comparison macros.xml @ 4:184dfd9e113d draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit f5db2969e8602eff32ec799d237875b911578fe5"
author iuc
date Thu, 09 Jan 2020 10:03:02 -0500
parents fd59d783248a
children a64dc31ab7f2
comparison
equal deleted inserted replaced
3:fd59d783248a 4:184dfd9e113d
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <token name="@CIRCOS_VERSION@">0.69.8</token> 3 <token name="@CIRCOS_VERSION@">0.69.8</token>
4 4
5 <token name="@WRAPPER_VERSION@">@CIRCOS_VERSION@+galaxy2</token> 5 <token name="@WRAPPER_VERSION@">@CIRCOS_VERSION@+galaxy3</token>
6 6
7 <xml name="requirements"> 7 <xml name="requirements">
8 <requirements> 8 <requirements>
9 <requirement type="package" version="@CIRCOS_VERSION@">circos</requirement> 9 <requirement type="package" version="@CIRCOS_VERSION@">circos</requirement>
10 <requirement type="package" version="2.7">python</requirement> 10 <requirement type="package" version="2.7">python</requirement>
139 <option value="set2-8-qual">Qualitative: Set2</option> 139 <option value="set2-8-qual">Qualitative: Set2</option>
140 <option value="set3-12-qual">Qualitative: Set3</option> 140 <option value="set3-12-qual">Qualitative: Set3</option>
141 </param> 141 </param>
142 </xml> 142 </xml>
143 143
144 <xml name="zdepth">
145 <param name="zdepth" type="float" value="" optional="true" label="Z-depth"
146 help="Optional. Datasets with a higher z-depth value are drawn on top of data sets with a lower value. Only useful if plotting multiple tracks"/>
147 </xml>
148
144 <xml name="font_select" 149 <xml name="font_select"
145 token_normal="true" 150 token_normal="true"
146 token_bold="false"> 151 token_bold="false">
147 <param name="font" type="select" label="Font"> 152 <param name="font" type="select" label="Font">
148 <option value="light">light</option> 153 <option value="light">light</option>
157 </xml> 162 </xml>
158 163
159 <xml name="axes"> 164 <xml name="axes">
160 <section name="sec_axes" title="Axes"> 165 <section name="sec_axes" title="Axes">
161 <repeat name="axes" title="Axis"> 166 <repeat name="axes" title="Axis">
162 <param name="y0" type="float" value="0" min="0" max="1" label="Inside Radius" help="Value must be between 1 (outer edge of track) and 0 (inner edge of the track)"/> 167 <param name="y0" type="float" value="0" label="Inside Radius" help="Values are according to minimum and maximum values of dataset. E.g. if your dataset goes from -10 to 10, y0 should be -10"/>
163 <param name="y1" type="float" value="1" min="0" max="1" label="Outside Radius" help="Value must be between 1 (outer edge of track) and 0 (inner edge of the track)"/> 168 <param name="y1" type="float" value="1" label="Outside Radius" help="Values are according to minimum and maximum values of dataset. E.g. if your dataset goes from -10 to 10, y1 should be 10"/>
164 169
165 <expand macro="circos_color"/> 170 <expand macro="circos_color"/>
166 <param name="thickness" type="integer" value="1" label="Thickness"/> 171 <param name="thickness" type="integer" value="1" label="Thickness"/>
167 <param name="spacing" type="float" value="0.1" label="Spacing" help="Relative spacing between each concentric arc"/> 172 <param name="spacing" type="float" value="0.1" label="Spacing" help="Relative spacing between each concentric arc"/>
168 </repeat> 173 </repeat>
193 <option value="var">Apply based on qualifier value (when available)</option> 198 <option value="var">Apply based on qualifier value (when available)</option>
194 </param> 199 </param>
195 <when value="1"> 200 <when value="1">
196 </when> 201 </when>
197 <when value="on"> 202 <when value="on">
198 <param name="on_genomes" type="text" label="Comma separated list of contig IDs"/> 203 <param name="on_genomes" type="text" label="Contig IDs" help="Pipe | separated list of contig IDs">
204 <sanitizer>
205 <valid initial="string.letters,string.digits">
206 <add value="|" />
207 </valid>
208 </sanitizer>
209 </param>
199 </when> 210 </when>
200 <when value="pos"> 211 <when value="pos">
201 <param name="pos_gt" type="float" label="Greater than this base" optional="true"/> 212 <param name="pos_gt" type="float" label="Greater than this base" optional="true"/>
202 <param name="pos_lt" type="float" label="Less than this base" optional="true"/> 213 <param name="pos_lt" type="float" label="Less than this base" optional="true"/>
203 <param name="pos_lt_sub" type="boolean" truevalue="yes" falsevalue="no" label="Count 'Less than this base' from end of chromosome" /> 214 <param name="pos_lt_sub" type="boolean" truevalue="yes" falsevalue="no" label="Count 'Less than this base' from end of chromosome" />
230 <add value="%" /> 241 <add value="%" />
231 </valid> 242 </valid>
232 </sanitizer> 243 </sanitizer>
233 </param> 244 </param>
234 245
235 <param name="varvalue" type="text" label="Qualifier value to compare against"/> 246 <param name="varvalue" type="text" label="Qualifier value to compare against">
247 <sanitizer>
248 <valid initial="string.letters,string.digits">
249 </valid>
250 </sanitizer>
251 </param>
236 </when> 252 </when>
237 </conditional> 253 </conditional>
238 </repeat> 254 </repeat>
239 <repeat name="actions" title="Actions to Apply"> 255 <repeat name="actions" title="Actions to Apply">
240 <conditional name="action"> 256 <conditional name="action">