annotate macros.xml @ 7:4b519282a05b draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit ef20b4968a6d00c49209de6b723f8b96d8bd128a"
author iuc
date Mon, 25 May 2020 10:52:02 -0400
parents 740057a5126d
children e6cbe3190642
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1 <?xml version="1.0"?>
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2 <macros>
2
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3 <token name="@CIRCOS_VERSION@">0.69.8</token>
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4
7
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5 <token name="@WRAPPER_VERSION@">@CIRCOS_VERSION@+galaxy6</token>
2
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6
0
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7 <xml name="requirements">
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8 <requirements>
2
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9 <requirement type="package" version="@CIRCOS_VERSION@">circos</requirement>
0
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10 <requirement type="package" version="2.7">python</requirement>
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11 <requirement type="package" version="0.6.4">bcbiogff</requirement>
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12 <requirement type="package" version="1.70">biopython</requirement>
2
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13 <requirement type="package" version="0.3.13">pybigwig</requirement>
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14 <requirement type="package" version="0.23">circos-tools</requirement>
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15 <requirement type="package" version="3.4">grep</requirement>
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16 <requirement type="package" version="5.1.0">gawk</requirement>
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17 <requirement type="package" version="1.29">tar</requirement>
2
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18 <yield />
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19 </requirements>
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20 </xml>
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21
2
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22 <token name="@UTILS@">
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23 #def circosColor($value)
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24 #set $value = str($value)
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25 #set $r = int($value[1:3], 16)
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26 #set $g = int($value[3:5], 16)
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27 #set $b = int($value[5:], 16)
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28 $r, $g, $b
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29 #end def
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30 #def circosColorAlpha($value, $alpha)
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31 #set $value = str($value)
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32 #set $r = int($value[1:3], 16)
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33 #set $g = int($value[3:5], 16)
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34 #set $b = int($value[5:], 16)
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35 #set $a = float($alpha)
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36 $r, $g, $b, $a
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37 #end def
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38 #def chromosomesToOrder($value)
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39 #set $q = ','.join([x if ':' not in x else x[x:x.index(':')] for x in str($value).split(';')])
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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40 $q
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41 #end def
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42 </token>
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43
0
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44 <xml name="citations">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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45 <citations>
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46 <citation type="doi">10.1101/gr.092759.109</citation>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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47 </citations>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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48 </xml>
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49
2
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50 <xml name="stroke_opts">
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51 <expand macro="circos_color_alpha" name="stroke_color" value="#000000" label="Stroke Color"/>
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52 <param name="stroke_thickness" type="integer" value="1" label="Stroke Thickness"/>
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53 </xml>
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54
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55 <xml name="minmax">
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56 <conditional name="minmax">
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57 <param name="minmax_select" type="select" label="Minimum / maximum options">
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58 <option value="yes">Supply min/max values</option>
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59 <option value="no" selected="true">Plot all values</option>
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60 </param>
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61 <when value="yes">
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62 <param name="min_value" type="float" value="1.0" label="Minimum value" />
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63 <param name="max_value" type="float" value="5.0" label="Maximum value" />
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64 </when>
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65 <when value="no">
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66 </when>
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67 </conditional>
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68 </xml>
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69
0
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70 <xml name="circos_color"
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71 token_label="Color"
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72 token_name="color"
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73 token_value="#000000"
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74 token_help=""
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75 >
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76 <param label="@LABEL@" type="color" name="@NAME@" value="@VALUE@" help="@HELP@">
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77 <sanitizer>
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78 <valid initial="string.letters,string.digits">
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79 <add value="#" />
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80 </valid>
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81 </sanitizer>
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82 </param>
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83 </xml>
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84
6
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85 <xml name="chrom_units"
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86 token_label="Position"
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87 token_help="In bases (e.g. 1000) or chromosome units (e.g. 1u)"
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88 token_value="5u"
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diff changeset
89 token_name="position"
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
90 >
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
91 <param name="@NAME@" type="text" value="@VALUE@" label="@LABEL@" help="@HELP@">
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
92 <sanitizer>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
93 <valid initial="string.digits">
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
