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comparison circos.xml @ 3:fd59d783248a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit f04fe62fb7dbad75e597da8cd674cfe36ed3d80a"
author iuc
date Mon, 02 Dec 2019 08:14:29 -0500
parents 014a21767ac4
children 184dfd9e113d
comparison
equal deleted inserted replaced
2:014a21767ac4 3:fd59d783248a
60 #if str($plot_options.colour_profile) == 'cg': 60 #if str($plot_options.colour_profile) == 'cg':
61 cat '$__tool_directory__/colours/cg.conf' >> circos/conf/karyotype-colors.conf && 61 cat '$__tool_directory__/colours/cg.conf' >> circos/conf/karyotype-colors.conf &&
62 #end if 62 #end if
63 #end if 63 #end if
64 64
65 mv '$circos_conf' circos/conf/circos.conf && 65 cp '$circos_conf' circos/conf/circos.conf &&
66 mv '$ticks_conf' circos/conf/ticks.conf && 66 cp '$ticks_conf' circos/conf/ticks.conf &&
67 mv '$ideogram_conf' circos/conf/ideogram.conf && 67 cp '$ideogram_conf' circos/conf/ideogram.conf &&
68 mv '$data_conf' circos/conf/data.conf && 68 cp '$data_conf' circos/conf/data.conf &&
69 mv '$highlight_conf' circos/conf/highlight.conf && 69 cp '$highlight_conf' circos/conf/highlight.conf &&
70 mv '$links_conf' circos/conf/links.conf && 70 cp '$links_conf' circos/conf/links.conf &&
71 mv '$test_case_conf' circos/conf/galaxy_test_case.json && 71 cp '$test_case_conf' circos/conf/galaxy_test_case.json &&
72 72
73 ## Highlights 73 ## Highlights
74 #for $hi, $data in enumerate($sec_highlight.data): 74 #for $hi, $data in enumerate($sec_highlight.data):
75 cp '${data.data_source}' circos/data/highlight-${hi}.txt && 75 cp '${data.data_source}' circos/data/highlight-${hi}.txt &&
76 #end for 76 #end for
84 #for $hi, $data in enumerate($sec_links.data): 84 #for $hi, $data in enumerate($sec_links.data):
85 cp '${data.data_source}' circos/data/links-${hi}.txt && 85 cp '${data.data_source}' circos/data/links-${hi}.txt &&
86 #end for 86 #end for
87 87
88 #if $outputs.tar == "yes" 88 #if $outputs.tar == "yes"
89 tar cvfz circos.tar.gz circos >/dev/null 89 tar -czf circos.tar.gz circos &&
90 #else
91 echo ''
92 #end if 90 #end if
93 91
94 #if $outputs.svg == "yes" or $outputs.png == "yes": 92 #if $outputs.svg == "yes" or $outputs.png == "yes":
95 && circos -conf circos/conf/circos.conf -noparanoid 93 circos -conf circos/conf/circos.conf -noparanoid
96 #end if 94 #end if
97 ]]></command> 95 ]]></command>
98 <configfiles> 96 <configfiles>
99 <expand macro="configfile_circos_conf" /> 97 <expand macro="configfile_circos_conf" />
100 <expand macro="configfile_ticks_conf" /> 98 <expand macro="configfile_ticks_conf" />