Mercurial > repos > eric-rasche > circos

annotate macros_conffiles.xml @ 8:eb3af6e9f633 draft

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planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 3ac672baa4a93250828fd4a450cb5689b0b03474
author eric-rasche
date Sat, 10 Jun 2017 16:21:01 -0400
parents b72f2db6d417
children e6440d0201f7
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e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
1 <?xml version="1.0"?>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
2 <macros>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
3 <xml name="configfile_circos_conf">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
4 <configfile name="circos_conf"><![CDATA[
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
5 <<include colors_fonts_patterns.conf>>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
6 <<include housekeeping.conf>>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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7 karyotype = karyotype.txt
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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parents:
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8
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
9 <image>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
10 <<include etc/image.conf>>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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11 </image>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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parents:
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12
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
13 <<include ticks.conf>>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
14 <<include ideogram.conf>>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
15 <plots>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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16 <<include 2d.conf>>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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17 <<include plot_highlight.conf>>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
18 </plots>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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19 <links>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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20 <<include links.conf>>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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21 </links>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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parents:
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22
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
23 <<include highlight.conf>>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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24 ]]></configfile>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
25 </xml>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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26 <xml name="configfile_ticks_conf">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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27 <configfile name="ticks_conf"><![CDATA[
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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28 show_ticks = ${ticks.show_ticks}
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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29 show_tick_labels = yes
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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30
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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31 #def circosColor($value)
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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32 #set $value = str($value)
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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33 #set $r = int($value[1:3], 16)
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
34 #set $g = int($value[3:5], 16)
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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35 #set $b = int($value[5:], 16)
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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36 $r, $g, $b
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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37 #end def
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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parents:
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38
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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39
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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40 <ticks>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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41 radius = ${ticks.radius}r
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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42 color = $circosColor($ticks.color)
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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43 thickness = 2p
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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44 multiplier = ${ticks.multiplier}
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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parents:
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45
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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46 #for $tick_group in $ticks.tick_group:
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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47 <tick>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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48 spacing = ${tick_group.spacing}
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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49 size = ${tick_group.size}p
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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50 show_label = ${tick_group.show_tick_labels}
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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51 label_size = ${tick_group.label_size}p
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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52 label_offset = ${tick_group.label_offset}p
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
53 format = ${tick_group.format} kb
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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54 ## TODO: figure out automated tick labels
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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55 ##if ${ticks.multiplier} * ${tick_group.spacing}
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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56 </tick>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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57 #end for
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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58 </ticks>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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parents:
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59 ]]>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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60 </configfile>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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61 </xml>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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62 <xml name="configfile_ideogram_conf">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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63 <configfile name="ideogram_conf"><![CDATA[
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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64
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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65 <ideogram>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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66
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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67 <spacing>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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68 ## spacing between ideograms