94 <add value="u"/>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
95 <add value="b"/>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
96 <add value="."/>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
97 </valid>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
98 </sanitizer>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
99 </param>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
100 </xml>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
101
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
102 <xml name="circos_color_alpha"
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
103 token_label="Color"
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
104 token_name="color"
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
105 token_value="#000000"
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
106 token_help=""
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
107 >
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
108 <param label="@LABEL@" type="color" name="@NAME@" value="@VALUE@" help="@HELP@">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
109 <sanitizer>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
110 <valid initial="string.letters,string.digits">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
111 <add value="#" />
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
112 </valid>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
113 </sanitizer>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
114 </param>
6
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
115 <param name="@NAME@_alpha" type="float" label="@LABEL@ Transparency" value="1" min="0" max="1" help="1 = fully opaque, 0 = fully transparent"/>
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
116 </xml>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
117
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
118 <xml name="brewer_scale"
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
119 token_name="color"
6
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
120 token_label="Color"
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
121 token_help="">
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
122 <param name="@NAME@" type="select" label="@LABEL@" help="@HELP@">
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
123 <option value="purples-13-seq">Sequential: Purples</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
124 <option value="reds-13-seq">Sequential: Reds</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
125 <option value="oranges-13-seq">Sequential: Oranges</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
126 <option value="greens-13-seq">Sequential: Greens</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
127 <option value="blues-13-seq">Sequential: Blues</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
128 <option value="greys-13-seq">Sequential: Greys</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
129
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
130 <option value="bugn-13-seq">Sequential: Blue - Green</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
131 <option value="bupu-13-seq">Sequential: Blue - Purple</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
132 <option value="gnbu-13-seq">Sequential: Green - Blue</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
133 <option value="orrd-13-seq">Sequential: Orange - Red</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
134 <option value="pubu-13-seq">Sequential: Purple - Blue</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
135 <option value="pubugn-13-seq">Sequential: Purple - Blue - Green</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
136 <option value="purd-13-seq">Sequential: Purple - Red</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
137 <option value="rdpu-13-seq">Sequential: Red - Purple</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
138 <option value="ylgn-13-seq">Sequential: Yellow - Green</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
139 <option value="ylgnbu-13-seq">Sequential: Yellow - Green - Blue</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
140 <option value="ylorbr-13-seq">Sequential: Yellow - Orange - Brown</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
141 <option value="ylorrd-13-seq">Sequential: Yellow - Orange - Red</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
142
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
143 <option value="brbg-15-div">Diverging: Brown - Blue Green</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
144 <option value="piyg-15-div">Diverging: Pink - Yellow Green</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
145 <option value="prgn-15-div">Diverging: Purple - Green</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
146 <option value="puor-15-div">Diverging: Purple - Orange</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
147 <option value="rdbu-15-div">Diverging: Red - Blue</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
148 <option value="rdgy-15-div">Diverging: Red - Grey</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
149 <option value="rdylbu-15-div">Diverging: Red - Yellow - Blue</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
150 <option value="rdylgn-15-div">Diverging: Red - Yellow - Green</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
151 <option value="spectral-15-div">Diverging: Spectral</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
152
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
153 <option value="accent-8-qual">Qualitative: Accent</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
154 <option value="dark2-8-qual">Qualitative: Dark2</option>
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
155 <option value="paired-12-qual" selected="true">Qualitative: Paired</option>
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
156 <option value="pastel1-9-qual">Qualitative: Pastel1</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
157 <option value="pastel2-8-qual">Qualitative: Pastel2</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
158 <option value="set1-9-qual">Qualitative: Set1</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
159 <option value="set2-8-qual">Qualitative: Set2</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
160 <option value="set3-12-qual">Qualitative: Set3</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
161 </param>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
162 </xml>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
163
6
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
164 <xml name="zdepth"
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
165 token_name="zdepth"
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
166 >
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
167 <param name="@NAME@" type="integer" value="0" optional="true" label="Z-index"
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
168 help="Datasets with a higher z-index value are drawn on top of data sets with a lower value. 0 is the default and plots added lower in the configuration file will be plotted above."/>
4
184dfd9e113d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit f5db2969e8602eff32ec799d237875b911578fe5"
iuc
parents: 3
diff changeset
169 </xml>
184dfd9e113d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit f5db2969e8602eff32ec799d237875b911578fe5"
iuc
parents: 3
diff changeset
170
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
171 <xml name="font_select"
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
172 token_normal="true"
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
173 token_bold="false">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
174 <param name="font" type="select" label="Font">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
175 <option value="light">light</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
176 <option value="normal" selected="@NORMAL@">normal</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
177 <option value="default">default</option>
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178 <option value="semibold">semibold</option>
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179 <option value="bold" selected="@BOLD@">bold</option>
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180 <option value="italic">italic</option>
