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comparison deepTools_macros.xml @ 10:135f3bae5c56 draft

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author bgruening
date Sat, 14 Dec 2013 03:29:29 -0500
parents c53a73b8eef9
children baf4283e2d7f
comparison
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9:c53a73b8eef9 10:135f3bae5c56
41 <macro name="requirements"> 41 <macro name="requirements">
42 <requirements> 42 <requirements>
43 <requirement type="package" >samtools</requirement> 43 <requirement type="package" >samtools</requirement>
44 <requirement type="package" >deepTools</requirement> 44 <requirement type="package" >deepTools</requirement>
45 <requirement type="package" >ucsc_tools</requirement> 45 <requirement type="package" >ucsc_tools</requirement>
46 <requirement type="package" version="1.5.4_fada41ab04f78c4c78d10c7a216e5c3160e8c36e">deepTools</requirement> 46 <requirement type="package" version="1.5.4_6765c227d9628f8e6ba690e6fde7f1d86c497b49">deepTools</requirement>
47 <requirement type="package" version="0.1">ucsc_tools</requirement> 47 <requirement type="package" version="0.1">ucsc_tools</requirement>
48 <requirement type="package" version="1.7.1">numpy</requirement> 48 <requirement type="package" version="1.7.1">numpy</requirement>
49 <requirement type="package" version="0.7.7">pysam</requirement> 49 <requirement type="package" version="0.7.7">pysam</requirement>
50 <requirement type="package" version="0.12.0">scipy</requirement>
50 <requirement type="package" version="1.2.1">matplotlib</requirement> 51 <requirement type="package" version="1.2.1">matplotlib</requirement>
51 <requirement type="package" version="0.1.19">samtools</requirement> 52 <requirement type="package" version="0.1.19">samtools</requirement>
52 <requirement type="package" version="12-2013">bx-python</requirement> 53 <requirement type="package" version="12-2013">bx-python</requirement>
53 <yield /> 54 <yield />
54 </requirements> 55 </requirements>
55 </macro> 56 </macro>
56 57 <macro name="stdio">
58 <stdio>
59 <exit_code range="1:" />
60 <exit_code range=":-1" />
61 <exit_code range="0" level="warning" description="Warning" />
62 <regex match="Error:" />
63 <regex match="Exception:" />
64 <regex match="EXception:" />
65 </stdio>
66 </macro>
57 <token name="@REFERENCES@"> 67 <token name="@REFERENCES@">
58 68
59 For more informations, please visit our `project site`_. 69 For more informations, please visit our `project site`_.
60 70
61 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com 71 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
140 </param> 150 </param>
141 <when value="specific"> 151 <when value="specific">
142 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" /> 152 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" />
143 </when> 153 </when>
144 </conditional> 154 </conditional>
155 </macro>
156
157 <macro name="image_file_format">
158 <param name="outFileFormat" type="select" label="Image file format">
159 <option value="png" selected="true">png</option>
160 <option value="pdf">pdf</option>
161 <option value="svg">svg</option>
162 <option value="eps">eps</option>
163 <option value="emf">emf</option>
164 </param>
145 </macro> 165 </macro>
146 166
147 <macro name="graphic_output_settings"> 167 <macro name="graphic_output_settings">
148 <conditional name="output" > 168 <conditional name="output" >
149 <param name="showOutputSettings" type="select" label="Show advanced output settings" > 169 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
164 <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping 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."/> 184 <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping 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."/>
165 </when> 185 </when>
166 </conditional> 186 </conditional>
167 </macro> 187 </macro>
168 188
189 <macro name="output_graphic_outputs">
190 <data format="png" name="outFileName" label="${tool.name} image">
191 <change_format>
192 <when input="output.outFileFormat" value="pdf" format="pdf" />
193 <when input="output.outFileFormat" value="svg" format="svg" />
194 <when input="output.outFileFormat" value="eps" format="eps" />
195 <when input="output.outFileFormat" value="emf" format="emf" />
196 </change_format>
197 </data>
198 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
199 <filter>
200 ((
201 output['showOutputSettings'] == 'yes' and
202 output['saveData'] is True
203 ))
204 </filter>
205 </data>
206 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
207 <filter>
208 ((
209 output['showOutputSettings'] == 'yes' and
210 output['saveMatrix'] is True
211 ))
212 </filter>
213 </data>
214 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
215 <filter>
216 ((
217 output['showOutputSettings'] == 'yes' and
218 output['saveSortedRegions'] is True
219 ))
220 </filter>
221 </data>
222 </macro>
223
169 <macro name="colormap"> 224 <macro name="colormap">
170
171 <param name="colorMap" type="select" label="Color map to use for the heatmap" help=" Available color map names can be found here: http://www.astro.lsa.umich.edu/~msshin/science/code/matplotlib_cm/"> 225 <param name="colorMap" type="select" label="Color map to use for the heatmap" help=" Available color map names can be found here: http://www.astro.lsa.umich.edu/~msshin/science/code/matplotlib_cm/">
172 <option value="RdYlBu" selected="true">RdYlBu</option> 226 <option value="RdYlBu" selected="true">RdYlBu</option>
173 <option value="Accent">Accent</option> 227 <option value="Accent">Accent</option>
174 <option value="Spectral">Spectral</option> 228 <option value="Spectral">Spectral</option>
175 <option value="Set1">Set1</option> 229 <option value="Set1">Set1</option>