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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69 default = ${ideogram.spacing}r
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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70 </spacing>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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71
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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72 # ideogram position, thickness and fill
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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73 radius = ${ideogram.radius}r
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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74 thickness = ${ideogram.thickness}p
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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75 fill = yes
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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parents:
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76
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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parents:
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77 show_label = ${ideogram.ideogram_labels.show_label}
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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78 label_radius = dims(ideogram,radius) + 0.075r
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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79 label_size = 24
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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80 label_parallel = ${ideogram.ideogram_labels.parallel}
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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81
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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82 show_bands = yes
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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83 fill_bands = yes
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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84 band_transparency = 4
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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parents:
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85
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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parents:
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86 </ideogram>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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parents:
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87 ]]></configfile>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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88 </xml>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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89 <xml name="configfile_data_conf">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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90 <configfile name="data_conf"><![CDATA[
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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91 #for $hi, $data in enumerate($sec_tdd.data):
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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92 <plot>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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93 #set plot_type = str($data.plot_format.plot_format_select)
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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94 #def circosColor($value)
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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95 #set $value = str($value)
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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96 #set $r = int($value[1:3], 16)
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
97 #set $g = int($value[3:5], 16)
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
98 #set $b = int($value[5:], 16)
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
99 $r, $g, $b
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
100 #end def
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
101
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
102 type = ${plot_type}
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
103 file = data/data-${hi}.txt
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
104
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
105 r1 = ${data.r1}r
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
106 r0 = ${data.r0}r
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
107 orientation = ${data.orientation}
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
108
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
109 #if str($plot_type) == 'histogram':
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
110 extend_bin = ${data.plot_format.format_specific.extend_bins}
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
111 fill_color = ${data.plot_format.format_specific.fill_color}
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
112 #else if str($plot_type) == 'heatmap':
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
113 fill_color = $circosColor($data.plot_format.format_specific.fill_color)
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
114 scale_log_base = ${data.plot_format.format_specific.scale_log_base}
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
115 #else if str($plot_type) == 'line':
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
116 color = $circosColor($data.plot_format.format_specific.color)
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
117 thickness = ${data.plot_format.format_specific.thickness}
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
118 #else if str($plot_type) == 'scatter':
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
119 glyph = ${data.plot_format.format_specific.glyph}
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
120 glyph_size = ${data.plot_format.format_specific.glyph_size}
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
121 color = $circosColor($data.plot_format.format_specific.color)
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
122 stroke_color = $circosColor($data.plot_format.format_specific.stroke_color)
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
123 stroke_thickness = ${data.plot_format.format_specific.stroke_thickness}
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
124 #else if str($plot_type) == 'tile':
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
125 color = ${data.plot_format.format_specific.color}
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
126 stroke_color = $circosColor($data.plot_format.format_specific.color)
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
127 stroke_thickness = ${data.plot_format.format_specific.stroke_thickness}
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
128 layers = ${data.plot_format.format_specific.layers}
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
129 thickness = ${data.plot_format.format_specific.thickness}
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
130 padding = ${data.plot_format.format_specific.padding}
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
131
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
132 layers_overflow = ${data.plot_format.format_specific.overflow.overflow_behavior}
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
133 #if str($data.plot_format.format_specific.overflow.overflow_behavior) != "hide":
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
134 layers_overflow_color = $circosColor($data.plot_format.format_specific.overflow.layer_overflow_color)
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
135 #end if
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
136 #end if
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
137
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
138 <rules>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
139 #for $rule in $data.sec_rule.rules:
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
140 <rule>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
141 #for $condition in $rule.conditions
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
142 #if str($condition.application.application_select) == "1":
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
143 condition = 1