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181 <option value="bolditalic">bolditalic</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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182 <option value="italicbold">italicbold</option>
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183 </param>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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184 </xml>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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185
6
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186 <xml name="radial_position">
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
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187 <conditional name="radial_position">
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
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188 <param name="select" type="select" label="Radial Position">
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
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189 <option value="plot">Relative position</option>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
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190 <option value="data" selected="True">Absolute position (values match data values)</option>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
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191 </param>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
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192 <when value="plot">
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193 <param name="y0" type="float" value="0" label="y0" help="Values are relative (0=inside of track, 1=outside of track)"/>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
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194 <param name="y1" type="float" value="1" label="y1" help="Values are relative (0=inside of track, 1=outside of track)"/>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
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195 </when>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
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196 <when value="data">
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197 <param name="y0" type="float" value="0" label="y0" help="Values are according to minimum and maximum values of dataset. E.g. if your dataset goes from -10 to 10, y0 should be -10."/>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
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198 <param name="y1" type="float" value="1" label="y1" help="Values are according to minimum and maximum values of dataset. E.g. if your dataset goes from -10 to 10, y1 should be 10."/>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
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199 </when>
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200 </conditional>
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201 </xml>
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202
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
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203 <xml name="radial_position_axes">
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204 <conditional name="radial_position">
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205 <param name="select" type="select" label="Radial Position">
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
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206 <option value="plot">Relative position</option>
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207 <option value="data" selected="True">Absolute position (values match data values)</option>
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208 </param>
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209 <when value="plot">
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210 <param name="spacing" type="float" value="0.1" min="0" max="1" label="Spacing" help="This many % of the distance between axis lines, set between the data minimum/maximum. If data goes from -1 to 1, and this is set to 0.33, and y0/y1 radius are 0/1, this produces two bands [0.33, 1]. If the y0/y1 radius are set to -1/1, this produces 4 bands: [-1, -0.33, 0.33, 1]. The y0/y1 radius act as clipping."/>
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211 </when>
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212 <when value="data">
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213 <param name="spacing" type="float" value="0.1" label="Spacing" help="Equal to data value difference. E.g. 0.25 here when data goes from -1 to 1 and y0/y1 are 0/1 produces 5 bands at [0, 0.25, 0.5, 0.75, 1]. If y0/y1 and radius are -1/1 produces 9 bands at [-1, -0.75, -0.5, -0.25, 0, 0.25, 0.5, 0.75, 1]. The y0/y1 radius act as clipping."/>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
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214 </when>
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215 </conditional>
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216 <param name="y0" type="float" value="0" label="y0" help="Values are according to minimum and maximum values of dataset. E.g. if your dataset goes from -10 to 10, y0 should be -10. These clip the axes, any axes which would be drawn on the data outside of these bounds will not be drawn."/>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
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217 <param name="y1" type="float" value="1" label="y1" help="Values are according to minimum and maximum values of dataset. E.g. if your dataset goes from -10 to 10, y1 should be 10. These clip the axes, any axes which would be drawn on the data outside of these bounds will not be drawn."/>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
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218 </xml>
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219
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
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220 <xml name="minsize">
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221 <param name="minsize" type="float" value="0" label="Minimum size (in chromosome units)" min="0"/>
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222 </xml>
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223
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
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224 <xml name="only_if_data">
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225 <param name="only_if_data" type="select" label="When to show">
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226 <option value="always" selected="True">Always</option>
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227 <option value="data">Only when data is present on the ideogram</option>
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228 </param>
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229 </xml>
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230
0
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231 <xml name="axes">
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232 <section name="sec_axes" title="Axes">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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233 <repeat name="axes" title="Axis">
6
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234 <expand macro="radial_position_axes" />
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235 <expand macro="circos_color_alpha"/>
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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236 <param name="thickness" type="integer" value="1" label="Thickness"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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237 </repeat>
6
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238 <expand macro="only_if_data" />
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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239 </section>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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240 </xml>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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241
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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242 <xml name="backgrounds">
