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comparison computeMatrix.xml @ 9:c53a73b8eef9 draft

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author bgruening
date Tue, 10 Dec 2013 12:13:18 -0500
parents d957e25e18a3
children 135f3bae5c56
comparison
equal deleted inserted replaced
8:1c5ed9126db6 9:c53a73b8eef9
113 </conditional> 113 </conditional>
114 </when> 114 </when>
115 115
116 <when value="reference-point"> 116 <when value="reference-point">
117 <param name="referencePoint" type="select" label="The reference point for the plotting"> 117 <param name="referencePoint" type="select" label="The reference point for the plotting">
118 <option value="TSS" selected="true">region start (TSS)</option> 118 <option value="TSS" selected="true">beginning of region (e.g. TSS)</option>
119 <option value="TES" selected="true">region end (TES)</option> 119 <option value="TES">end of region (e.g. TES)</option>
120 <option value="center" selected="true">center of the region</option> 120 <option value="center">center of region</option>
121 </param> 121 </param>
122
122 <param name="nanAfterEnd" type="boolean" truevalue="--nanAfterEnd" falsevalue="" label="Discard any values after the region end" help="This is useful to visualize the region end when not using the scale-regions mode and when the reference-point is set to the TSS."/> 123 <param name="nanAfterEnd" type="boolean" truevalue="--nanAfterEnd" falsevalue="" label="Discard any values after the region end" help="This is useful to visualize the region end when not using the scale-regions mode and when the reference-point is set to the TSS."/>
123 <param name="beforeRegionStartLength" type="integer" value="1000" min="1" label="Distance upstream of the start site of the regions defined in the region file" help="If the regions are genes, this would be the distance upstream of the transcription start site."/> 124 <param name="beforeRegionStartLength" type="integer" value="1000" min="1" label="Distance upstream of the start site of the regions defined in the region file" help="If the regions are genes, this would be the distance upstream of the transcription start site."/>
124 125
125 <param name="afterRegionStartLength" type="integer" value="1000" min="1" label="Distance downstream of the end site of the given regions" help="If the regions are genes, this would be the distance downstream of the transcription end site."/> 126 <param name="afterRegionStartLength" type="integer" value="1000" min="1" label="Distance downstream of the end site of the given regions" help="If the regions are genes, this would be the distance downstream of the transcription end site."/>
126 </when> 127 </when>
127 </conditional> 128 </conditional>
128 129
129 <conditional name="output" > 130 <conditional name="output" >
130 <param name="showOutputSettings" type="select" label="Show additional output options" > 131 <param name="showOutputSettings" type="select" label="Show additional output options" >
131 <option value="no" selected="true">no</option> 132 <option value="no" selected="true">no</option>
132 <option value="yes">yes</option> 133 <option value="yes">yes</option>
133 </param> 134 </param>
134 <when value="no" /> 135 <when value="no" />
135 <when value="yes"> 136 <when value="yes">
136 <param name="saveData" type="boolean" label="Save the averages per matrix column into a text file" help="This corresponds to the underlying data used to plot a summary profile."/> 137 <param name="saveData" type="boolean" label="Save the averages per matrix column into a text file" help="This corresponds to the underlying data used to plot a summary profile."/>
137 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap" help="This matrix can easily be loaded into R or other programs."/> 138 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap" help="This matrix can easily be loaded into R or other programs."/>
138 <param name="saveSortedRegions" type="boolean" label="Save the regions after skiping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/> 139 <param name="saveSortedRegions" type="boolean" label="Save the regions after skiping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
139 </when> 140 </when>
140 </conditional> 141 </conditional>
141 142
142 <conditional name="advancedOpt" > 143 <conditional name="advancedOpt" >
143 <param name="showAdvancedOpt" type="select" label="Show advanced options" > 144 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
144 <option value="no" selected="true">no</option> 145 <option value="no" selected="true">no</option>
180 </when> 181 </when>
181 </conditional> 182 </conditional>
182 183
183 </inputs> 184 </inputs>
184 <outputs> 185 <outputs>
185 <data format="bgzip" name="outFileName" label="${tool.name} on ${on_string}: matrix"> 186 <data format="bgzip" name="outFileName" label="${tool.name} on ${on_string}: Matrix">
186 </data> 187 </data>
187 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: raw data"> 188 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
188 <filter>(output['showOutputSettings'] == 'yes' and output['saveData'] == True)</filter> 189 <filter>
189 </data> 190 ((
190 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: matrix of values"> 191 output['showOutputSettings'] == 'yes' and
191 <filter>(output['showOutputSettings'] == 'yes' and output['saveMatrix'] == True)</filter> 192 output['saveData'] is True
193 ))
194 </filter>
195 </data>
196 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
197 <filter>
198 ((
199 output['showOutputSettings'] == 'yes' and
200 output['saveMatrix'] is True
201 ))
202 </filter>
192 </data> 203 </data>
193 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions"> 204 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
194 <filter>(output['showOutputSettings'] == 'yes' and output['saveSortedRegions'] == True)</filter> 205 <filter>
195 </data> 206 ((
207 output['showOutputSettings'] == 'yes' and
208 output['saveSortedRegions'] is True
209 ))
210 </filter>
211 </data>
196 </outputs> 212 </outputs>
197 <!-- 213 <!--
198 computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1 214 computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1
199 --> 215 -->
200 <tests> 216 <tests>