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
144 #elif str($condition.application.application_select) == "on":
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
145 #set on_str = ' '.join([ "on(%s)" % $chr.strip() for $chr in $condition.application.on_genomes.split(',') ])
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
146 condition = $on_str
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
147 #elif str($condition.application.application_select) == "pos":
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
148 #if $condition.application.pos_gt != 0:
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
149 condition = var(start) > $condition.application.pos_gt
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
150 #end if
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
151
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
152 #if $condition.application.pos_lt != 0:
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
153 condition = var(start) < $condition.application.pos_lt
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
154 #end if
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
155 #elif str($condition.application.application_select) == "value":
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
156 #if $condition.application.pos_gt != 0:
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
157 condition = var(value) > $condition.application.pos_gt
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
158 #end if
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
159
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
160 #if $condition.application.pos_lt != 0:
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
161 condition = var(value) < $condition.application.pos_lt
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
162 #end if
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
163 #elif str($condition.application.application_select) == "var":
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
164 condition = var(${condition.application.varname}) ${condition.application.cond_select} "${condition.application.varvalue}"
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
165 #end if
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
166 #end for
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
167
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
168 #for $action in $rule.actions:
8
eb3af6e9f633 planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 3ac672baa4a93250828fd4a450cb5689b0b03474
eric-rasche
parents: 7
diff changeset
169 #if str($action.action.action_select) == "fill_color_value" or str($action.action.action_select) == "color_value" :
eb3af6e9f633 planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 3ac672baa4a93250828fd4a450cb5689b0b03474
eric-rasche
parents: 7
diff changeset
170 #set x_fill_color = $action.action.action_value
eb3af6e9f633 planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 3ac672baa4a93250828fd4a450cb5689b0b03474
eric-rasche
parents: 7
diff changeset
171 #set x_fill_color_count = int(str($x_fill_color).split('-')[1])
eb3af6e9f633 planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 3ac672baa4a93250828fd4a450cb5689b0b03474
eric-rasche
parents: 7
diff changeset
172 #set x_min = $x_fill_color_count if $action.action.invert else 1
eb3af6e9f633 planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 3ac672baa4a93250828fd4a450cb5689b0b03474
eric-rasche
parents: 7
diff changeset
173 #set x_max = 1 if $action.action.invert else $x_fill_color_count
0
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
174
8
eb3af6e9f633 planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 3ac672baa4a93250828fd4a450cb5689b0b03474
eric-rasche
parents: 7
diff changeset
175 fill_color = eval(sprintf("${action.action.action_value}-%d", remap_int(var(value), ${action.action.min_value}, ${action.action.max_value}, ${x_min}, ${x_max})))
0
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
176 #else
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
177 $action.action.action_select = ${action.action.action_value}
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
178 #end if
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
179 #end for
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
180 $rule.continue_flow
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
181 </rule>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
182 #end for
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
183 </rules>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
184
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
185 <axes>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
186 #for $axis in $data.sec_axes.axes:
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
187 <axis>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
188 color = $circosColor($axis.color)
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
189 thickness = ${axis.thickness}
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
190 spacing = ${axis.spacing}r
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
191 y0 = ${axis.y0}r
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
192 y1 = ${axis.y1}r
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
193 </axis>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
194 #end for
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
195 </axes>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
196 <backgrounds>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
197 #for $bkg in $data.sec_bkgs.backgrounds:
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
198 <background>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
199 color = $circosColor($bkg.color)
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
200 y0 = ${bkg.y0}r
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
201 y1 = ${bkg.y1}r
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
202 </background>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
203 #end for
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
204 </backgrounds>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
205 </plot>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
206 #end for
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
207 ]]></configfile>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
208 </xml>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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209
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
210 <xml name="configfile_links_conf">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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211 <configfile name="links_conf"><![CDATA[
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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212 #for $hi, $data in enumerate($sec_links.data):
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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213 <link>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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214 #def circosColor($value)
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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215 #set $value = str($value)
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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parents:
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216 #set $r = int($value[1:3], 16)
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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217 #set $g = int($value[3:5], 16)
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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218 #set $b = int($value[5:], 16)
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
219 $r, $g, $b
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
220 #end def
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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parents:
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221
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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222 file = data/links-${hi}.txt
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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parents:
diff changeset
223
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
224 radius = ${data.radius}r
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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225 ribbon = ${data.linktype.ribbon}
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
226 #if $data.linktype.ribbon == 'yes'
