Mercurial > repos > iuc > circos

annotate macros_conffiles.xml @ 2:014a21767ac4 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
author iuc
date Tue, 17 Sep 2019 16:54:57 -0400
parents ef5f8bbf7730
children 184dfd9e113d
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rev   line source
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
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diff changeset
1 <?xml version="1.0"?>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
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2 <macros>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
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3 <xml name="configfile_circos_conf">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
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4 <configfile name="circos_conf"><![CDATA[
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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5 @UTILS@
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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6
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
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7 <<include colors_fonts_patterns.conf>>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
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8 <<include housekeeping.conf>>
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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9
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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10 <colors>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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11 <<include karyotype-colors.conf>>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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12
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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13 #for $hi, $data in enumerate($sec_tdd.data):
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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14 #set plot_type = str($data.plot_format.plot_format_select)
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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15 #if str($plot_type) == 'tile':
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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16 color-tile-$hi = $circosColor($data.plot_format.format_specific.fill_color)
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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17 #end if
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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18 #end for
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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19 </colors>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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20
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
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21 karyotype = karyotype.txt
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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22 #if str($ideogram.units) == 'bases':
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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23 chromosomes_units = 1
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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24 #else if str($ideogram.units) == 'kb':
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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25 chromosomes_units = 1000
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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26 #else if str($ideogram.units) == 'mb':
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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27 chromosomes_units = 1000000
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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28 #else:
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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29 chromosomes_units = 1000000000
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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30 #end if
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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31
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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32 #if $ideogram.limit_chromosomes:
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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33 chromosomes = $ideogram.limit_chromosomes
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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34 chromosomes_order = $chromosomesToOrder($ideogram.limit_chromosomes)
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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35 chromosomes_display_default = no
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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36 #end if
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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37
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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38 #if $ideogram.chromosomes_reverse:
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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39 chromosomes_reverse = $ideogram.chromosomes_reverse
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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40 #end if
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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41
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
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42 <image>
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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43 # Transcluded from etc/image.generic.conf
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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44 dir = .
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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45 file = circos.png
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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46 #if $outputs.png:
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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47 png = yes
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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48 #end if
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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49 #if $outputs.svg:
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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50 svg = yes
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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51 #end if
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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52 # by default angle = 0 is at 3 o'clock position
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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53 angle_offset = -90
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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54 auto_alpha_colors = yes
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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55 auto_alpha_steps = 5
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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56 #if str($plot_options.background.background_select) == 'transparent':
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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57 background = transparent
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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58 #else
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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59 background = $circosColor($plot_options.background.background_color)
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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60 #end if
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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61 radius* = ${plot_options.radius}p
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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62 </image>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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63
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
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64 <<include ticks.conf>>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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65 <<include ideogram.conf>>
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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66 <<include data.conf>>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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67 <<include highlight.conf>>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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68 <<include links.conf>>
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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69
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
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70 ]]></configfile>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
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71 </xml>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
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72 <xml name="configfile_ticks_conf">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
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73 <configfile name="ticks_conf"><![CDATA[
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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74 @UTILS@
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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75
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
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76 show_ticks = ${ticks.show_ticks}
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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77 show_tick_labels = yes
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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78
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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79
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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80 <ticks>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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81 radius = ${ticks.radius}r
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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82 color = black
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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83 skip_first_label = ${ticks.skip_first_label}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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84 skip_last_label = ${ticks.skip_last_label}
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
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85 thickness = 2p
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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86
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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87 # Multiplier controls how 'u' behaves when used in numbers.
