Mercurial > repos > bgruening > deeptools

comparison deepTools_macros.xml @ 22:8710187d1eb5 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bgruening
date Thu, 12 Dec 2013 18:11:46 -0500
parents 8436c195dd6c
children b8ba675a5895
comparison
equal deleted inserted replaced
21:8436c195dd6c 22:8710187d1eb5
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_fada41ab04f78c4c78d10c7a216e5c3160e8c36e">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
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>
145 </macro> 155 </macro>
146 156
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>
165 </macro>
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" >
150 <option value="no" selected="true">no</option> 170 <option value="no" selected="true">no</option>
151 <option value="yes">yes</option> 171 <option value="yes">yes</option>
152 </param> 172 </param>
153 <when value="no" /> 173 <when value="no" />
154 <when value="yes"> 174 <when value="yes">
155 <param name="outFileFormat" type="select" label="Image file format"> 175 <yield />
156 <option value="png" selected="true">png</option>
157 <option value="pdf">pdf</option>
158 <option value="svg">svg</option>
159 <option value="eps">eps</option>
160 <option value="emf">emf</option>
161 </param>
162 <param name="saveData" type="boolean" label="Save the data underlying data for the average profile"/> 176 <param name="saveData" type="boolean" label="Save the data underlying data for the average profile"/>
163 <param name="saveMatrix" type="boolean" label="Save the the matrix of values underlying the heatmap"/> 177 <param name="saveMatrix" type="boolean" label="Save the the matrix of values underlying the heatmap"/>
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."/> 178 <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> 179 </when>
166 </conditional> 180 </conditional>
167 </macro> 181 </macro>
168 182
183 <macro name="output_graphic_outputs">
184 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
185 <filter>
186 ((
187 output['showOutputSettings'] == 'yes' and
188 output['saveData'] is True
189 ))
190 </filter>
191 </data>
192 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
193 <filter>
194 ((
195 output['showOutputSettings'] == 'yes' and
196 output['saveMatrix'] is True
197 ))
198 </filter>
199 </data>
200 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
201 <filter>
202 ((
203 output['showOutputSettings'] == 'yes' and
204 output['saveSortedRegions'] is True
205 ))
206 </filter>
207 </data>
208 </macros>
209
169 <macro name="colormap"> 210 <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/"> 211 <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> 212 <option value="RdYlBu" selected="true">RdYlBu</option>
173 <option value="Accent">Accent</option> 213 <option value="Accent">Accent</option>
174 <option value="Spectral">Spectral</option> 214 <option value="Spectral">Spectral</option>
175 <option value="Set1">Set1</option> 215 <option value="Set1">Set1</option>