Mercurial > repos > eric-rasche > circos
comparison macros_conffiles.xml @ 9:e6440d0201f7 draft default tip
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 7e335df423e3e06da3d33a5378a336a149e6cc6c
| author | eric-rasche |
|---|---|
| date | Fri, 30 Jun 2017 06:48:38 -0400 |
| parents | eb3af6e9f633 |
| children |
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| 8:eb3af6e9f633 | 9:e6440d0201f7 |
|---|---|
| 108 | 108 |
| 109 #if str($plot_type) == 'histogram': | 109 #if str($plot_type) == 'histogram': |
| 110 extend_bin = ${data.plot_format.format_specific.extend_bins} | 110 extend_bin = ${data.plot_format.format_specific.extend_bins} |
| 111 fill_color = ${data.plot_format.format_specific.fill_color} | 111 fill_color = ${data.plot_format.format_specific.fill_color} |
| 112 #else if str($plot_type) == 'heatmap': | 112 #else if str($plot_type) == 'heatmap': |
| 113 fill_color = $circosColor($data.plot_format.format_specific.fill_color) | 113 color = $circosColor($data.plot_format.format_specific.fill_color) |
| 114 scale_log_base = ${data.plot_format.format_specific.scale_log_base} | 114 scale_log_base = ${data.plot_format.format_specific.scale_log_base} |
| 115 #else if str($plot_type) == 'line': | 115 #else if str($plot_type) == 'line': |
| 116 color = $circosColor($data.plot_format.format_specific.color) | 116 color = $circosColor($data.plot_format.format_specific.color) |
| 117 thickness = ${data.plot_format.format_specific.thickness} | 117 thickness = ${data.plot_format.format_specific.thickness} |
| 118 #else if str($plot_type) == 'scatter': | 118 #else if str($plot_type) == 'scatter': |
| 143 condition = 1 | 143 condition = 1 |
| 144 #elif str($condition.application.application_select) == "on": | 144 #elif str($condition.application.application_select) == "on": |
| 145 #set on_str = ' '.join([ "on(%s)" % $chr.strip() for $chr in $condition.application.on_genomes.split(',') ]) | 145 #set on_str = ' '.join([ "on(%s)" % $chr.strip() for $chr in $condition.application.on_genomes.split(',') ]) |
| 146 condition = $on_str | 146 condition = $on_str |
| 147 #elif str($condition.application.application_select) == "pos": | 147 #elif str($condition.application.application_select) == "pos": |
| 148 #if $condition.application.pos_gt != 0: | 148 #if float($condition.application.pos_gt) != 0: |
| 149 condition = var(start) > $condition.application.pos_gt | 149 condition = var(start) > $condition.application.pos_gt |
| 150 #end if | 150 #end if |
| 151 | 151 |
| 152 #if $condition.application.pos_lt != 0: | 152 #if float($condition.application.pos_lt) != 0: |
| 153 condition = var(start) < $condition.application.pos_lt | 153 condition = var(start) < $condition.application.pos_lt |
| 154 #end if | 154 #end if |
| 155 #elif str($condition.application.application_select) == "value": | 155 #elif str($condition.application.application_select) == "value": |
| 156 #if $condition.application.pos_gt != 0: | 156 #if float($condition.application.pos_gt) != 0: |
| 157 condition = var(value) > $condition.application.pos_gt | 157 condition = var(value) > $condition.application.pos_gt |
| 158 #end if | 158 #end if |
| 159 | 159 |
| 160 #if $condition.application.pos_lt != 0: | 160 #if float($condition.application.pos_lt) != 0: |
| 161 condition = var(value) < $condition.application.pos_lt | 161 condition = var(value) < $condition.application.pos_lt |
| 162 #end if | 162 #end if |
| 163 #elif str($condition.application.application_select) == "var": | 163 #elif str($condition.application.application_select) == "var": |
| 164 condition = var(${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 |
| 169 #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" : |
| 170 #set x_fill_color = $action.action.action_value | 170 #set x_fill_color = $action.action.action_value |
| 171 #set x_fill_color_count = int(str($x_fill_color).split('-')[1]) | 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 | 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 | 173 #set x_max = 1 if $action.action.invert else $x_fill_color_count |
| 174 | 174 #set color_action = "fill_color" if str($plot_type) == 'histogram' else "color" |
| 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 |
| 176 $color_action = eval(sprintf("${action.action.action_value}-%d", remap_int(var(value), ${action.action.min_value}, ${action.action.max_value}, ${x_min}, ${x_max}))) | |
| 176 #else | 177 #else |
| 177 $action.action.action_select = ${action.action.action_value} | 178 $action.action.action_select = ${action.action.action_value} |
| 178 #end if | 179 #end if |
| 179 #end for | 180 #end for |
| 180 $rule.continue_flow | 181 $rule.continue_flow |
| 288 #set x_fill_color_count = int(str($x_fill_color).split('-')[1]) | 289 #set x_fill_color_count = int(str($x_fill_color).split('-')[1]) |
| 289 #set x_min = $x_fill_color_count if $action.action.dynamic.invert else 1 | 290 #set x_min = $x_fill_color_count if $action.action.dynamic.invert else 1 |
| 290 #set x_max = 1 if $action.action.dynamic.invert else $x_fill_color_count | 291 #set x_max = 1 if $action.action.dynamic.invert else $x_fill_color_count |
| 291 | 292 |
| 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}))) | 293 $actiontype = eval(sprintf("${action.action.dynamic.action_value}-%d", remap_int(var(value), ${action.action.dynamic.min_value}, ${action.action.dynamic.max_value}, ${x_min}, ${x_max}))) |
| 294 #end if | |
| 295 #elif $actiontype == 'z': | |
| 296 #if $action.action.dynamic.dynamic_select == "static": | |
| 297 #set actionval = $action.action.dynamic.action_value | |
| 298 $actiontype = $actionval | |
| 299 #else | |
| 300 #set x_min = 1000 if $action.action.dynamic.invert else 1 | |
| 301 #set x_max = 1 if $action.action.dynamic.invert else 1000 | |
| 302 $actiontype = eval(remap_int(var(value), ${action.action.dynamic.min_value}, ${action.action.dynamic.max_value}, ${x_min}, ${x_max})) | |
| 293 #end if | 303 #end if |
| 294 #else | 304 #else |
| 295 #set actionval = $action.action.action_value | 305 #set actionval = $action.action.action_value |
| 296 $actiontype = $actionval | 306 $actiontype = $actionval |
| 297 #end if | 307 #end if |