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
227 ${data.linktype.twist}
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
228 #end if
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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229 color = $circosColor($data.color)
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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230 bezier_radius = ${data.bezier_radius}r
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
231 thickness = ${data.thickness}
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
232 crest = ${data.advanced.crest}
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
233 bezier_radius_purity = ${data.advanced.bezier_radius_purity}
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
234
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
235 #if $data.advanced.perturbation.perturb == 'yes'
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
236 perturb = yes
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
237 perturb_crest = ${data.advanced.perturbation.perturb_crest_min},${data.advanced.perturbation.perturb_crest_max}
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
238 perturb_bezier_radius = ${data.advanced.perturbation.perturb_bezier_radius_min},${data.advanced.perturbation.perturb_bezier_radius_max}
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
239 perturb_bezier_radius_purity = ${data.advanced.perturbation.perturb_bezier_radius_purity_min},${data.advanced.perturbation.perturb_bezier_radius_purity_max}
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
240 #end if
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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parents:
diff changeset
241
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
242 #if $data.advanced.zdepth
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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243 z = ${data.advanced.zdepth}
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
244 #end if
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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parents:
diff changeset
245
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
246 <rules>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
247 #for $rule in $data.sec_link_rule.rules:
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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diff changeset
248 <rule>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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parents:
diff changeset
249 #for $condition in $rule.conditions
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
250 #set cond = $condition.application.application_select
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
251 #if $cond == 'interchr' or $cond == 'intrachr' or $cond == 'inv' or $cond == 'rev'
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
252 condition = var($cond)
6
169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec
eric-rasche
parents: 5
diff changeset
253 #elif $cond == 'always'
169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec
eric-rasche
parents: 5
diff changeset
254 condition = 1
0
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
255 #else
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
256 #set op = $condition.application.comparison.compare
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
257 #set val = $condition.application.comparison.compval
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
258 #if $cond == 'chr'
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
259 #if $op == 'between' or $op == 'fromto'
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
260 #set val2 = $condition.application.comparison.compval2
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
261 #set c=''.join([str($op),"(",str($val),",",str($val2),")"])
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
262 #else
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
263 #set c=''.join([str($op),"(",str($val),")"])
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
264 #end if
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
265 condition = $c
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
266 #else
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
267 #if $cond == 'dist' and $op == 'lt'
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
268 condition = abs(var(pos1) - var(pos2)) < $val
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
269 #elif $cond == 'dist' and $op == 'gt'
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
270 condition = abs(var(pos1) - var(pos2)) > $val
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
271 #elif $op == 'lt'
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
272 condition = var($cond) < $val
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
273 #elif $op == 'gt'
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
274 condition = var($cond) > $val
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
275 #end if
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
276 #end if
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
277 #end if
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
278 #end for
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
279
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
280 #for $action in $rule.actions:
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
281 #set actiontype = $action.action.action_select
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
282 #if $actiontype == 'color':
6
169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec
eric-rasche
parents: 5
diff changeset
283 #if $action.action.dynamic.dynamic_select == "static":
7
b72f2db6d417 planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 86fb40a41d9e6012ea0b02d1cd77675f4bd971fb
eric-rasche
parents: 6
diff changeset
284 #set actionval = $circosColor($action.action.dynamic.action_value)
6
169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec
eric-rasche
parents: 5
diff changeset
285 $actiontype = $actionval
169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec
eric-rasche
parents: 5
diff changeset
286 #else
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287 #set x_fill_color = $action.action.dynamic.action_value
8
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288 #set x_fill_color_count = int(str($x_fill_color).split('-')[1])
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289 #set x_min = $x_fill_color_count if $action.action.dynamic.invert else 1
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290 #set x_max = 1 if $action.action.dynamic.invert else $x_fill_color_count
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291
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292 $actiontype = eval(sprintf("${action.action.dynamic.action_value}-%d", remap_int(var(value), ${action.action.dynamic.min_value}, ${action.action.dynamic.max_value}, ${x_min}, ${x_max})))
6
169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec
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293 #end if
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294 #else
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295 #set actionval = $action.action.action_value
6
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296 $actiontype = $actionval
0
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297 #end if
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298 #end for
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299
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300 $rule.continue_flow
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301
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302 </rule>
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303 #end for
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304 </rules>
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305 </link>
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306 #end for
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307 ]]></configfile>
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308 </xml>
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309
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310 <xml name="configfile_plot_highlight_conf">
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311 <configfile name="plot_highlight_conf"><![CDATA[
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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312 ###for $hi, $highlight in enumerate($sec_heat.highlights):
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313 ## #if $highlight.type_select == "plot_highlights":
