Mercurial > repos > iuc > circos

annotate macros.xml @ 3:a2b4b1b1a88e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit f04fe62fb7dbad75e597da8cd674cfe36ed3d80a"
author iuc
date Mon, 02 Dec 2019 13:13:27 +0000
parents 890ef899a3d7
children 6d45ebe16927
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8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
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1 <?xml version="1.0"?>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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2 <macros>
2
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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3 <token name="@CIRCOS_VERSION@">0.69.8</token>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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4
3
a2b4b1b1a88e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit f04fe62fb7dbad75e597da8cd674cfe36ed3d80a"
iuc
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5 <token name="@WRAPPER_VERSION@">@CIRCOS_VERSION@+galaxy2</token>
2
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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6
0
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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7 <xml name="requirements">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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8 <requirements>
2
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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9 <requirement type="package" version="@CIRCOS_VERSION@">circos</requirement>
0
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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10 <requirement type="package" version="2.7">python</requirement>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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11 <requirement type="package" version="0.6.4">bcbiogff</requirement>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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12 <requirement type="package" version="1.70">biopython</requirement>
2
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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13 <requirement type="package" version="0.3.13">pybigwig</requirement>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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14 <requirement type="package" version="0.23">circos-tools</requirement>
3
a2b4b1b1a88e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit f04fe62fb7dbad75e597da8cd674cfe36ed3d80a"
iuc
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15 <requirement type="package" version="1.29">tar</requirement>
2
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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16 <yield />
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8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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17 </requirements>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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18 </xml>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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19
2
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20 <token name="@UTILS@">
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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21 #def circosColor($value)
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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22 #set $value = str($value)
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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23 #set $r = int($value[1:3], 16)
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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24 #set $g = int($value[3:5], 16)
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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25 #set $b = int($value[5:], 16)
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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26 $r, $g, $b
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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27 #end def
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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28 #def circosColorAlpha($value, $alpha)
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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29 #set $value = str($value)
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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30 #set $r = int($value[1:3], 16)
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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31 #set $g = int($value[3:5], 16)
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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32 #set $b = int($value[5:], 16)
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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33 #set $a = float($alpha)
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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34 $r, $g, $b, $a
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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35 #end def
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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36 #def chromosomesToOrder($value)
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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37 #set $q = ','.join([x if ':' not in x else x[x:x.index(':')] for x in str($value).split(';')])
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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38 $q
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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39 #end def
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
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40 </token>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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41
0
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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42 <xml name="citations">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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43 <citations>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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44 <citation type="doi">10.1101/gr.092759.109</citation>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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45 </citations>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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46 </xml>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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47
2
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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48 <xml name="stroke_opts">
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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49 <expand macro="circos_color_alpha" name="stroke_color" value="#000000" label="Stroke Color"/>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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50 <param name="stroke_thickness" type="integer" value="1" label="Stroke Thickness"/>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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51 </xml>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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52
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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53 <xml name="minmax">
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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54 <conditional name="minmax">
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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55 <param name="minmax_select" type="select" label="Minimum / maximum options">
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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56 <option value="yes">Supply min/max values</option>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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57 <option value="no" selected="true">Plot all values</option>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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58 </param>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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59 <when value="yes">
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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60 <param name="min_value" type="float" value="1.0" label="Minimum value" />
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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61 <param name="max_value" type="float" value="5.0" label="Maximum value" />
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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62 </when>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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63 <when value="no">