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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88 #if str($ideogram.units) == 'bases':
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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89 multiplier = 1
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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90 #else if str($ideogram.units) == 'kb':
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
91 multiplier = 1e-3
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
92 #else if str($ideogram.units) == 'mb':
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
93 multiplier = 1e-6
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
94 #else if str($ideogram.units) == 'gb':
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
95 multiplier = 1e-9
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
96 #end if
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
97
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
98 #for $tick_group in $ticks.tick_group:
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
99 <tick>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
100 spacing = ${tick_group.spacing}
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
101 size = ${tick_group.size}p
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
102 show_label = ${tick_group.ticks.show_tick_labels}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
103 color = $circosColor($tick_group.color)
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
104
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
105 #if str($tick_group.ticks.show_tick_labels) == 'yes':
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
106 label_size = ${tick_group.ticks.label_size}p
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
107 label_offset = ${tick_group.ticks.label_offset}p
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
108 #if $tick_group.ticks.format_ext:
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
109 #if str($ideogram.units) == 'bases':
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
110 format = ${tick_group.ticks.format}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
111 #else if str($ideogram.units) == 'kb':
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
112 format = ${tick_group.ticks.format} Kb
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
113 #else if str($ideogram.units) == 'mb':
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
114 format = ${tick_group.ticks.format} Mb
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
115 #else if str($ideogram.units) == 'gb':
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
116 format = ${tick_group.ticks.format} Gb
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
117 #end if
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
118 #else
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
119 format = ${tick_group.ticks.format}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
120 #end if
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
121 #end if
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
122 </tick>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
123 #end for
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
124 </ticks>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
125 ]]>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
126 </configfile>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
127 </xml>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
128 <xml name="configfile_ideogram_conf">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
129 <configfile name="ideogram_conf"><![CDATA[
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
130 @UTILS@
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
131 <ideogram>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
132 <spacing>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
133 ## spacing between ideograms
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
134 default = ${ideogram.spacing}r
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
135 </spacing>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
136
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
137 # ideogram position, thickness and fill
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
138 radius = ${ideogram.radius}r
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
139 thickness = ${ideogram.thickness}p
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
140 fill = yes
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
141 show_label = ${ideogram.ideogram_labels.show_label}
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
142 label_radius = dims(ideogram,radius) + ${ideogram.ideogram_labels.radius_offset}r
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
143 label_size = ${ideogram.ideogram_labels.size}
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
144 label_parallel = ${ideogram.ideogram_labels.parallel}
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
145
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
146 #if $ideogram.bands.bands:
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
147 show_bands = yes
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
148 #else
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
149 show_bands = no
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
150 #end if
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
151 fill_bands = ${ideogram.bands.fill_bands}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
152 #if int($ideogram.bands.band_transparency) > 0:
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
153 band_transparency = ${ideogram.bands.band_transparency}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
154 #end if
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
155 band_stroke_color = $circosColor($ideogram.bands.band_stroke_color)
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
156 band_stroke_thickness = ${ideogram.bands.band_stroke_thickness}
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
157 </ideogram>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
158 ]]></configfile>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
159 </xml>
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
160 <xml name="configfile_highlight_conf">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
161 <configfile name="highlight_conf"><![CDATA[
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
162 @UTILS@
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
163 <highlights>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
164 #for $hi, $data in enumerate($sec_highlight.data):
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
165 <highlight>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
166 file = data/highlight-${hi}.txt # ${data.data_source.element_identifier}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
167 r1 = ${data.r1}r
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
168 r0 = ${data.r0}r
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
169 fill_color = $circosColor($data.fill_color)
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
170
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
171 <rules>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
172 #for $rule in $data.sec_rule.rules:
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
173 <rule>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
174 #for $condition in $rule.conditions
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
175 #if str($condition.application.application_select) == "1":
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
176 condition = 1
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
177 #elif str($condition.application.application_select) == "on":
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
178 #set on_str = ' '.join([ "on(%s)" % $chr.strip() for $chr in $condition.application.on_genomes.split(',') ])
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
179 condition = $on_str
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
180 #elif str($condition.application.application_select) == "pos":
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
181 #if $condition.application.pos_gt:
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
182 condition = var(start) > $condition.application.pos_gt
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
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183 #end if
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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diff changeset
184
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
185 #if $condition.application.pos_lt:
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
186 #if $condition.application.pos_lt_sub == 'yes':
