Mercurial > repos > fubar > jbrowse2
annotate macros.xml @ 113:878c27dfea9d draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 45375b64cbc99173525a2b374d71a13e650ce1b0
author | bgruening |
---|---|
date | Sun, 28 Jul 2024 02:42:43 +0000 |
parents | 56f9a6e0fe80 |
children |
rev | line source |
---|---|
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1 <macros> |
113
878c27dfea9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 45375b64cbc99173525a2b374d71a13e650ce1b0
bgruening
parents:
112
diff
changeset
|
2 <token name="@TOOL_VERSION@">2.13.0</token> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
3 <xml name="edamInc"> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
4 <edam_topics> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
5 <edam_topic>topic_3307</edam_topic> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
6 <edam_topic>topic_0092</edam_topic> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
7 </edam_topics> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
8 <edam_operations> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
9 <edam_operation>operation_0573</edam_operation> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
10 <edam_operation>operation_0564</edam_operation> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
11 </edam_operations> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
12 </xml> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
13 <xml name="requirements"> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
14 <requirements> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
15 <requirement type="package" version="@TOOL_VERSION@">jbrowse2</requirement> |
98
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
16 <requirement type="package" version="1.82">biopython</requirement> |
19
bde6b1d09f7d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
fubar
parents:
17
diff
changeset
|
17 <requirement type="package" version="0.7.1">bcbio-gff</requirement> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
18 <requirement type="package" version="1.19">samtools</requirement> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
19 <requirement type="package" version="6.0.1">pyyaml</requirement> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
20 <requirement type="package" version="1.11">tabix</requirement> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
21 <requirement type="package" version="4.6.0">findutils</requirement> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
89
diff
changeset
|
22 <requirement type="package" version="0.0.12-0">hictk</requirement> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
89
diff
changeset
|
23 <requirement type="package" version="3.0">zip</requirement> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
24 <yield/> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
25 </requirements> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
26 </xml> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
27 <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token> |
106
0082924757b0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
fubar
parents:
105
diff
changeset
|
28 <token name="@VERSION_SUFFIX@">0</token> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
29 <xml name="creators"> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
30 <creator> |
98
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
31 <person givenName="Helena" familyName="Rasche" url="https://github.com/hexylena"/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
32 <person givenName="Anthony" familyName="Bretaudeau" url="https://github.com/abretaud"/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
33 <person givenName="Ross" familyName="Lazarus" url="https://github.com/fubar2/"/> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
34 </creator> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
35 </xml> |
98
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
36 <xml name="genome_selector" token_help="" token_label="Fasta sequences" token_optional="False"> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
37 <conditional name="reference_genome"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
38 <param name="genome_type_select" type="select" label="Reference genome to display" help="Built-in references"> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
39 <option selected="True" value="indexed">Use a built-in genome</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
40 <option value="history">Use a genome from history</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
41 </param> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
42 <when value="indexed"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
43 <param name="genomes" type="select" optional="@OPTIONAL@" label="@LABEL@" help="@HELP@"> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
44 <options from_data_table="all_fasta"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
45 <filter column="2" type="sort_by"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
46 <validator message="No genomes are available for the selected input dataset" type="no_options"/> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
47 </options> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
48 </param> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
49 </when> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
50 <when value="history"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
51 <param name="genomes" type="data" format="fasta" optional="@OPTIONAL@" label="@LABEL@" help="@HELP@" multiple="True"/> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
52 </when> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
53 </conditional> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
54 </xml> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
55 <xml name="auto_manual_tk" token_cond_label="Color" token_cond_name="color" token_select_label="Color Specification" token_select_name="color_select" token_automatic_label="Automatically selected" token_manual_label="Manual Color Selection"> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
56 <conditional name="@COND_NAME@" label="@COND_LABEL@"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
57 <param name="@SELECT_NAME@" type="select" label="@SELECT_LABEL@"> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
58 <option value="automatic" selected="true">@AUTOMATIC_LABEL@</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
59 <option value="manual">@MANUAL_LABEL@</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
60 </param> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
61 <when value="automatic"> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
62 </when> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
63 <when value="manual"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
64 <yield/> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
65 </when> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
66 </conditional> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
67 </xml> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
68 <xml name="jb_color" token_label="JBrowse style.color" token_name="style_color" token_value="goldenrod" token_help="Basic color of features. Most glyphs interpret this as the fill color of the rectangle they draw. Color syntax is the same as that used for CSS"> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
69 <param name="@NAME@" type="color" value="@VALUE@" label="@LABEL@" help="@HELP@"> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
70 <sanitizer> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
71 <valid initial="string.letters,string.digits"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
72 <add value="#"/> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
