Mercurial > repos > iuc > circos

comparison macros_conffiles.xml @ 4:6d45ebe16927 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit f5db2969e8602eff32ec799d237875b911578fe5"
author iuc
date Thu, 09 Jan 2020 15:02:34 +0000
parents 890ef899a3d7
children 5d7a5119a8e7
comparison
equal deleted inserted replaced
3:a2b4b1b1a88e 4:6d45ebe16927
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':