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annotate macros.xml @ 7:b72f2db6d417 draft

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planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 86fb40a41d9e6012ea0b02d1cd77675f4bd971fb
author eric-rasche
date Sat, 10 Jun 2017 14:16:41 -0400
parents 169adf243c0a
children eb3af6e9f633
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e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
1 <?xml version="1.0"?>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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2 <macros>
6
169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec
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3 <token name="@WRAPPER_VERSION@">0.9-RC2</token>
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4 <xml name="requirements">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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5 <requirements>
5
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6 <requirement type="package" version="0.69.4">circos</requirement>
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7 <requirement type="package" version="2.2.3">libgd</requirement>
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8 <requirement type="package" version="2.7">python</requirement>
5
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9 <requirement type="package" version="0.6.4">bcbiogff</requirement>
b25b3518c2ce planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 7561690774be81155d79a3c38a77c098c59aa9a2
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10 <requirement type="package" version="1.67">biopython</requirement>
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11 </requirements>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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12 </xml>
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13
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14 <xml name="citations">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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15 <citations>
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16 <citation type="doi">10.1101/gr.092759.109</citation>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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17 </citations>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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18 </xml>
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19
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20 <xml name="circos_color"
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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21 token_label="Color"
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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22 token_name="color"
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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23 token_value="#000000"
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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24 token_help=""
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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25 >
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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26 <param label="@LABEL@" type="color" name="@NAME@" value="@VALUE@" help="@HELP@">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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27 <sanitizer>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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28 <valid initial="string.letters,string.digits">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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29 <add value="#" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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30 </valid>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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31 </sanitizer>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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32 </param>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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33 </xml>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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34
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35 <xml name="auto_color"
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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36 token_name="color"
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37 token_label="Color">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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38 <conditional name="@NAME@" label="@LABEL@">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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39 <param name="@NAME@_select" type="select" label="@LABEL@">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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40 <option value="automatic" selected="true">Automatic Selection</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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41 <option value="manual">Manual Specification</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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42 </param>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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43 <when value="automatic">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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44 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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45 <when value="manual">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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46 <param name="@NAME@" label="@LABEL@" type="color" value="#000000">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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47 <sanitizer>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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48 <valid initial="string.letters,string.digits">
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49 <add value="#" />
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50 </valid>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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51 </sanitizer>
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52 </param>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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53 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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54 </conditional>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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55 </xml>
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56
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57 <xml name="brewer_scale"
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58 token_name="color"
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59 token_label="Color">
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60 <param name="@NAME@" type="select" label="@LABEL@">
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61 <option value="purples-13-seq">Sequential: Purples</option>
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62 <option value="reds-13-seq">Sequential: Reds</option>
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63 <option value="oranges-13-seq">Sequential: Oranges</option>
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64 <option value="greens-13-seq">Sequential: Greens</option>
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65 <option value="blues-13-seq">Sequential: Blues</option>
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66 <option value="greys-13-seq">Sequential: Greys</option>
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67
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68 <option value="bugn-13-seq">Sequential: Blue - Green</option>
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69 <option value="bupu-13-seq">Sequential: Blue - Purple</option>
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70 <option value="gnbu-13-seq">Sequential: Green - Blue</option>
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71 <option value="orrd-13-seq">Sequential: Orange - Red</option>
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72 <option value="pubu-13-seq">Sequential: Purple - Blue</option>
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73 <option value="pubugn-13-seq">Sequential: Purple - Blue - Green</option>
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74 <option value="purd-13-seq">Sequential: Purple - Red</option>
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75 <option value="rdpu-13-seq">Sequential: Red - Purple</option>
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76 <option value="ylgn-13-seq">Sequential: Yellow - Green</option>
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77 <option value="ylgnbu-13-seq">Sequential: Yellow - Green - Blue</option>
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78 <option value="ylorbr-13-seq">Sequential: Yellow - Orange - Brown</option>
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79 <option value="ylorrd-13-seq">Sequential: Yellow - Orange - Red</option>
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80
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81 <option value="brbg-15-div">Diverging: Brown - Blue Green</option>
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82 <option value="piyg-15-div">Diverging: Pink - Yellow Green</option>
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83 <option value="prgn-15-div">Diverging: Purple - Green</option>
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84 <option value="puor-15-div">Diverging: Purple - Orange</option>
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85 <option value="rdbu-15-div">Diverging: Red - Blue</option>
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86 <option value="rdgy-15-div">Diverging: Red - Grey</option>
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87 <option value="rdylbu-15-div">Diverging: Red - Yellow - Blue</option>
