Mercurial > repos > eric-rasche > circos
comparison macros_conffiles.xml @ 8:eb3af6e9f633 draft
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 3ac672baa4a93250828fd4a450cb5689b0b03474
| author | eric-rasche |
|---|---|
| date | Sat, 10 Jun 2017 16:21:01 -0400 |
| parents | b72f2db6d417 |
| children | e6440d0201f7 |
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| 7:b72f2db6d417 | 8:eb3af6e9f633 |
|---|---|
| 164 condition = var(${condition.application.varname}) ${condition.application.cond_select} "${condition.application.varvalue}" | 164 condition = var(${condition.application.varname}) ${condition.application.cond_select} "${condition.application.varvalue}" |
| 165 #end if | 165 #end if |
| 166 #end for | 166 #end for |
| 167 | 167 |
| 168 #for $action in $rule.actions: | 168 #for $action in $rule.actions: |
| 169 #set x_fill_color = $action.action.action_value | |
| 170 #set x_fill_color_count = int(str($x_fill_color).split('-')[1]) + 1 | |
| 171 #set x_fill_color_qw = ' '.join(["%s-%s" % ($action.action.action_value, $i) for i in range(1, $x_fill_color_count)]) | |
| 172 | |
| 173 #if str($action.action.action_select) == "fill_color_value" or str($action.action.action_select) == "color_value" : | 169 #if str($action.action.action_select) == "fill_color_value" or str($action.action.action_select) == "color_value" : |
| 174 fill_color = eval(qw(${x_fill_color_qw})[remap_int(var(value), ${action.action.min_value}, ${action.action.max_value}, 0, ${x_fill_color_count - 1})]) | 170 #set x_fill_color = $action.action.action_value |
| 171 #set x_fill_color_count = int(str($x_fill_color).split('-')[1]) | |
| 172 #set x_min = $x_fill_color_count if $action.action.invert else 1 | |
| 173 #set x_max = 1 if $action.action.invert else $x_fill_color_count | |
| 174 | |
| 175 fill_color = eval(sprintf("${action.action.action_value}-%d", remap_int(var(value), ${action.action.min_value}, ${action.action.max_value}, ${x_min}, ${x_max}))) | |
| 175 #else | 176 #else |
| 176 $action.action.action_select = ${action.action.action_value} | 177 $action.action.action_select = ${action.action.action_value} |
| 177 #end if | 178 #end if |
| 178 #end for | 179 #end for |
| 179 $rule.continue_flow | 180 $rule.continue_flow |
| 282 #if $action.action.dynamic.dynamic_select == "static": | 283 #if $action.action.dynamic.dynamic_select == "static": |
| 283 #set actionval = $circosColor($action.action.dynamic.action_value) | 284 #set actionval = $circosColor($action.action.dynamic.action_value) |
| 284 $actiontype = $actionval | 285 $actiontype = $actionval |
| 285 #else | 286 #else |
| 286 #set x_fill_color = $action.action.dynamic.action_value | 287 #set x_fill_color = $action.action.dynamic.action_value |
| 287 #set x_fill_color_count = int(str($x_fill_color).split('-')[1]) + 1 | 288 #set x_fill_color_count = int(str($x_fill_color).split('-')[1]) |
| 288 #set x_fill_color_qw = ' '.join(["%s-%s" % ($action.action.dynamic.action_value, $i) for i in range(1, $x_fill_color_count)]) | 289 #set x_min = $x_fill_color_count if $action.action.dynamic.invert else 1 |
| 289 $actiontype = eval(qw(${x_fill_color_qw})[remap_int(var(value), ${action.action.dynamic.min_value}, ${action.action.dynamic.max_value}, 0, ${x_fill_color_count - 1})]) | 290 #set x_max = 1 if $action.action.dynamic.invert else $x_fill_color_count |
| 291 | |