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243 <section name="sec_bkgs" title="Backgrounds">
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244 <repeat name="backgrounds" title="Background">
6
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245 <expand macro="radial_position" />
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246 <expand macro="circos_color_alpha"/>
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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247 </repeat>
6
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248 <expand macro="only_if_data" />
0
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249 </section>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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250 </xml>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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251
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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252 <xml name="rules">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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253 <section name="sec_rule" title="Rules">
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254 <repeat name="rules" title="Rule">
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255 <repeat name="conditions" title="Conditions to Apply">
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256 <conditional name="application">
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257 <param name="application_select" type="select" label="Condition">
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258 <option value="always">Apply to Every Point</option>
2
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259 <option value="random">Randomly</option>
6
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260 <option value="on">Check for presence/absence per chromosome</option>
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261 <option value="pos">Based on position on chromosome</option>
7
4b519282a05b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit ef20b4968a6d00c49209de6b723f8b96d8bd128a"
iuc
parents: 6
diff changeset
262 <option value="value">Based on value (ONLY for scatter/histogram/heatmap/line)</option>
6
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
263 <option value="var">Based on qualifier value (when available)</option>
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
264 </param>
6
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
265 <when value="always">
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
266 </when>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
267 <when value="on">
6
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
268 <param name="on_genomes" type="text" label="Chromosome IDs" help="Pipe | separated list of chromosome IDs">
4
184dfd9e113d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit f5db2969e8602eff32ec799d237875b911578fe5"
iuc
parents: 3
diff changeset
269 <sanitizer>
184dfd9e113d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit f5db2969e8602eff32ec799d237875b911578fe5"
iuc
parents: 3
diff changeset
270 <valid initial="string.letters,string.digits">
184dfd9e113d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit f5db2969e8602eff32ec799d237875b911578fe5"
iuc
parents: 3
diff changeset
271 <add value="|" />
6
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
272 <add value="-" />
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
273 <add value="." />
4
184dfd9e113d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit f5db2969e8602eff32ec799d237875b911578fe5"
iuc
parents: 3
diff changeset
274 </valid>
184dfd9e113d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit f5db2969e8602eff32ec799d237875b911578fe5"
iuc
parents: 3
diff changeset
275 </sanitizer>
184dfd9e113d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit f5db2969e8602eff32ec799d237875b911578fe5"
iuc
parents: 3
diff changeset
276 </param>
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
277 </when>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
278 <when value="pos">
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
279 <param name="pos_gt" type="float" label="Greater than this base" optional="true"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
280 <param name="pos_lt" type="float" label="Less than this base" optional="true"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
281 <param name="pos_lt_sub" type="boolean" truevalue="yes" falsevalue="no" label="Count 'Less than this base' from end of chromosome" />
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
282 </when>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
283 <when value="random">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
284 <param name="value" type="float" label="Percentage of bins" value="0.5" min="0" max="1" help="Randomly apply with this probability"/>
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
285 </when>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
286 <when value="value">
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
287 <param name="pos_gt" type="float" label="Points above this value" optional="true"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
288 <param name="pos_lt" type="float" label="Points below this value" optional="true"/>
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
289 </when>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
290 <when value="var">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
291 <param name="varname" type="text" label="Qualifier name"
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
292 help="Set to the name of the qualifier in the file you wish to compare against" />
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
293
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
294 <param name="cond_select" type="select" label="Condition">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
295 <option value="eq">Equal to (string)</option>
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
296 <option value="==">Equal to (numeric)</option>
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
297 <option value="ne">Not equal to (string)</option>
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
298 <option value="!=">Not equal to (numeric)</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
299 <option value="&lt;">Less than (numeric)</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
300 <option value="&gt;">Greater than (numeric)</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
301 <option value="%">Modulus (numeric)</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
302 <sanitizer>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
303 <valid initial="string.letters">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
304 <add value="&gt;" />
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
305 <add value="&lt;" />
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
306 <add value="!" />
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
307 <add value="=" />
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
308 <add value="%" />
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
309 </valid>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
310 </sanitizer>
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
311 </param>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
312
4
184dfd9e113d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit f5db2969e8602eff32ec799d237875b911578fe5"
iuc
parents: 3
diff changeset
313 <param name="varvalue" type="text" label="Qualifier value to compare against">
184dfd9e113d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit f5db2969e8602eff32ec799d237875b911578fe5"
iuc
parents: 3
diff changeset
314 <sanitizer>
184dfd9e113d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit f5db2969e8602eff32ec799d237875b911578fe5"
iuc
parents: 3
diff changeset
315 <valid initial="string.letters,string.digits">
184dfd9e113d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit f5db2969e8602eff32ec799d237875b911578fe5"
iuc
parents: 3
diff changeset
316 </valid>
184dfd9e113d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit f5db2969e8602eff32ec799d237875b911578fe5"
iuc
parents: 3
diff changeset
317 </sanitizer>