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314 ##<plot>
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315 ## type = highlight
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316 ## file = data/highlight-${hi}.txt
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317 ## r1 = ${highlight.r1}r
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318 ## r0 = ${highlight.r0}r
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319 ## color = ${highlight.fill_color}
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320 ##</plot>
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321 ## #end if
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322 ###end for
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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323 ]]></configfile>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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324 </xml>
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325 <xml name="configfile_highlight_conf">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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326 <configfile name="highlight_conf"><![CDATA[
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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327 ##<highlights>
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328 ###for $hi, $highlight in enumerate($sec_heat.highlights):
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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329 ## #if $highlight.type_select == "normal":
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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330 ## <highlight>
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331 ## file = data/highlight-${hi}.txt
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332 ## r1 = ${highlight.r1}r
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333 ## r0 = ${highlight.r0}r
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334 ## color = ${highlight.fill_color}
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335 ## </highlight>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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336 ## #end if
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337 ###end for
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338 ##</highlights>
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339 ]]></configfile>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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340 </xml>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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341 <xml name="test_case">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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342 <configfile name="test_case_conf"><![CDATA[
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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343 <!--
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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344 mkdir -p test-data/my-test-case/;
5
b25b3518c2ce planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 7561690774be81155d79a3c38a77c098c59aa9a2
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345 #if $reference_genome.reference_genome_source == 'history':
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346 cp ${genome_fasta} test-data/my-test-case/input.fa;
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347 #end if
8
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348
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349 #if $reference_genome.reference_genome_source != 'karyotype':
eb3af6e9f633 planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 3ac672baa4a93250828fd4a450cb5689b0b03474
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350 #if $reference_genome.bands:
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351 cp ${reference_genome.bands} test-data/my-test-case/bands.${reference_genome.bands.ext};
0
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352 #end if
8
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353 #end if
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354
0
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355 #for $idx, $data in enumerate($sec_tdd.data):
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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356 #if str($data.plot_format.plot_format_select) in ('histogram', 'heatmap'):
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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357 #for $jdx, $file in enumerate($data.plot_format.data_source):
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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358 cp ${file} test-data/my-test-case/${idx}-${jdx}.${file.ext};
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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359 #end for
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360 #else
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361 cp ${data.plot_format.data_source} test-data/my-test-case/${idx}.${data.plot_format.data_source.ext};
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362 #end if
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363 #end for
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364 cp "$output_png" test-data/my-test-case/output.png;
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365 cp "$output_svg" test-data/my-test-case/output.svg;
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366 -->
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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367 <test>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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368 <param name="reference_genome|reference_genome_source" value="${reference_genome.reference_genome_source}"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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369 <param name="reference_genome|genome_fasta" value="my-test-case/input.fa" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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370 <!-- ideograms -->
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371 <param name="ideogram|spacing" value="${ideogram.spacing}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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372 <param name="ideogram|radius" value="${ideogram.radius}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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373 <param name="ideogram|thickness" value="${ideogram.thickness}" />
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374 <param name="ideogram|ideogram_labels|show_label" value="${ideogram.ideogram_labels.show_label}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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375 <param name="ideogram|ideogram_labels|parallel" value="${ideogram.ideogram_labels.parallel}" />
8
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376 #if $reference_genome.reference_genome_source != 'karyotype':
eb3af6e9f633 planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 3ac672baa4a93250828fd4a450cb5689b0b03474
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377 #if $reference_genome.bands:
eb3af6e9f633 planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 3ac672baa4a93250828fd4a450cb5689b0b03474
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378 <param name="reference_genome.bands" value="my-test-case/bands.${reference_genome.bands.ext}" />
eb3af6e9f633 planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 3ac672baa4a93250828fd4a450cb5689b0b03474
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379 #end if
0
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
380 #end if
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
381 <!-- Ticks -->
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
382 <param name="ticks|show_ticks" value="${ticks.show_ticks}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
383 <param name="ticks|radius" value="${ticks.radius}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
384 <param name="ticks|color" value="${ticks.color}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
385 <param name="ticks|multiplier" value="${ticks.multiplier}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
386 #for $idx, $tick_group in enumerate($ticks.tick_group):
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