| 292 $actiontype = eval(sprintf("${action.action.dynamic.action_value}-%d", remap_int(var(value), ${action.action.dynamic.min_value}, ${action.action.dynamic.max_value}, ${x_min}, ${x_max}))) | |
| 290 #end if | 293 #end if |
| 291 #else | 294 #else |
| 292 #set actionval = $action.action.action_value | 295 #set actionval = $action.action.action_value |
| 293 $actiontype = $actionval | 296 $actiontype = $actionval |
| 294 #end if | 297 #end if |
| 340 <!-- | 343 <!-- |
| 341 mkdir -p test-data/my-test-case/; | 344 mkdir -p test-data/my-test-case/; |
| 342 #if $reference_genome.reference_genome_source == 'history': | 345 #if $reference_genome.reference_genome_source == 'history': |
| 343 cp ${genome_fasta} test-data/my-test-case/input.fa; | 346 cp ${genome_fasta} test-data/my-test-case/input.fa; |
| 344 #end if | 347 #end if |
| 345 #if $ideogram.bands: | 348 |
| 346 cp ${ideogram.bands} test-data/my-test-case/bands.${ideogram.bands.ext}; | 349 #if $reference_genome.reference_genome_source != 'karyotype': |
| 350 #if $reference_genome.bands: | |
| 351 cp ${reference_genome.bands} test-data/my-test-case/bands.${reference_genome.bands.ext}; | |
| 347 #end if | 352 #end if |
| 353 #end if | |
| 354 | |
| 348 #for $idx, $data in enumerate($sec_tdd.data): | 355 #for $idx, $data in enumerate($sec_tdd.data): |
| 349 #if str($data.plot_format.plot_format_select) in ('histogram', 'heatmap'): | 356 #if str($data.plot_format.plot_format_select) in ('histogram', 'heatmap'): |
| 350 #for $jdx, $file in enumerate($data.plot_format.data_source): | 357 #for $jdx, $file in enumerate($data.plot_format.data_source): |
| 351 cp ${file} test-data/my-test-case/${idx}-${jdx}.${file.ext}; | 358 cp ${file} test-data/my-test-case/${idx}-${jdx}.${file.ext}; |
| 352 #end for | 359 #end for |
| 364 <param name="ideogram|spacing" value="${ideogram.spacing}" /> | 371 <param name="ideogram|spacing" value="${ideogram.spacing}" /> |
| 365 <param name="ideogram|radius" value="${ideogram.radius}" /> | 372 <param name="ideogram|radius" value="${ideogram.radius}" /> |
| 366 <param name="ideogram|thickness" value="${ideogram.thickness}" /> | 373 <param name="ideogram|thickness" value="${ideogram.thickness}" /> |
| 367 <param name="ideogram|ideogram_labels|show_label" value="${ideogram.ideogram_labels.show_label}" /> | 374 <param name="ideogram|ideogram_labels|show_label" value="${ideogram.ideogram_labels.show_label}" /> |
| 368 <param name="ideogram|ideogram_labels|parallel" value="${ideogram.ideogram_labels.parallel}" /> | 375 <param name="ideogram|ideogram_labels|parallel" value="${ideogram.ideogram_labels.parallel}" /> |
| 369 #if $ideogram.bands: | 376 #if $reference_genome.reference_genome_source != 'karyotype': |
| 370 <param name="ideogram|bands" value="my-test-case/bands.${ideogram.bands.ext}" /> | 377 #if $reference_genome.bands: |
| 378 <param name="reference_genome.bands" value="my-test-case/bands.${reference_genome.bands.ext}" /> | |
| 379 #end if | |
| 371 #end if | 380 #end if |
| 372 <!-- Ticks --> | 381 <!-- Ticks --> |
| 373 <param name="ticks|show_ticks" value="${ticks.show_ticks}" /> | 382 <param name="ticks|show_ticks" value="${ticks.show_ticks}" /> |
| 374 <param name="ticks|radius" value="${ticks.radius}" /> | 383 <param name="ticks|radius" value="${ticks.radius}" /> |
| 375 <param name="ticks|color" value="${ticks.color}" /> | 384 <param name="ticks|color" value="${ticks.color}" /> |