184dfd9e113d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit f5db2969e8602eff32ec799d237875b911578fe5"
iuc
parents: 3
diff changeset
318 </param>
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
319 </when>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
320 </conditional>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
321 </repeat>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
322 <repeat name="actions" title="Actions to Apply">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
323 <conditional name="action">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
324 <param name="action_select" type="select" label="Action">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
325 <option value="show">Change Visibility</option>
6
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
326 <option value="z">Change Z-index</option>
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
327 <option value="fill_color">Change Fill Color for all points</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
328 <option value="fill_color_value">Change Fill Color based on Value</option>
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
329 <option value="stroke_color">Change Stroke Color</option>
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
330 <option value="color_value">Change Stroke Color based on Value</option>
6
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
331 <option value="value_from_attr">Change value of point based on attribute</option>
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
332 </param>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
333 <when value="show">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
334 <param name="action_value" type="boolean" truevalue="yes" falsevalue="no" label="Show"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
335 </when>
6
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
336 <when value="value_from_attr">
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
337 <param name="action_value" type="text" label="Attribute to pull value from" help="From the optional x1=y1;x2=y2... formatted attributes in the last column">
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
338 <sanitizer>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
339 <valid initial="string.letters,string.digits">
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
340 </valid>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
341 </sanitizer>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
342 </param>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
343 </when>
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
344 <when value="fill_color">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
345 <expand macro="circos_color" name="action_value" label="Fill Color"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
346 </when>
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
347 <when value="stroke_color">
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
348 <expand macro="circos_color" name="action_value" label="Stroke Color"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
349 </when>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
350 <when value="fill_color_value">
6
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
351 <expand macro="brewer_scale" name="action_value" label="Fill Color" help="Fill will be changed based on a mapping of dataset values to colours, but to do this the mapping needs to be defined. Minimum and maximum values are defined below, and will map to the minimum and maximum values of this brewer scale."/>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
352 <param name="min_value" type="float" value="-1" label="Minimum value of dataset"/>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
353 <param name="max_value" type="float" value="1" label="Maximum value of dataset"/>
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
354 <param name="invert" type="boolean" truevalue="True" falsevalue="False" label="Invert Color Scale" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
355 </when>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
356 <when value="color_value">
6
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
357 <expand macro="brewer_scale" name="action_value" label="Stroke Color" help="Stroke will be changed based on a mapping of dataset values to colours, but to do this the mapping needs to be defined. Minimum and maximum values are defined below, and will map to the minimum and maximum values of this brewer scale."/>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
358 <param name="min_value" type="float" value="-1" label="Minimum value of dataset"/>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
359 <param name="max_value" type="float" value="1" label="Maximum value of dataset"/>
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
360 <param name="invert" type="boolean" truevalue="True" falsevalue="False" label="Invert Color Scale" />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
361 </when>
6
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
362 <when value="z">
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
363 <conditional name="dynamic">
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
364 <param name="dynamic_select" type="select" label="Static or Dynamic Z-Index">
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
365 <option value="static">Static</option>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
366 <option value="dynamic">Dynamic (based on value)</option>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
367 </param>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
368 <when value="static">
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
369 <expand macro="zdepth" name="action_value"/>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
370 </when>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
371 <when value="dynamic">
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
372 <param name="min_value" type="float" value="-1" label="Expected minimum value of dataset"/>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
373 <param name="max_value" type="float" value="1" label="Expected maximum value of dataset"/>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
374 <param name="invert" type="boolean" truevalue="True" falsevalue="False" label="Invert Z-Index Mapping" />
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
375 </when>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
376 </conditional>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
377 </when>
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
378 </conditional>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
379 </repeat>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
380 <param name="continue_flow" type="boolean" truevalue="flow = continue" falsevalue="" label="Continue flow"
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
381 help="Allow rules after this one to be applied in addition to this rule. E.g. if one rule modifies font size, and another font colour, with continued flow they could both be applied rather than whichever was encountered first."/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
382 </repeat>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
383 </section>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
384 </xml>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
385
6
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
386 <xml name="link_color_action_options"
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
387 token_section="ERROR">
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
388
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
389 <conditional name="dynamic">
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
390 <param name="dynamic_select" type="select" label="Static / Dynamic Change">
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
391 <option value="static">Color is always applied</option>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
392 <option value="dynamic">Color is applied based on value</option>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
393 <option value="source">Color based on source chromosome color</option>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
