Mercurial > repos > iuc > circos
comparison macros_conffiles.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 | 014a21767ac4 |
| children | a64dc31ab7f2 |
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| 3:fd59d783248a | 4:184dfd9e113d |
|---|---|
| 161 <configfile name="highlight_conf"><![CDATA[ | 161 <configfile name="highlight_conf"><![CDATA[ |
| 162 @UTILS@ | 162 @UTILS@ |
| 163 <highlights> | 163 <highlights> |
| 164 #for $hi, $data in enumerate($sec_highlight.data): | 164 #for $hi, $data in enumerate($sec_highlight.data): |
| 165 <highlight> | 165 <highlight> |
| 166 file = data/highlight-${hi}.txt # ${data.data_source.element_identifier} | 166 file = data/highlight-${hi}.txt # ${data.data_source.element_identifier} |
| 167 r1 = ${data.r1}r | 167 r1 = ${data.r1}r |
| 168 r0 = ${data.r0}r | 168 r0 = ${data.r0}r |
| 169 fill_color = $circosColor($data.fill_color) | 169 fill_color = $circosColorAlpha($data.fill_color) |
| 170 stroke_color = $circosColorAlpha($data.stroke_color) | |
| 171 stroke_thickness = ${data.stroke_thickness} | |
| 170 | 172 |
| 171 <rules> | 173 <rules> |
| 172 #for $rule in $data.sec_rule.rules: | 174 #for $rule in $data.sec_rule.rules: |
| 173 <rule> | 175 <rule> |
| 174 #for $condition in $rule.conditions | 176 #for $condition in $rule.conditions |
| 175 #if str($condition.application.application_select) == "1": | 177 #if str($condition.application.application_select) == "1": |
| 176 condition = 1 | 178 condition = 1 |
| 177 #elif str($condition.application.application_select) == "on": | 179 #elif str($condition.application.application_select) == "on": |
| 178 #set on_str = ' '.join([ "on(%s)" % $chr.strip() for $chr in $condition.application.on_genomes.split(',') ]) | 180 condition = on($condition.application.on_genomes) |
| 179 condition = $on_str | |
| 180 #elif str($condition.application.application_select) == "pos": | 181 #elif str($condition.application.application_select) == "pos": |
| 181 #if $condition.application.pos_gt: | 182 #if $condition.application.pos_gt: |
| 182 condition = var(start) > $condition.application.pos_gt | 183 condition = var(start) > $condition.application.pos_gt |
| 183 #end if | 184 #end if |
| 184 | 185 |
| 414 <configfile name="links_conf"><![CDATA[ | 415 <configfile name="links_conf"><![CDATA[ |
| 415 @UTILS@ | 416 @UTILS@ |
| 416 <links> | 417 <links> |
| 417 #for $hi, $data in enumerate($sec_links.data): | 418 #for $hi, $data in enumerate($sec_links.data): |
| 418 <link> | 419 <link> |
| 419 file = data/links-${hi}.txt | 420 file = data/links-${hi}.txt # ${data.data_source.element_identifier} |
| 420 radius = ${data.radius}r | 421 radius = ${data.radius}r |
| 421 ribbon = ${data.linktype.ribbon} | 422 ribbon = ${data.linktype.ribbon} |
| 422 #if $data.linktype.ribbon == 'yes' | 423 #if $data.linktype.ribbon == 'yes' |
| 423 ${data.linktype.twist} | 424 ${data.linktype.twist} |
| 424 #if $data.linktype.pattern != 'solid': | 425 #if $data.linktype.pattern != 'solid': |