387 <param name="ticks|tick_group_${idx}|tickspacing" value="${tick_group.spacing}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
388 <param name="ticks|tick_group_${idx}|size" value="${tick_group.size}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
389 <param name="ticks|tick_group_${idx}|show_tick_labels" value="${tick_group.show_tick_labels}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
390 <param name="ticks|tick_group_${idx}|label_size" value="${tick_group.label_size}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
391 <param name="ticks|tick_group_${idx}|label_offset" value="${tick_group.label_offset}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
392 <param name="ticks|tick_group_${idx}|label_format" value="${tick_group.format}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
393 #end for
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
394 <!-- Data -->
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
395 #for $idx, $data_group in enumerate($sec_tdd.data):
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
396 <param name="sec_tdd|data_${idx}|r0" value="${data_group.r0}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
397 <param name="sec_tdd|data_${idx}|r1" value="${data_group.r1}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
398 <param name="sec_tdd|data_${idx}|orientation" value="${data_group.orientation}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
399 <param name="sec_tdd|data_${idx}|plot_format|plot_format_select" value="${data_group.plot_format.plot_format_select}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
400 <!-- Note, please double check your files -->
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
401 #if str($data_group.plot_format.plot_format_select) == 'histogram':
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
402 #set my_files = ','.join([ "my-test-case/%s-%s.%s" % ($idx, $j, $file.ext) for ($j, $file) in enumerate($data_group.plot_format.data_source)])
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
403 <param name="sec_tdd|data_${idx}|plot_format|data_source" value="${my_files}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
404 <param name="sec_tdd|data_${idx}|plot_format|format_specific|fill_color" value="${data_group.plot_format.format_specific.fill_color}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
405 <param name="sec_tdd|data_${idx}|plot_format|format_specific|extend_bins" value="${data_group.plot_format.format_specific.extend_bins}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
406 #else if str($data_group.plot_format.plot_format_select) == 'heatmap':
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
407 #set my_files = ','.join([ "my-test-case/%s-%s.%s" % ($idx, $j, $file.ext) for ($j, $file) in enumerate($data_group.plot_format.data_source)])
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
408 <param name="sec_tdd|data_${idx}|plot_format|data_source" value="${my_files}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
409 <param name="sec_tdd|data_${idx}|plot_format|format_specific|fill_color" value="${data_group.plot_format.format_specific.fill_color}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
410 <param name="sec_tdd|data_${idx}|plot_format|format_specific|scale_log_base" value="${data_group.plot_format.format_specific.scale_log_base}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
411 #else if str($data_group.plot_format.plot_format_select) == 'line':
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
412 <param name="sec_tdd|data_${idx}|plot_format|data_source" value="my-test-case/${idx}.${data.plot_format.data_source.ext}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
413 <param name="sec_tdd|data_${idx}|plot_format|format_specific|color" value="${data_group.plot_format.format_specific.color}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
414 <param name="sec_tdd|data_${idx}|plot_format|format_specific|stroke" value="${data_group.plot_format.format_specific.stroke}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
415 #else if str($data_group.plot_format.plot_format_select) == 'scatter':
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
416 <param name="sec_tdd|data_${idx}|plot_format|data_source" value="my-test-case/${idx}.${data.plot_format.data_source.ext}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
417 <param name="sec_tdd|data_${idx}|plot_format|format_specific|glyph" value="${data_group.plot_format.format_specific.glyph}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
418 <param name="sec_tdd|data_${idx}|plot_format|format_specific|glyph_size" value="${data_group.plot_format.format_specific.glyph_size}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
419 <param name="sec_tdd|data_${idx}|plot_format|format_specific|data_min" value="${data_group.plot_format.format_specific.data_min}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
420 <param name="sec_tdd|data_${idx}|plot_format|format_specific|data_max" value="${data_group.plot_format.format_specific.data_max}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
421 <param name="sec_tdd|data_${idx}|plot_format|format_specific|color" value="${data_group.plot_format.format_specific.color}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
422 <param name="sec_tdd|data_${idx}|plot_format|format_specific|stroke_color" value="${data_group.plot_format.format_specific.stroke_color}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
423 <param name="sec_tdd|data_${idx}|plot_format|format_specific|stroke_thickness" value="${data_group.plot_format.format_specific.stroke_thickness}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
424 #else if str($data_group.plot_format.plot_format_select) == 'tile':
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
425 <param name="sec_tdd|data_${idx}|plot_format|data_source" value="my-test-case/${idx}.${data.plot_format.data_source.ext}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
426 <param name="sec_tdd|data_${idx}|plot_format|format_specific|fill_color" value="${data_group.plot_format.format_specific.fill_color}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
427 <param name="sec_tdd|data_${idx}|plot_format|format_specific|color" value="${data_group.plot_format.format_specific.color}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
428 <param name="sec_tdd|data_${idx}|plot_format|format_specific|stroke_thickness" value="${data_group.plot_format.format_specific.stroke_thickness}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
429 <param name="sec_tdd|data_${idx}|plot_format|format_specific|layers" value="${data_group.plot_format.format_specific.layers}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
430 <param name="sec_tdd|data_${idx}|plot_format|format_specific|thickness" value="${data_group.plot_format.format_specific.thickness}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
431 <param name="sec_tdd|data_${idx}|plot_format|format_specific|padding" value="${data_group.plot_format.format_specific.padding}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
432 <param name="sec_tdd|data_${idx}|plot_format|format_specific|overflow|overflow_behavior" value="${data_group.plot_format.format_specific.overflow.overflow_behavior}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
433 #if str($data_group.plot_format.format_specific.overflow.overflow_behavior) != 'hide':
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
434 <param name="sec_tdd|data_${idx}|plot_format|format_specific|overflow|layer_overflow_color" value="${data_group.plot_format.format_specific.overflow.layer_overflow_color}" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
435 #end if
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
436 #end if
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
437 ## Next line intentionally blank
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
438
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
439 #end for
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
440
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
441
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
442 <!-- Outputs -->
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
443 <output name="output_png" file="my-test-case/output.png" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
444 <output name="output_svg" file="my-test-case/output.svg" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
445 </test>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
446 ]]></configfile>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
447 </xml>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
448 </macros>