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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64 </when>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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65 </conditional>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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66 </xml>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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67
0
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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68 <xml name="circos_color"
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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69 token_label="Color"
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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70 token_name="color"
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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71 token_value="#000000"
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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72 token_help=""
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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73 >
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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74 <param label="@LABEL@" type="color" name="@NAME@" value="@VALUE@" help="@HELP@">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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75 <sanitizer>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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76 <valid initial="string.letters,string.digits">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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77 <add value="#" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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78 </valid>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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79 </sanitizer>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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80 </param>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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81 </xml>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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82
2
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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83 <xml name="circos_color_alpha"
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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84 token_label="Color"
0
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
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85 token_name="color"
2
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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86 token_value="#000000"
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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87 token_help=""
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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diff changeset
88 >
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
89 <param label="@LABEL@" type="color" name="@NAME@" value="@VALUE@" help="@HELP@">
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
90 <sanitizer>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
91 <valid initial="string.letters,string.digits">
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
92 <add value="#" />
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
93 </valid>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
94 </sanitizer>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
95 </param>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
96 <param name="@NAME@_alpha" type="float" label="Transparency" value="1" min="0" max="1" help="1 = fully opaque, 0 = fully transparent"/>
0
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
97 </xml>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
98
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
99 <xml name="brewer_scale"
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
100 token_name="color"
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
101 token_label="Color">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
102 <param name="@NAME@" type="select" label="@LABEL@">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
103 <option value="purples-13-seq">Sequential: Purples</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
104 <option value="reds-13-seq">Sequential: Reds</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
105 <option value="oranges-13-seq">Sequential: Oranges</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
106 <option value="greens-13-seq">Sequential: Greens</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
107 <option value="blues-13-seq">Sequential: Blues</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
108 <option value="greys-13-seq">Sequential: Greys</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
109
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
110 <option value="bugn-13-seq">Sequential: Blue - Green</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
111 <option value="bupu-13-seq">Sequential: Blue - Purple</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
112 <option value="gnbu-13-seq">Sequential: Green - Blue</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
113 <option value="orrd-13-seq">Sequential: Orange - Red</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
114 <option value="pubu-13-seq">Sequential: Purple - Blue</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
115 <option value="pubugn-13-seq">Sequential: Purple - Blue - Green</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
116 <option value="purd-13-seq">Sequential: Purple - Red</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
117 <option value="rdpu-13-seq">Sequential: Red - Purple</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
118 <option value="ylgn-13-seq">Sequential: Yellow - Green</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
119 <option value="ylgnbu-13-seq">Sequential: Yellow - Green - Blue</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
120 <option value="ylorbr-13-seq">Sequential: Yellow - Orange - Brown</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
121 <option value="ylorrd-13-seq">Sequential: Yellow - Orange - Red</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
122
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
123 <option value="brbg-15-div">Diverging: Brown - Blue Green</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
124 <option value="piyg-15-div">Diverging: Pink - Yellow Green</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
125 <option value="prgn-15-div">Diverging: Purple - Green</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
126 <option value="puor-15-div">Diverging: Purple - Orange</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
127 <option value="rdbu-15-div">Diverging: Red - Blue</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
128 <option value="rdgy-15-div">Diverging: Red - Grey</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
129 <option value="rdylbu-15-div">Diverging: Red - Yellow - Blue</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
130 <option value="rdylgn-15-div">Diverging: Red - Yellow - Green</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
131 <option value="spectral-15-div">Diverging: Spectral</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
132
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
133 <option value="accent-8-qual">Qualitative: Accent</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
134 <option value="dark2-8-qual">Qualitative: Dark2</option>
2
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
135 <option value="paired-12-qual" selected="true">Qualitative: Paired</option>
0
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
136 <option value="pastel1-9-qual">Qualitative: Pastel1</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
137 <option value="pastel2-8-qual">Qualitative: Pastel2</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
138 <option value="set1-9-qual">Qualitative: Set1</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
139 <option value="set2-8-qual">Qualitative: Set2</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
140 <option value="set3-12-qual">Qualitative: Set3</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
141 </param>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
142 </xml>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
143
2
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
144 <xml name="font_select"
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
145 token_normal="true"
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
146 token_bold="false">
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
147 <param name="font" type="select" label="Font">
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
148 <option value="light">light</option>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