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
187 condition = var(end) < chrlen(var(chr)) - $condition.application.pos_lt
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
188 #else
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
189 condition = var(end) < $condition.application.pos_lt
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
190 #end if
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
191 #end if
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
192 #elif str($condition.application.application_select) == "value":
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
193 #if $condition.application.pos_gt:
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
194 condition = var(value) > $condition.application.pos_gt
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
195 #end if
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
196
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
197 #if $condition.application.pos_lt:
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
198 condition = var(value) < $condition.application.pos_lt
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
199 #end if
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
200 #elif str($condition.application.application_select) == "var":
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
201 condition = var(${condition.application.varname}) ${condition.application.cond_select} "${condition.application.varvalue}"
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
202 #elif str($condition.application.application_select) == "random":
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
203 condition = rand() < ${condition.application.value}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
204 #end if
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
205 #end for
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
206
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
207 #for $action in $rule.actions:
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
208 #if str($action.action.action_select) == "fill_color_value" or str($action.action.action_select) == "color_value" :
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
209 #set x_fill_color = $action.action.action_value
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
210 #set x_fill_color_count = int(str($x_fill_color).split('-')[1])
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
211 #set x_min = $x_fill_color_count if $action.action.invert else 1
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
212 #set x_max = 1 if $action.action.invert else $x_fill_color_count
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
213 #set color_action = "fill_color" if str($plot_type) in ('histogram', 'histogram-stacked') else "color"
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
214
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
215 $color_action = eval(sprintf("${action.action.action_value}-%d", remap_int(var(value), ${action.action.min_value}, ${action.action.max_value}, ${x_min}, ${x_max})))
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
216 #else
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
217 $action.action.action_select = $circosColor($action.action.action_value)
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
218 #end if
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
219 #end for
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
220 $rule.continue_flow
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
221 </rule>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
222 #end for
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
223 </rules>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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224 </highlight>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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225 #end for
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
226 </highlights>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
227 ]]></configfile>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
228 </xml>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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229
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
230
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
231 <xml name="configfile_data_conf">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
232 <configfile name="data_conf"><![CDATA[
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
233 <plots>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
234 @UTILS@
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
235
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
236 #for $hi, $data in enumerate($sec_tdd.data):
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
237 <plot>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
238 #set plot_type = str($data.plot_format.plot_format_select)
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
239 file = data/data-${hi}.txt # ${data.plot_format.data_source.element_identifier}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
240 r1 = ${data.r1}r
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
241 r0 = ${data.r0}r
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
242 orientation = ${data.orientation}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
243 #if str($data.minmax.minmax_select) == 'yes':
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
244 min = ${$data.minmax.min_value}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
245 max = ${$data.minmax.max_value}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
246 #end if
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
247
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
248 #if str($plot_type) in ('histogram', 'histogram-stacked'):
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
249 type = histogram
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
250 extend_bin = ${data.plot_format.format_specific.extend_bins}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
251 #if str($plot_type) == 'histogram':
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
252 fill_color = $circosColorAlpha($data.plot_format.format_specific.fill_color, $data.plot_format.format_specific.fill_color_alpha)
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
253 #else:
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
254 fill_color = $data.plot_format.format_specific.fill_color
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
255 #end if
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
256 fill_under = ${data.plot_format.format_specific.fill_under}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
257 color = $circosColorAlpha($data.plot_format.format_specific.stroke_color, $data.plot_format.format_specific.stroke_color_alpha)
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
258 thickness = ${data.plot_format.format_specific.stroke_thickness}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
259 #else if str($plot_type) == 'heatmap':
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
260 type = ${plot_type}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
261 color = ${data.plot_format.format_specific.fill_color}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
262 scale_log_base = ${data.plot_format.format_specific.scale_log_base}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
263 #else if str($plot_type) == 'line':
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
264 type = ${plot_type}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
265 color = $circosColor($data.plot_format.format_specific.stroke_color)
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
266 thickness = ${data.plot_format.format_specific.stroke_thickness}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
267 #else if str($plot_type) == 'scatter':
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
268 type = ${plot_type}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
269 glyph = ${data.plot_format.format_specific.glyph}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
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270 glyph_size = ${data.plot_format.format_specific.glyph_size}
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diff changeset
271 # So this option is ignored, and we have added an always-on rule in the
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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272 # first place to override the colour. This is because this color option will
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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273 # only accept named colours, while you can override the colour in a rule
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diff changeset
274 # block with an RGB colour.
