend">descending order</option> 130 <option value="descend">descending order</option>
130 <option value="ascend">ascending order</option> 131 <option value="ascend">ascending order</option>
131 </param> 132 </param>
132 133
170 </data> 171 </data>
171 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions"> 172 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
172 <filter>(output['showOutputSettings'] == 'yes' and output['saveSortedRegions'] == True)</filter> 173 <filter>(output['showOutputSettings'] == 'yes' and output['saveSortedRegions'] == True)</filter>
173 </data> 174 </data>
174 </outputs> 175 </outputs>
176 <!--
177 computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1
178 -->
179 <tests>
180 <test>
181 <param name="regionsFile" value="test2.bed" ftype="bed" />
182 <param name="scoreFile" value="test.bw" ftype="bigwig" />
183 <param name="advancedOpt.binSize" value="1" />
184 <param name="mode.beforeRegionStartLength" value="100" />
185 <param name="mode.afterRegionStartLength" value="100" />
186 <output name="outFileName" file="master.mat.gz" ftype="bgzip" compare="sim_size" delta="100" />
187 </test>
188 </tests>
175 <help> 189 <help>
176 **What it does** 190 **What it does**
177 191
178 This tool summarizes and prepares an intermediary file containing scores associated with genomic regions that can be used afterwards to plot a heatmap or a profile. Typically, these genomic regions are genes, but any other regions defined in a BED or GFF format can be used. This tool can also be used to filter and sort regions according to their score. 192 This tool summarizes and prepares an intermediary file containing scores associated with genomic regions that can be used afterwards to plot a heatmap or a profile. Typically, these genomic regions are genes, but any other regions defined in a BED or GFF format can be used. This tool can also be used to filter and sort regions according to their score.
179 193