Mercurial > repos > iuc > circos

annotate macros.xml @ 1:95664f8de269 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 24c6ef0ca00b91b3f184a5cce3ad0f9435b27b46
author iuc
date Thu, 04 Oct 2018 06:05:11 -0400
parents 8464186c8503
children 890ef899a3d7
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
2 <macros>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
3 <token name="@WRAPPER_VERSION@">0.9-RC2</token>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
4 <xml name="requirements">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
5 <requirements>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
6 <requirement type="package" version="0.69.5">circos</requirement>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
7 <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
iuc
parents:
diff changeset
8 <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
iuc
parents:
diff changeset
9 <requirement type="package" version="1.70">biopython</requirement>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
10 </requirements>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
11 </xml>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
12
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
13 <xml name="citations">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
14 <citations>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
15 <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
iuc
parents:
diff changeset
16 </citations>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
17 </xml>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
18
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
19 <xml name="circos_color"
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
20 token_label="Color"
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
21 token_name="color"
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
22 token_value="#000000"
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
23 token_help=""
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
24 >
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
25 <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
iuc
parents:
diff changeset
26 <sanitizer>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
27 <valid initial="string.letters,string.digits">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
28 <add value="#" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
29 </valid>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
30 </sanitizer>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
31 </param>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
32 </xml>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
33
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
34 <xml name="auto_color"
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
35 token_name="color"
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
36 token_label="Color">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
37 <conditional name="@NAME@" label="@LABEL@">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
38 <param name="@NAME@_select" 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
39 <option value="automatic" selected="true">Automatic Selection</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
40 <option value="manual">Manual Specification</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
41 </param>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
42 <when value="automatic">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
43 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
44 <when value="manual">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
45 <param name="@NAME@" label="@LABEL@" type="color" value="#000000">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
46 <sanitizer>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
47 <valid initial="string.letters,string.digits">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
48 <add value="#" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
49 </valid>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
50 </sanitizer>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
51 </param>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
52 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
53 </conditional>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
54 </xml>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
55
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
56 <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
57 token_name="color"
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
58 token_label="Color">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
59 <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
60 <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
61 <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
62 <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
63 <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
64 <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
65 <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
66
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
67 <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
68 <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
69 <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
70 <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
71 <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
72 <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
73 <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
74 <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
75 <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
76 <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
77 <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
78 <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
79
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
80 <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
81 <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
82 <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
83 <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
84 <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
85 <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
86 <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
87 <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
88 <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
89
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
90 <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
91 <option value="dark2-8-qual">Qualitative: Dark2</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
92 <option value="paired-12-qual">Qualitative: Paired</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
93 <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
94 <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
95 <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
96 <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
97 <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
98 </param>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
99 </xml>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
100
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
101 <xml name="axes">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
102 <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
103 <repeat name="axes" title="Axis">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
104 <param name="y0" type="float" value="0.0" label="Inside Radius (y0)" help="This is relative to the subplot you are currently in."/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
105 <param name="y1" type="float" value="1" label="Outside Radius (y1)" help="This is relative to the subplot you are currently in."/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
106
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
107 <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
108 <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
109 <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
110 </repeat>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
111 </section>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
112 </xml>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
113
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
114 <xml name="backgrounds">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
115 <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
116 <repeat name="backgrounds" title="Background">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
117 <param name="y0" type="float" value="0.0" label="Inside Radius (y0)" help="This is relative to the subplot you are currently in."/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
118 <param name="y1" type="float" value="1" label="Outside Radius (y1)" help="This is relative to the subplot you are currently in."/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
119 <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
120 </repeat>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
121 </section>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
122 </xml>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
123
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
124 <xml name="rules">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
125 <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
126 <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
127 <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
128 <conditional name="application">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
129 <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
130 <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
131 <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
132 <option value="pos">Based on numerical position</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
133 <option value="value">Apply based on point value</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="var">Apply based on GFF3 qualifier value (when available)</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
135 </param>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
136 <when value="1">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
137 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
138 <when value="on">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
139 <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
140 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
141 <when value="pos">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
142 <param name="pos_gt" type="float" label="Greater than this base" value="1000.0" help="Leave as zero to disable this test"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
143 <param name="pos_lt" type="float" label="Less than this base" value="0.0" help="Leave as zero to disable this test"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
144 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
145 <when value="value">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
146 <param name="pos_gt" type="float" label="Points above this value" value="0.0" help="Leave as zero to disable this test"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
147 <param name="pos_lt" type="float" label="Points below this value" value="0.0" help="Leave as zero to disable this test"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
148 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
149 <when value="var">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
150 <param name="varname" type="text" label="Qualifier name"
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
151 help="Set to the name of the qualifier in the GFF3 file you wish to compare against" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
152
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
153 <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
154 <option value="eq">Equal to (string)</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
155 <option value="ne">Not equal to (string)</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
156 </param>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
157
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
158 <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
159 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
160 </conditional>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
161 </repeat>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
162 <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
163 <conditional name="action">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
164 <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