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275 #
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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276 # Additionally it is named "color" in a scatter track whilst in the rule
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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277 # you must override it with "fill_color"
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278 color = $circosColor($data.plot_format.format_specific.fill_color)
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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279 stroke_color = $circosColor($data.plot_format.format_specific.stroke_color)
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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280 stroke_thickness = ${data.plot_format.format_specific.stroke_thickness}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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diff changeset
281 #else if str($plot_type) == 'tile':
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282 type = ${plot_type}
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283 color = color-tile-$hi
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284 stroke_color = $circosColor($data.plot_format.format_specific.stroke_color)
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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285 stroke_thickness = ${data.plot_format.format_specific.stroke_thickness}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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286 layers = ${data.plot_format.format_specific.layers}
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287 thickness = ${data.plot_format.format_specific.thickness}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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288 padding = ${data.plot_format.format_specific.padding}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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289 margin = ${data.plot_format.format_specific.margin}u
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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290 layers_overflow = ${data.plot_format.format_specific.overflow.overflow_behavior}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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291 #if str($data.plot_format.format_specific.overflow.overflow_behavior) != "hide":
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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292 layers_overflow_color = $circosColor($data.plot_format.format_specific.overflow.layer_overflow_color)
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293 #end if
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294 #else if str($plot_type) == 'text':
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295 type = ${plot_type}
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296 #if $data.plot_format.format_specific.link.show_link == "yes":
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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297 show_links = yes
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298 link_dims = ${data.plot_format.format_specific.link.link_dims}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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299 link_thickness = ${data.plot_format.format_specific.link.link_thickness}p
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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300 link_color = ${data.plot_format.format_specific.link.link_color}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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diff changeset
301 #else
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302 show_links = no
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303 #end if
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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304
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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305 #if $data.plot_format.format_specific.snuggle.label_snuggle == "yes":
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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306 label_snuggle = ${data.plot_format.format_specific.snuggle.label_snuggle}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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307 max_snuggle_distance = ${data.plot_format.format_specific.snuggle.max_snuggle_distance}r
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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308 snuggle_sampling = ${data.plot_format.format_specific.snuggle.snuggle_sampling}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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309 snuggle_tolerance = ${data.plot_format.format_specific.snuggle.snuggle_tolerance}r
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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310 snuggle_link_overlap_test = ${data.plot_format.format_specific.snuggle.snuggle_link_overlap_test}
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311 snuggle_link_overlap_tolerance = ${data.plot_format.format_specific.snuggle.snuggle_link_overlap_tolerance}p
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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312 snuggle_refine = ${data.plot_format.format_specific.snuggle.snuggle_refine}
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313 #end if
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314
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315 label_size = ${data.plot_format.format_specific.label_size}p
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316 label_font = condensed
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317 padding = 0p
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318 rpadding = 0p
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319 #end if
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diff changeset
320
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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321 <rules>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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322 #if str($plot_type) == 'scatter':
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323 <rule>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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diff changeset
324 # Workaround for above commented colour bug.