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88 <option value="rdylgn-15-div">Diverging: Red - Yellow - Green</option>
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89 <option value="spectral-15-div">Diverging: Spectral</option>
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90
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91 <option value="accent-8-qual">Qualitative: Accent</option>
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eric-rasche
parents:
diff changeset
92 <option value="dark2-8-qual">Qualitative: Dark2</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
93 <option value="paired-12-qual">Qualitative: Paired</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
94 <option value="pastel1-9-qual">Qualitative: Pastel1</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
95 <option value="pastel2-8-qual">Qualitative: Pastel2</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
96 <option value="set1-9-qual">Qualitative: Set1</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
97 <option value="set2-8-qual">Qualitative: Set2</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
98 <option value="set3-12-qual">Qualitative: Set3</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
99 </param>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
100 </xml>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
101
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
102 <xml name="axes">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
103 <section name="sec_axes" title="Axes">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
104 <repeat name="axes" title="Axis">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
105 <param name="y0" type="float" value="0.0" label="Inside Radius (y0)" help="This is relative to the subplot you are currently in."/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
106 <param name="y1" type="float" value="1" label="Outside Radius (y1)" help="This is relative to the subplot you are currently in."/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
107
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
108 <expand macro="circos_color"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
109 <param name="thickness" type="integer" value="1" label="Thickness"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
110 <param name="spacing" type="float" value="0.1" label="Spacing" help="Relative spacing between each concentric arc"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
111 </repeat>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
112 </section>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
113 </xml>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
114
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
115 <xml name="backgrounds">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
116 <section name="sec_bkgs" title="Backgrounds">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
117 <repeat name="backgrounds" title="Background">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
118 <param name="y0" type="float" value="0.0" label="Inside Radius (y0)" help="This is relative to the subplot you are currently in."/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
119 <param name="y1" type="float" value="1" label="Outside Radius (y1)" help="This is relative to the subplot you are currently in."/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
120 <expand macro="circos_color"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
121 </repeat>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
122 </section>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
123 </xml>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
124
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
125 <xml name="rules">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
126 <section name="sec_rule" title="Rules">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
127 <repeat name="rules" title="Rule">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
128 <repeat name="conditions" title="Conditions to Apply">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
129 <conditional name="application">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
130 <param name="application_select" type="select" label="Condition">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
131 <option value="1">Apply to Every Point</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
132 <option value="on">Check for presence/absence per chromosome</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
133 <option value="pos">Based on numerical position</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
134 <option value="value">Apply based on point value</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
135 <option value="var">Apply based on GFF3 qualifier value (when available)</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
136 </param>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
137 <when value="1">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
138 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
139 <when value="on">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
140 <param name="on_genomes" type="text" label="Comma separated list of contig IDs"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
141 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
142 <when value="pos">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
143 <param name="pos_gt" type="float" label="Greater than this base" value="1000.0" help="Leave as zero to disable this test"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
144 <param name="pos_lt" type="float" label="Less than this base" value="0.0" help="Leave as zero to disable this test"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
145 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
146 <when value="value">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
147 <param name="pos_gt" type="float" label="Points above this value" value="0.0" help="Leave as zero to disable this test"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
148 <param name="pos_lt" type="float" label="Points below this value" value="0.0" help="Leave as zero to disable this test"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
149 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
150 <when value="var">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
151 <param name="varname" type="text" label="Qualifier name"
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
152 help="Set to the name of the qualifier in the GFF3 file you wish to compare against" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
153
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
154 <param name="cond_select" type="select" label="Condition">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
155 <option value="eq">Equal to (string)</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
156 <option value="ne">Not equal to (string)</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
157 </param>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
158
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
159 <param name="varvalue" type="text" label="Qualifier value to compare against"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
160 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
161 </conditional>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
162 </repeat>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
163 <repeat name="actions" title="Actions to Apply">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
164 <conditional name="action">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
165 <param name="action_select" type="select" label="Action">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
166 <option value="show">Change Visibility</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
167 <option value="fill_color">Change Fill Color for all points</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
168 <option value="fill_color_value">Change Fill Color based on Value</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
169 <option value="color">Change Stroke Color</option>
5
b25b3518c2ce planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 7561690774be81155d79a3c38a77c098c59aa9a2
eric-rasche
parents: 4
diff changeset
170 <option value="color_value">Change Stroke Color based on Value</option>
0
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
171 </param>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
172 <when value="show">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
173 <param name="action_value" type="boolean" truevalue="yes" falsevalue="no" label="Show"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
174 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
175 <when value="fill_color">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
176 <expand macro="circos_color" name="action_value" label="Fill Color"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
177 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
178 <when value="color">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
179 <expand macro="circos_color" name="action_value" label="Stroke Color"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
180 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
181 <when value="fill_color_value">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
182 <expand macro="brewer_scale" name="action_value" label="Fill Color"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
183 <param name="min_value" type="float" value="-1" label="Expected minimum value of dataset"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
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184 <param name="max_value" type="float" value="1" label="Expected maximum value of dataset"/>
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185 </when>
5
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186 <when value="color_value">
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187 <expand macro="brewer_scale" name="action_value" label="Stroke Color"/>
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188 <param name="min_value" type="float" value="-1" label="Expected minimum value of dataset"/>