165 <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
166 <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
167 <option value="fill_color_value">Change Fill 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
168 <option value="color">Change Stroke Color</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
169 <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
170 </param>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
171 <when value="show">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
172 <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
173 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
174 <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
175 <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
176 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
177 <when value="color">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
178 <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
179 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
180 <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
181 <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
182 <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
183 <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
184 <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
185 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
186 <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
187 <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
188 <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
189 <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
190 <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
191 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
192 </conditional>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
193 </repeat>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
194 <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
195 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
196 </repeat>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
197 </section>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
198 </xml>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
199
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
200 <xml name="linkrules">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
201 <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
202 <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
203 <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
204 <conditional name="application">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
205 <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
206 <option value="always">True / Always Applied</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
207 <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
208 <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
209 <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
210 <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
211 <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
212 <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
213 <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
214 <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
215 <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
216 <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
217 <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
218 <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
219 <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
220 <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
221 <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
222 </param>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
223 <when value="chr">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
224 <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
225 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
226 <when value="start1">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
227 <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
228 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
229 <when value="end1">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
230 <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
231 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
232 <when value="pos1">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
233 <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
234 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
235 <when value="size1">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
236 <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
237 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
238 <when value="start2">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
239 <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
240 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
241 <when value="end2">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
242 <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
243 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
244 <when value="pos2">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
245 <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
246 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
247 <when value="size2">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
248 <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
249 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
250 <when value="dist">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
251 <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
252 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
253 <when value="rev1"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
254 <when value="rev2"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
255 <when value="inv"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
256 <when value="interchr"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
257 <when value="intrachr"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
258 <when value="always"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
259 </conditional>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
260 </repeat>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
261 <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
262 <conditional name="action">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
263 <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
264 <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
265 <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
266 <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
267 <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
268 </param>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
269 <when value="show">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
270 <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
271 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
272 <when value="color">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
273 <conditional name="dynamic">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
274 <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
275 <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
276 <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
277 </param>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
278 <when value="static">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
279 <expand macro="circos_color" label="Link 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
280 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
281 <when value="dynamic">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
282 <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
283 <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
284 <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
285 <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
286 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
287 </conditional>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
288 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
289 <when value="thickness">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
290 <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
291 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
292 <when value="z">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
293 <conditional name="dynamic">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
294 <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
295 <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
296 <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
297 </param>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
298 <when value="static">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
299 <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
300 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
301 <when value="dynamic">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
302 <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
303 <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
304 <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
305 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
306 </conditional>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
307 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
308 </conditional>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
309 </repeat>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
310
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
311 <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
312 </repeat>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
313 </section>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
314 </xml>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
315
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
316 <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
317 <conditional name="comparison" >
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
318 <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
319 <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
320 <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
321 </param>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
322 <when value="lt">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
323 <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
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="gt">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
326 <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
327 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
328 </conditional>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
329 </xml>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
330
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
331 <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
332 <conditional name="comparison" >
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
333 <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
334 <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
335 <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
336 <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
337 <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
338 <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
339 </param>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
340 <!-- 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
341 <when value="on">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
342 <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
343 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
344 <when value="from">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
345 <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
346 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
347 <when value="to">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
348 <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
349 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
350 <when value="fromto">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
351 <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
352 <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
353 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
354 <when value="between">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
355 <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
356 <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
357 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
358 </conditional>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
359 </xml>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
360
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8
iuc
parents:
diff changeset
361 </macros>