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325 condition = 1
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326 fill_color = $circosColor($data.plot_format.format_specific.fill_color)
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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327 flow = continue
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diff changeset
328 </rule>
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329 #end if
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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330 #for $rule in $data.sec_rule.rules:
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331 <rule>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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diff changeset
332 #for $condition in $rule.conditions
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diff changeset
333 #if str($condition.application.application_select) == "1":
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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334 condition = 1
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335 #elif str($condition.application.application_select) == "on":
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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336 #set on_str = ' '.join([ "on(%s)" % $chr.strip() for $chr in $condition.application.on_genomes.split(',') ])
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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337 condition = $on_str
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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diff changeset
338 #elif str($condition.application.application_select) == "pos":
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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diff changeset
339 #if $condition.application.pos_gt:
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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340 condition = var(start) > $condition.application.pos_gt
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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341 #end if
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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342
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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diff changeset
343 #if $condition.application.pos_lt:
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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diff changeset
344 condition = var(start) < $condition.application.pos_lt
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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diff changeset
345 #end if
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
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diff changeset
346 #elif str($condition.application.application_select) == "value":
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
347 #if $condition.application.pos_gt:
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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diff changeset
348 condition = var(value) > $condition.application.pos_gt
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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diff changeset
349 #end if
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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diff changeset
350
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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diff changeset
351 #if $condition.application.pos_lt:
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
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diff changeset
352 condition = var(value) < $condition.application.pos_lt
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
353 #end if
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
354 #elif str($condition.application.application_select) == "var":
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
355 condition = var(${condition.application.varname}) ${condition.application.cond_select} "${condition.application.varvalue}"
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
356 #end if
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
357 #end for
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
358
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
359 #for $action in $rule.actions:
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
360 #if str($action.action.action_select) == "fill_color_value" or str($action.action.action_select) == "color_value" :
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
361 #set x_fill_color = $action.action.action_value
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
362 #set x_fill_color_count = int(str($x_fill_color).split('-')[1])
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
363 #set x_min = $x_fill_color_count if $action.action.invert else 1
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
364 #set x_max = 1 if $action.action.invert else $x_fill_color_count
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
365 #set color_action = "fill_color" if str($plot_type) in ('histogram', 'histogram-stacked') else "color"
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
366
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
367 $color_action = eval(sprintf("${action.action.action_value}-%d", remap_int(var(value), ${action.action.min_value}, ${action.action.max_value}, ${x_min}, ${x_max})))
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
368 #elif str($action.action.action_select) in ('fill_color', 'stroke_color'):
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
369 #if str($plot_type) in ('tile', ):
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
370 color = $circosColor($action.action.action_value)
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
371 #else:
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
372 #if str($action.action.action_select) == "stroke_color" and str($plot_type) == "histogram":
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
373 color = $circosColor($action.action.action_value)
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
374 #else
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
375 $action.action.action_select = $circosColor($action.action.action_value)
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
376 #end if
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
377 #end if
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
378 #else
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
379 $action.action.action_select = ${action.action.action_value}
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
380 #end if
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
381 #end for
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
382 $rule.continue_flow
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
383 </rule>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
384 #end for
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
385 </rules>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
386
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
387 <axes>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
388 #for $axis in $data.sec_axes.axes:
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
389 <axis>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
390 color = $circosColor($axis.color)
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
391 thickness = ${axis.thickness}
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
392 spacing = ${axis.spacing}r
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
393 y0 = ${axis.y0}r
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
394 y1 = ${axis.y1}r
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
395 </axis>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
396 #end for
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
397 </axes>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
398 <backgrounds>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
399 #for $bkg in $data.sec_bkgs.backgrounds:
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
400 <background>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
401 color = $circosColor($bkg.color)
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
402 y0 = ${bkg.y0}r
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
403 y1 = ${bkg.y1}r
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
404 </background>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
405 #end for
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
406 </backgrounds>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
407 </plot>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
408 #end for
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
409 </plots>
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
410 ]]></configfile>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
411 </xml>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
412
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
413 <xml name="configfile_links_conf">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
414 <configfile name="links_conf"><![CDATA[
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
415 @UTILS@
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
416 <links>
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
417 #for $hi, $data in enumerate($sec_links.data):
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
418 <link>
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