149 <option value="normal" selected="@NORMAL@">normal</option>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
150 <option value="default">default</option>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
151 <option value="semibold">semibold</option>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
152 <option value="bold" selected="@BOLD@">bold</option>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
153 <option value="italic">italic</option>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
154 <option value="bolditalic">bolditalic</option>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
155 <option value="italicbold">italicbold</option>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
156 </param>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
157 </xml>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
158
0
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
159 <xml name="axes">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
160 <section name="sec_axes" title="Axes">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
161 <repeat name="axes" title="Axis">
2
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
162 <param name="y0" type="float" value="0" min="0" max="1" label="Inside Radius" help="Value must be between 1 (outer edge of track) and 0 (inner edge of the track)"/>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
163 <param name="y1" type="float" value="1" min="0" max="1" label="Outside Radius" help="Value must be between 1 (outer edge of track) and 0 (inner edge of the track)"/>
0
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
164
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
165 <expand macro="circos_color"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
166 <param name="thickness" type="integer" value="1" label="Thickness"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
167 <param name="spacing" type="float" value="0.1" label="Spacing" help="Relative spacing between each concentric arc"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
168 </repeat>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
169 </section>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
170 </xml>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
171
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
172 <xml name="backgrounds">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
173 <section name="sec_bkgs" title="Backgrounds">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
174 <repeat name="backgrounds" title="Background">
2
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
175 <param name="y0" type="float" value="0" min="0" max="1" label="Inside Radius" help="Value must be between 1 (outer edge of track) and 0 (inner edge of the track)"/>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
176 <param name="y1" type="float" value="1" min="0" max="1" label="Outside Radius" help="Value must be between 1 (outer edge of track) and 0 (inner edge of the track)"/>
0
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
177 <expand macro="circos_color"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
178 </repeat>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
179 </section>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
180 </xml>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
181
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
182 <xml name="rules">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
183 <section name="sec_rule" title="Rules">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
184 <repeat name="rules" title="Rule">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
185 <repeat name="conditions" title="Conditions to Apply">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
186 <conditional name="application">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
187 <param name="application_select" type="select" label="Condition">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
188 <option value="1">Apply to Every Point</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
189 <option value="on">Check for presence/absence per chromosome</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
190 <option value="pos">Based on numerical position</option>
2
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
191 <option value="random">Randomly</option>
0
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
192 <option value="value">Apply based on point value</option>
2
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
193 <option value="var">Apply based on qualifier value (when available)</option>
0
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
194 </param>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
195 <when value="1">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
196 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
197 <when value="on">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
198 <param name="on_genomes" type="text" label="Comma separated list of contig IDs"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
199 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
200 <when value="pos">
2
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
201 <param name="pos_gt" type="float" label="Greater than this base" optional="true"/>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
202 <param name="pos_lt" type="float" label="Less than this base" optional="true"/>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
203 <param name="pos_lt_sub" type="boolean" truevalue="yes" falsevalue="no" label="Count 'Less than this base' from end of chromosome" />
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
204 </when>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
205 <when value="random">
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
206 <param name="value" type="float" label="Percentage of bins" value="0.5" min="0" max="1" help="Randomly apply with this probability"/>
0
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
207 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
208 <when value="value">
2
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
209 <param name="pos_gt" type="float" label="Points above this value" optional="true"/>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
210 <param name="pos_lt" type="float" label="Points below this value" optional="true"/>
0
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
211 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
212 <when value="var">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
213 <param name="varname" type="text" label="Qualifier name"
2
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
214 help="Set to the name of the qualifier in the file you wish to compare against" />
0
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
215
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
216 <param name="cond_select" type="select" label="Condition">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
217 <option value="eq">Equal to (string)</option>
2
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
218 <option value="==">Equal to (numeric)</option>
0
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
219 <option value="ne">Not equal to (string)</option>
2
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
220 <option value="!=">Not equal to (numeric)</option>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
221 <option value="&lt;">Less than (numeric)</option>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
222 <option value="&gt;">Greater than (numeric)</option>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
223 <option value="%">Modulus (numeric)</option>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
224 <sanitizer>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
225 <valid initial="string.letters">
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
226 <add value="&gt;" />
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
227 <add value="&lt;" />
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
228 <add value="!" />
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
229 <add value="=" />
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
230 <add value="%" />
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
231 </valid>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
232 </sanitizer>
0
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
233 </param>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
234
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
235 <param name="varvalue" type="text" label="Qualifier value to compare against"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
236 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
237 </conditional>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
238 </repeat>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
239 <repeat name="actions" title="Actions to Apply">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
240 <conditional name="action">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
241 <param name="action_select" type="select" label="Action">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
242 <option value="show">Change Visibility</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