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189 <param name="max_value" type="float" value="1" label="Expected maximum value of dataset"/>
b25b3518c2ce planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 7561690774be81155d79a3c38a77c098c59aa9a2
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190 </when>
0
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191 </conditional>
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192 </repeat>
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193 <param name="continue_flow" type="boolean" truevalue="flow = continue" falsevalue="" label="Continue flow"
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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194 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."/>
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195 </repeat>
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196 </section>
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197 </xml>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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198
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199 <xml name="linkrules">
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200 <section name="sec_link_rule" title="Rules">
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201 <repeat name="rules" title="Rule">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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202 <repeat name="conditions" title="Conditions to Apply" help="Multiple conditions will be combined using AND">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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203 <conditional name="application">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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204 <param name="application_select" type="select" label="Condition">
6
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205 <option value="always">True / Always Applied</option>
0
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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206 <option value="interchr">Interchromosomal</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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207 <option value="intrachr">Intrachromosomal</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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208 <option value="chr">Chromosome</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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209 <option value="dist">Distance between sides</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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210 <option value="start1">Start position Left</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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211 <option value="end1">End Position Left</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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212 <option value="pos1">Middle position Left</option>
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213 <option value="size1">Size Left</option>
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214 <option value="start2">Start position Right</option>
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eric-rasche
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215 <option value="end2">End Position Right</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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216 <option value="pos2">Middle position Right</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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217 <option value="size2">Size Right</option>
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218 <option value="rev1">Reversed Left (link end is reversed (e.g. start &gt; end) </option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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219 <option value="rev2">Reversed Right (link end is reversed (e.g. start &gt; end) </option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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220 <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>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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221 </param>
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222 <when value="chr">
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223 <expand macro="chromosome_comparison"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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224 </when>
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225 <when value="start1">
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226 <expand macro="integer_comparison"/>
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227 </when>
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228 <when value="end1">
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229 <expand macro="integer_comparison"/>
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230 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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231 <when value="pos1">
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232 <expand macro="integer_comparison"/>
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233 </when>
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234 <when value="size1">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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235 <expand macro="integer_comparison"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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236 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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237 <when value="start2">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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238 <expand macro="integer_comparison"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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239 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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240 <when value="end2">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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241 <expand macro="integer_comparison"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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242 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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243 <when value="pos2">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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244 <expand macro="integer_comparison"/>
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245 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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246 <when value="size2">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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247 <expand macro="integer_comparison"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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248 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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249 <when value="dist">
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eric-rasche
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250 <expand macro="integer_comparison"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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251 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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252 <when value="rev1"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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253 <when value="rev2"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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254 <when value="inv"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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255 <when value="interchr"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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256 <when value="intrachr"/>
6
169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec
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257 <when value="always"/>
0
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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258 </conditional>
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259 </repeat>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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260 <repeat name="actions" title="Actions to Apply">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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261 <conditional name="action">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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262 <param name="action_select" type="select" label="Action">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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263 <option value="show">Change Visibility</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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264 <option value="color">Change Link Color</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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265 <option value="thickness">Change Thickness</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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266 <option value="z">Change Z-depth</option>
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267 </param>
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268 <when value="show">
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eric-rasche
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269 <param name="action_value" type="boolean" label="Show" truevalue="yes" falsevalue="no"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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270 </when>
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271 <when value="color">
6
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eric-rasche
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diff changeset
272 <conditional name="dynamic">
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eric-rasche