394 <option value="dest">Color based on destination chromosome color</option>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
395 </param>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
396 <when value="static">
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
397 <expand macro="circos_color_alpha" label="@SECTION@ Color" name="action_value"/>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
398 </when>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
399 <when value="dynamic">
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
400 <expand macro="brewer_scale" name="action_value" label="@SECTION@ Color" help="@SECTION@ will be changed based on a mapping of dataset values to colours, but to do this the mapping needs to be defined. Minimum and maximum values are defined below, and will map to the minimum and maximum values of this brewer scale."/>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
401 <param name="min_value" type="float" value="-1" label="Minimum value of dataset"/>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
402 <param name="max_value" type="float" value="1" label="Maximum value of dataset"/>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
403 <param name="invert" type="boolean" truevalue="True" falsevalue="False" label="Invert Color Scale" />
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
404 </when>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
405 <when value="source">
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
406 </when>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
407 <when value="dest">
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
408 </when>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
409 </conditional>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
410 </xml>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
411
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
412 <xml name="linkrules">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
413 <section name="sec_link_rule" title="Rules">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
414 <repeat name="rules" title="Rule">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
415 <repeat name="conditions" title="Conditions to Apply" help="Multiple conditions will be combined using AND">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
416 <conditional name="application">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
417 <param name="application_select" type="select" label="Condition">
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
418 <option value="always" selected="true">True / Always Applied</option>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
419 <option value="random">Randomly</option>
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
420 <option value="interchr">Interchromosomal</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
421 <option value="intrachr">Intrachromosomal</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
422 <option value="chr">Chromosome</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
423 <option value="dist">Distance between sides</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
424 <option value="start1">Start position Left</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
425 <option value="end1">End Position Left</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
426 <option value="pos1">Middle position Left</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
427 <option value="size1">Size Left</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
428 <option value="start2">Start position Right</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
429 <option value="end2">End Position Right</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
430 <option value="pos2">Middle position Right</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
431 <option value="size2">Size Right</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
432 <option value="rev1">Reversed Left (link end is reversed (e.g. start &gt; end) </option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
433 <option value="rev2">Reversed Right (link end is reversed (e.g. start &gt; end) </option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
434 <option value="inv">Inverted (link is inverted (i.e. one of its ends is reversed). If both ends are reversed, the link is not inverted )</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
435 </param>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
436 <when value="chr">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
437 <expand macro="chromosome_comparison"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
438 </when>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
439 <when value="start1">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
440 <expand macro="integer_comparison"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
441 </when>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
442 <when value="end1">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
443 <expand macro="integer_comparison"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
444 </when>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
445 <when value="pos1">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
446 <expand macro="integer_comparison"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
447 </when>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
448 <when value="size1">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
449 <expand macro="integer_comparison"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
450 </when>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
451 <when value="start2">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
452 <expand macro="integer_comparison"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
453 </when>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
454 <when value="end2">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
455 <expand macro="integer_comparison"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
456 </when>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
457 <when value="pos2">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
458 <expand macro="integer_comparison"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
459 </when>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
460 <when value="size2">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
461 <expand macro="integer_comparison"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
462 </when>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
463 <when value="dist">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
464 <expand macro="integer_comparison"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
465 </when>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
466 <when value="rev1"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
467 <when value="rev2"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
468 <when value="inv"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
469 <when value="interchr"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
470 <when value="intrachr"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
471 <when value="always"/>
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
472 <when value="random">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
473 <param name="value" type="float" label="Percentage" value="0.5" min="0" max="1" help="Randomly apply with this probability"/>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
474 </when>
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
475 </conditional>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
476 </repeat>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
477 <repeat name="actions" title="Actions to Apply">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
478 <conditional name="action">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
479 <param name="action_select" type="select" label="Action">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
480 <option value="show">Change Visibility</option>
6
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
481 <option value="z">Change Z-index</option>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
482 <option value="color">Change Fill Color</option>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
483 <option value="stroke_color">Change Stroke Color (Ribbons Only)</option>
