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comparison computeMatrix.xml @ 10:135f3bae5c56 draft

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author bgruening
date Sat, 14 Dec 2013 03:29:29 -0500
parents c53a73b8eef9
children b4c5dd45778a
comparison
equal deleted inserted replaced
9:c53a73b8eef9 10:135f3bae5c56
1 <tool id="deeptools_computeMatrix" name="computeMatrix" version="1.0"> 1 <tool id="deeptools_computeMatrix" name="computeMatrix" version="1.0.2">
2 <description>summarizes and prepares an intermediary file containing scores associated with genomic regions that can be used afterwards to plot a heatmap or a profile</description> 2 <description>summarizes and prepares an intermediary file containing scores associated with genomic regions that can be used afterwards to plot a heatmap or a profile</description>
3 <expand macro="requirements" /> 3 <expand macro="requirements" />
4 <expand macro="stdio" />
4 <macros> 5 <macros>
5 <import>deepTools_macros.xml</import> 6 <import>deepTools_macros.xml</import>
6 </macros> 7 </macros>
7 <command> 8 <command>
8 #import tempfile 9 #import tempfile
114 </when> 115 </when>
115 116
116 <when value="reference-point"> 117 <when value="reference-point">
117 <param name="referencePoint" type="select" label="The reference point for the plotting"> 118 <param name="referencePoint" type="select" label="The reference point for the plotting">
118 <option value="TSS" selected="true">beginning of region (e.g. TSS)</option> 119 <option value="TSS" selected="true">beginning of region (e.g. TSS)</option>
119 <option value="TES">end of region (e.g. TES)</option> 120 <option value="TES">end of region (e.g. TES)</option>
120 <option value="center">center of region</option> 121 <option value="center">center of region</option>
121 </param> 122 </param>
122 123
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."/> 124 <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."/>
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."/> 125 <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."/>
125 126
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."/> 127 <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."/>
127 </when> 128 </when>
128 </conditional> 129 </conditional>
129 130
130 <conditional name="output" > 131 <expand macro="graphic_output_settings" />
131 <param name="showOutputSettings" type="select" label="Show additional output options" >
132 <option value="no" selected="true">no</option>
133 <option value="yes">yes</option>
134 </param>
135 <when value="no" />
136 <when value="yes">
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."/>
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."/>
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."/>
140 </when>
141 </conditional>
142 132
143 <conditional name="advancedOpt" > 133 <conditional name="advancedOpt" >
144 <param name="showAdvancedOpt" type="select" label="Show advanced options" > 134 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
145 <option value="no" selected="true">no</option> 135 <option value="no" selected="true">no</option>
146 <option value="yes">yes</option> 136 <option value="yes">yes</option>
181 </when> 171 </when>
182 </conditional> 172 </conditional>
183 173
184 </inputs> 174 </inputs>
185 <outputs> 175 <outputs>
186 <data format="bgzip" name="outFileName" label="${tool.name} on ${on_string}: Matrix"> 176 <data format="bgzip" name="outFileName" label="${tool.name} on ${on_string}: Matrix" />
187 </data> 177 <expand macro="output_graphic_outputs" />
188 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
189 <filter>
190 ((
191 output['showOutputSettings'] == 'yes' and
192 output['saveData'] is True
193 ))
194 </filter>
195 </data>
196 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
197 <filter>
198 ((
199 output['showOutputSettings'] == 'yes' and
200 output['saveMatrix'] is True
201 ))
202 </filter>
203 </data>
204 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
205 <filter>
206 ((
207 output['showOutputSettings'] == 'yes' and
208 output['saveSortedRegions'] is True
209 ))
210 </filter>
211 </data>
212 </outputs> 178 </outputs>
213 <!-- 179 <!--
214 computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1 180 computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1
215 --> 181 -->
216 <tests> 182 <tests>