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273 <param name="dynamic_select" type="select" label="Static / Dynamic Change">
169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec
eric-rasche
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274 <option value="static">Static: Change is always applied</option>
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eric-rasche
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275 <option value="dynamic">Dynamic: Change is sometimes applied</option>
169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec
eric-rasche
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276 </param>
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eric-rasche
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277 <when value="static">
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eric-rasche
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278 <expand macro="circos_color" label="Link Color" name="action_value"/>
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eric-rasche
parents: 5
diff changeset
279 </when>
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280 <when value="dynamic">
7
b72f2db6d417 planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 86fb40a41d9e6012ea0b02d1cd77675f4bd971fb
eric-rasche
parents: 6
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281 <expand macro="brewer_scale" label="Fill Color" name="action_value"/>
6
169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec
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282 <param name="min_value" type="float" value="-1" label="Expected minimum value of dataset"/>
169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec
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parents: 5
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283 <param name="max_value" type="float" value="1" label="Expected maximum value of dataset"/>
169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec
eric-rasche
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284 </when>
169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec
eric-rasche
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285 </conditional>
0
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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286 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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287 <when value="thickness">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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288 <param name="action_value" type="integer" value="1" label="Thickness"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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289 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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290 <when value="z">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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291 <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"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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292 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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293 </conditional>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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294 </repeat>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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295
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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296 <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." />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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297 </repeat>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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298 </section>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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299 </xml>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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300
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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301 <xml name="integer_comparison">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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302 <conditional name="comparison" >
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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303 <param name="compare" type="select" label="Comparison">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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304 <option value="lt">less than</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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305 <option value="gt">greater than</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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306 </param>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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307 <when value="lt">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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308 <param name="compval" value="0" type="integer" label="value"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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309 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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310 <when value="gt">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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diff changeset
311 <param name="compval" value="0" type="integer" label="value"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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312 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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313 </conditional>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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314 </xml>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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315
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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316 <xml name="chromosome_comparison">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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317 <conditional name="comparison" >
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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318 <param name="compare" type="select" label="Comparison">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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319 <option value="on">on chromosome (either side)</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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320 <option value="from">from chromosome</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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321 <option value="to">to chromosome</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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322 <option value="fromto">from-to chromosome</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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323 <option value="between">between chromosomes</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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324 </param>
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325 <!-- TODO select chromosome from metadata/file column instead of text fields -->
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326 <when value="on">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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327 <param name="compval" value="chr1" type="text" label="Chromosome"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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328 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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329 <when value="from">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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330 <param name="compval" value="chr1" type="text" label="Chromosome"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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331 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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332 <when value="to">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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333 <param name="compval" value="chr1" type="text" label="Chromosome"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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334 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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335 <when value="fromto">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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336 <param name="compval" value="chr1" type="text" label="From Chromosome"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
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337 <param name="compval2" value="chr1" type="text" label="To Chromosome"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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338 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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339 <when value="between">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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340 <param name="compval" value="chr1" type="text" label="Chromosome"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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341 <param name="compval2" value="chr1" type="text" label="Chromosome"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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342 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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343 </conditional>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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344 </xml>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
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345
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346 </macros>