Mercurial > repos > iuc > circos
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 |
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| 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"> |