419 file = data/links-${hi}.txt
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
420 radius = ${data.radius}r
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
421 ribbon = ${data.linktype.ribbon}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
422 #if $data.linktype.ribbon == 'yes'
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
423 ${data.linktype.twist}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
424 #if $data.linktype.pattern != 'solid':
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
425 pattern = ${data.linktype.pattern}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
426 #end if
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
427 #end if
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
428 color = $circosColorAlpha($data.color, $data.color_alpha)
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
429 bezier_radius = ${data.bezier_radius}r
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
430 thickness = ${data.thickness}
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
431 crest = ${data.advanced.crest}
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
432 bezier_radius_purity = ${data.advanced.bezier_radius_purity}
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
433 #if $data.advanced.perturbation.perturb == 'yes'
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
434 perturb = yes
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
435 perturb_crest = ${data.advanced.perturbation.perturb_crest_min},${data.advanced.perturbation.perturb_crest_max}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
436 perturb_bezier_radius = ${data.advanced.perturbation.perturb_bezier_radius_min},${data.advanced.perturbation.perturb_bezier_radius_max}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
437 perturb_bezier_radius_purity = ${data.advanced.perturbation.perturb_bezier_radius_purity_min},${data.advanced.perturbation.perturb_bezier_radius_purity_max}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
438 #end if
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
439 #if $data.advanced.zdepth
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
440 z = ${data.advanced.zdepth}
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
441 #end if
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
442
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
443 <rules>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
444 #for $rule in $data.sec_link_rule.rules:
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
445 <rule>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
446 #for $condition in $rule.conditions
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
447 #set cond = $condition.application.application_select
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
448 #if $cond == 'interchr' or $cond == 'intrachr' or $cond == 'inv' or $cond == 'rev'
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
449 condition = var($cond)
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
450 #elif $cond == 'always'
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
451 condition = 1
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
452 #elif $cond == 'random'
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
453 condition = rand() < ${condition.application.value}
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
454 #else
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
455 #set op = $condition.application.comparison.compare
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
456 #set val = $condition.application.comparison.compval
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
457 #if $cond == 'chr'
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
458 #if $op == 'between' or $op == 'fromto'
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
459 #set val2 = $condition.application.comparison.compval2
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
460 #set c=''.join([str($op),"(",str($val),",",str($val2),")"])
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
461 #elif $op == 'on'
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
462 #set c='(var(chr1) eq "%s" or var(chr2) eq "%s")' % (str($val), str($val))
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
463 #else
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
464 #set c=''.join([str($op),"(",str($val),")"])
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
465 #end if
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
466 condition = $c
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
467 #else
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
468 #if $cond == 'dist' and $op == 'lt'
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
469 condition = abs(var(pos1) - var(pos2)) < $val
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
470 #elif $cond == 'dist' and $op == 'gt'
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
471 condition = abs(var(pos1) - var(pos2)) > $val
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
472 #elif $op == 'lt'
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
473 condition = var($cond) < $val
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
474 #elif $op == 'gt'
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
475 condition = var($cond) > $val
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
476 #end if
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
477 #end if
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
478 #end if
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
479 #end for
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
480
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
481 #for $action in $rule.actions:
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
482 #set actiontype = $action.action.action_select
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
483 #if $actiontype == 'color':
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
484 #if $action.action.dynamic.dynamic_select == "static":
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
485 #set actionval = $circosColorAlpha($action.action.dynamic.action_value, $action.action.dynamic.action_value_alpha)
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
486 $actiontype = $actionval
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
487 #else
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
488 #set x_fill_color = $action.action.dynamic.action_value
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
489 #set x_fill_color_count = int(str($x_fill_color).split('-')[1])
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
490 #set x_min = $x_fill_color_count if $action.action.dynamic.invert else 1
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
491 #set x_max = 1 if $action.action.dynamic.invert else $x_fill_color_count
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
492
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
493 $actiontype = eval(sprintf("${action.action.dynamic.action_value}-%d", remap_int(var(value), ${action.action.dynamic.min_value}, ${action.action.dynamic.max_value}, ${x_min}, ${x_max})))
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
494 #end if
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
495 #elif $actiontype == 'z':
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
496 #if $action.action.dynamic.dynamic_select == "static":
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
497 #set actionval = $action.action.dynamic.action_value
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
498 $actiontype = $actionval
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
499 #else
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
500 #set x_min = 1000 if $action.action.dynamic.invert else 1
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
501 #set x_max = 1 if $action.action.dynamic.invert else 1000
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
502 $actiontype = eval(remap_int(var(value), ${action.action.dynamic.min_value}, ${action.action.dynamic.max_value}, ${x_min}, ${x_max}))
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
503 #end if
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
504 #else
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
505 #set actionval = $action.action.action_value
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
506 $actiontype = $actionval
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
507 #end if
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
508 #end for
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
509
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
510 $rule.continue_flow
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
511
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
512 </rule>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
513 #end for
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
514 </rules>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
515 </link>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
516 #end for
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
517 </links>
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
518 ]]></configfile>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
519 </xml>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
520
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
521 <xml name="test_case">
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 0
diff changeset
522 <inputs name="test_case_conf" />
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
523 </xml>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
524 </macros>