243 <option value="fill_color">Change Fill Color for all points</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
244 <option value="fill_color_value">Change Fill Color based on Value</option>
2
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
245 <option value="stroke_color">Change Stroke Color</option>
0
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
246 <option value="color_value">Change Stroke Color based on Value</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
247 </param>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
248 <when value="show">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
249 <param name="action_value" type="boolean" truevalue="yes" falsevalue="no" label="Show"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
250 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
251 <when value="fill_color">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
252 <expand macro="circos_color" name="action_value" label="Fill Color"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
253 </when>
2
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
254 <when value="stroke_color">
0
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
255 <expand macro="circos_color" name="action_value" label="Stroke Color"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
256 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
257 <when value="fill_color_value">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
258 <expand macro="brewer_scale" name="action_value" label="Fill Color"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
259 <param name="min_value" type="float" value="-1" label="Expected minimum value of dataset"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
260 <param name="max_value" type="float" value="1" label="Expected maximum value of dataset"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
261 <param name="invert" type="boolean" truevalue="True" falsevalue="False" label="Invert Color Scale" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
262 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
263 <when value="color_value">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
264 <expand macro="brewer_scale" name="action_value" label="Stroke Color"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
265 <param name="min_value" type="float" value="-1" label="Expected minimum value of dataset"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
266 <param name="max_value" type="float" value="1" label="Expected maximum value of dataset"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
267 <param name="invert" type="boolean" truevalue="True" falsevalue="False" label="Invert Color Scale" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
268 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
269 </conditional>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
270 </repeat>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
271 <param name="continue_flow" type="boolean" truevalue="flow = continue" falsevalue="" label="Continue flow"
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
272 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."/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
273 </repeat>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
274 </section>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
275 </xml>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
276
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
277 <xml name="linkrules">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
278 <section name="sec_link_rule" title="Rules">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
279 <repeat name="rules" title="Rule">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
280 <repeat name="conditions" title="Conditions to Apply" help="Multiple conditions will be combined using AND">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
281 <conditional name="application">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
282 <param name="application_select" type="select" label="Condition">
2
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
283 <option value="always" selected="true">True / Always Applied</option>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
284 <option value="random">Randomly</option>
0
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
285 <option value="interchr">Interchromosomal</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
286 <option value="intrachr">Intrachromosomal</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
287 <option value="chr">Chromosome</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
288 <option value="dist">Distance between sides</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
289 <option value="start1">Start position Left</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
290 <option value="end1">End Position Left</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
291 <option value="pos1">Middle position Left</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
292 <option value="size1">Size Left</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
293 <option value="start2">Start position Right</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
294 <option value="end2">End Position Right</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
295 <option value="pos2">Middle position Right</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
296 <option value="size2">Size Right</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
297 <option value="rev1">Reversed Left (link end is reversed (e.g. start &gt; end) </option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
298 <option value="rev2">Reversed Right (link end is reversed (e.g. start &gt; end) </option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
299 <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>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
300 </param>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
301 <when value="chr">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
302 <expand macro="chromosome_comparison"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
303 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
304 <when value="start1">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
305 <expand macro="integer_comparison"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
306 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
307 <when value="end1">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
308 <expand macro="integer_comparison"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
309 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
310 <when value="pos1">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
311 <expand macro="integer_comparison"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
312 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
313 <when value="size1">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
314 <expand macro="integer_comparison"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
315 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
316 <when value="start2">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
317 <expand macro="integer_comparison"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
318 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
319 <when value="end2">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
320 <expand macro="integer_comparison"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
321 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
322 <when value="pos2">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
323 <expand macro="integer_comparison"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
324 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
325 <when value="size2">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
326 <expand macro="integer_comparison"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
327 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
328 <when value="dist">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
329 <expand macro="integer_comparison"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
330 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
331 <when value="rev1"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
332 <when value="rev2"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
333 <when value="inv"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
334 <when value="interchr"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
335 <when value="intrachr"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
336 <when value="always"/>
2
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
337 <when value="random">
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
338 <param name="value" type="float" label="Percentage" value="0.5" min="0" max="1" help="Randomly apply with this probability"/>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
339 </when>
0
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
340 </conditional>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
341 </repeat>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