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
484 <option value="thickness">Change Thickness</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
485 </param>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
486 <when value="show">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
487 <param name="action_value" type="boolean" label="Show" truevalue="yes" falsevalue="no"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
488 </when>
6
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
489 <when value="stroke_color">
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
490 <expand macro="link_color_action_options" section="Stroke"/>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
491 </when>
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
492 <when value="color">
6
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
493 <expand macro="link_color_action_options" section="Fill"/>
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
494 </when>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
495 <when value="thickness">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
496 <param name="action_value" type="integer" value="1" label="Thickness"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
497 </when>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
498 <when value="z">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
499 <conditional name="dynamic">
6
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
500 <param name="dynamic_select" type="select" label="Static or Dynamic Z-Index">
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
501 <option value="static">Static</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
502 <option value="dynamic">Dynamic (based on value)</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
503 </param>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
504 <when value="static">
6
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
505 <expand macro="zdepth" name="action_value"/>
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
506 </when>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
507 <when value="dynamic">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
508 <param name="min_value" type="float" value="-1" label="Expected minimum value of dataset"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
509 <param name="max_value" type="float" value="1" label="Expected maximum value of dataset"/>
6
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents: 5
diff changeset
510 <param name="invert" type="boolean" truevalue="True" falsevalue="False" label="Invert Z-Index Mapping" />
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
511 </when>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
512 </conditional>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
513 </when>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
514 </conditional>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
515 </repeat>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
516
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
517 <param name="continue_flow" type="boolean" label="Continue flow" truevalue="flow = continue" falsevalue="" help="Allow rules after this one to be applied in addition to this rule. E.g. if one rule modifies font size, and another font colour, with continued flow they could both be applied rather than whichever was encountered first." />
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
518 </repeat>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
519 </section>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
520 </xml>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
521
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
522 <xml name="integer_comparison">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
523 <conditional name="comparison" >
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
524 <param name="compare" type="select" label="Comparison">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
525 <option value="lt">less than</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
526 <option value="gt">greater than</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
527 </param>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
528 <when value="lt">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
529 <param name="compval" value="0" type="integer" label="value"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
530 </when>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
531 <when value="gt">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
532 <param name="compval" value="0" type="integer" label="value"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
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533 </when>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
534 </conditional>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
535 </xml>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
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536
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
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537 <xml name="chromosome_comparison">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
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538 <conditional name="comparison" >
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
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539 <param name="compare" type="select" label="Comparison">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
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540 <option value="on">on chromosome (either side)</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
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541 <option value="from">from chromosome</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
542 <option value="to">to chromosome</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
543 <option value="fromto">from-to chromosome</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
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544 <option value="between">between chromosomes</option>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
545 </param>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
546 <!-- TODO select chromosome from metadata/file column instead of text fields -->
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
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547 <when value="on">
2
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
548 <param name="compval" value="chr1" type="text" label="Chromosome" help="Comma separated values are supported in this field"/>
0
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
549 </when>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
550 <when value="from">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
551 <param name="compval" value="chr1" type="text" label="Chromosome"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
552 </when>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
553 <when value="to">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
554 <param name="compval" value="chr1" type="text" label="Chromosome"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
555 </when>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
556 <when value="fromto">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
557 <param name="compval" value="chr1" type="text" label="From Chromosome"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
558 <param name="compval2" value="chr1" type="text" label="To Chromosome"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
559 </when>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
560 <when value="between">
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
561 <param name="compval" value="chr1" type="text" label="Chromosome"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
562 <param name="compval2" value="chr1" type="text" label="Chromosome"/>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
563 </when>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
564 </conditional>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
565 </xml>
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
566
ef5f8bbf7730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
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567 </macros>