342 <repeat name="actions" title="Actions to Apply">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
343 <conditional name="action">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
344 <param name="action_select" type="select" label="Action">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
345 <option value="show">Change Visibility</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
346 <option value="color">Change Link Color</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
347 <option value="thickness">Change Thickness</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
348 <option value="z">Change Z-depth</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
349 </param>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
350 <when value="show">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
351 <param name="action_value" type="boolean" label="Show" truevalue="yes" falsevalue="no"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
352 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
353 <when value="color">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
354 <conditional name="dynamic">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
355 <param name="dynamic_select" type="select" label="Static / Dynamic Change">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
356 <option value="static">Static: Change is always applied</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
357 <option value="dynamic">Dynamic: Change is sometimes applied</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
358 </param>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
359 <when value="static">
2
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
360 <expand macro="circos_color_alpha" label="Link Color" name="action_value"/>
0
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
361 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
362 <when value="dynamic">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
363 <expand macro="brewer_scale" label="Fill Color" name="action_value"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
364 <param name="min_value" type="float" value="-1" label="Expected minimum value of dataset"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
365 <param name="max_value" type="float" value="1" label="Expected maximum value of dataset"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
366 <param name="invert" type="boolean" truevalue="True" falsevalue="False" label="Invert Color Scale" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
367 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
368 </conditional>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
369 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
370 <when value="thickness">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
371 <param name="action_value" type="integer" value="1" label="Thickness"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
372 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
373 <when value="z">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
374 <conditional name="dynamic">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
375 <param name="dynamic_select" type="select" label="Static or Dynamic Z-Depth">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
376 <option value="static">Static</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
377 <option value="dynamic">Dynamic (based on value)</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
378 </param>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
379 <when value="static">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
380 <param name="action_value" type="float" value="1" label="Z-depth" help="Datasets with a higher z-depth value are drawn on top of datasets with lower z value"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
381 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
382 <when value="dynamic">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
383 <param name="min_value" type="float" value="-1" label="Expected minimum value of dataset"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
384 <param name="max_value" type="float" value="1" label="Expected maximum value of dataset"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
385 <param name="invert" type="boolean" truevalue="True" falsevalue="False" label="Invert Z-Depth Mapping" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
386 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
387 </conditional>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
388 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
389 </conditional>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
390 </repeat>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
391
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
392 <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." />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
393 </repeat>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
394 </section>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
395 </xml>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
396
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
397 <xml name="integer_comparison">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
398 <conditional name="comparison" >
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
399 <param name="compare" type="select" label="Comparison">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
400 <option value="lt">less than</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
401 <option value="gt">greater than</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
402 </param>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
403 <when value="lt">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
404 <param name="compval" value="0" type="integer" label="value"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
405 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
406 <when value="gt">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
407 <param name="compval" value="0" type="integer" label="value"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
408 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
409 </conditional>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
410 </xml>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
411
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
412 <xml name="chromosome_comparison">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
413 <conditional name="comparison" >
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
414 <param name="compare" type="select" label="Comparison">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
415 <option value="on">on chromosome (either side)</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
416 <option value="from">from chromosome</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
417 <option value="to">to chromosome</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
418 <option value="fromto">from-to chromosome</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
419 <option value="between">between chromosomes</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
420 </param>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
421 <!-- TODO select chromosome from metadata/file column instead of text fields -->
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
422 <when value="on">
2
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
iuc
parents: 1
diff changeset
423 <param name="compval" value="chr1" type="text" label="Chromosome" help="Comma separated values are supported in this field"/>
0
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
424 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
425 <when value="from">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
426 <param name="compval" value="chr1" type="text" label="Chromosome"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
427 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
428 <when value="to">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
429 <param name="compval" value="chr1" type="text" label="Chromosome"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
430 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
431 <when value="fromto">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
432 <param name="compval" value="chr1" type="text" label="From Chromosome"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
433 <param name="compval2" value="chr1" type="text" label="To Chromosome"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
434 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
435 <when value="between">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
436 <param name="compval" value="chr1" type="text" label="Chromosome"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
437 <param name="compval2" value="chr1" type="text" label="Chromosome"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
438 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
439 </conditional>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
440 </xml>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
441
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
442 </macros>