73 </valid> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
74 </sanitizer> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
75 </param> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
76 </xml> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
77 <xml name="auto_color" token_cond_label="Color" token_cond_name="color" token_select_label="Color Selection" token_select_name="color_select" token_automatic_label="Automatically selected" token_manual_label="Manual Color Selection"> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
78 <expand macro="auto_manual_tk" cond_label="@COND_LABEL@" cond_name="@COND_NAME@" select_label="@SELECT_LABEL@" select_name="@SELECT_NAME@" automatic_label="@AUTOMATIC_LABEL@" manual_label="@MANUAL_LABEL@"> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
79 <expand macro="jb_color"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
80 <yield/> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
81 </expand> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
82 </xml> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
83 <xml name="brewer_scheme"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
84 <param name="brewer_scheme" type="select" label="Brewer color Scheme"> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
85 <option value="BrBg">BrBg: Brown - Blue Green</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
86 <option value="PiYg">PiYg: Pink - Yellow Green</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
87 <option value="PRGn">PRGn: Purple Red - Green</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
88 <option value="PuOr">PuOr: Purple - Orange</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
89 <option value="RdBu" selected="true">RdBu: Red - Blue</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
90 <option value="RdGy">RdGy: Red - Gray</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
91 <option value="RdYlBu">RdYlBu: Red - Yellow - Blue</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
92 <option value="RdYlGn">RdYlBu: Red - Yellow - Green</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
93 <option value="Spectral">Spectral</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
94 </param> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
95 </xml> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
96 <xml name="general_options"> |
101
e4ba5f1da6ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
fubar
parents:
100
diff
changeset
|
97 <section name="jbgen" title="Advanced JBrowse Options: collections, locations, colours, font size and default bp per pixel" expanded="false"> |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
45
diff
changeset
|
98 <conditional name="ucol"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
99 <param name="formcoll" type="select" label="Convert a collection of track files rather than filling in the tool form" help="A collection of bam/vcf and other track types will be converted into a JBrowse2 automatically"> |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
45
diff
changeset
|
100 <option value="form" selected="true">Fill in the tool form to specify tracks for the output JBrowse2</option> |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
45
diff
changeset
|
101 <option value="collect">Convert a collection of suitable track files</option> |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
45
diff
changeset
|
102 </param> |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
45
diff
changeset
|
103 <when value="collect"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
104 <param name="autoCollection" type="data_collection" label="Collection of bed, bam and other track files"/> |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
45
diff
changeset
|
105 </when> |
98
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
106 <when value="form"/> |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
45
diff
changeset
|
107 </conditional> |
98
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
108 <param name="zipOut" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Create a zip archive for downloading rather than viewing" help="Default is to make an interactive browser appear when the 'eye' icon is activated"/> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
109 <param name="defaultLocation" type="text" value="" label="Subset to display to new users" help="Initial subset to be shown for users who have never visited the browser before. Example: 'ctgA:1234..5678"/> |
98
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
110 <param name="session_name" type="text" value="New JBrowse2 session" label="Session name" help="Displayed at the top of the window"/> |
112
56f9a6e0fe80
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 566509061b742b73c8dd1a1db6813fbf6a7a3792
bgruening
parents:
108
diff
changeset
|
111 <param name="bpPerPx" type="integer" min="1" value="50" label="Base pairs per display pixel for default view" help="Make the default window show more or less BP of sequence. For some reason not automatable in JB2, sorry"/> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
112 <param name="enableAnalytics" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enable analytics" help="Will send usage data to Google Analytics, see https://github.com/GMOD/jbrowse-components/issues/1166"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
113 <param name="primary_color" type="color" value="#0D233F" label="Primary color"> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
114 <sanitizer> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
115 <valid initial="string.ascii_letters,string.digits"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
116 <add value="#"/> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
117 </valid> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
118 </sanitizer> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
119 </param> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
120 <param name="secondary_color" type="color" value="#721E63" label="Secondary color"> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
121 <sanitizer> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
122 <valid initial="string.ascii_letters,string.digits"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
123 <add value="#"/> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
124 </valid> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
125 </sanitizer> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
126 </param> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
127 <param name="tertiary_color" type="color" value="#135560" label="Tertiary color"> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
128 <sanitizer> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
129 <valid initial="string.ascii_letters,string.digits"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
130 <add value="#"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
131 </valid> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
132 </sanitizer> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
133 </param> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
134 <param name="quaternary_color" type="color" value="#FFB11D" label="Quaternary color"> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
135 <sanitizer> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
136 <valid initial="string.ascii_letters,string.digits"> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
137 <add value="#"/> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
138 </valid> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
139 </sanitizer> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
140 </param> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
141 <param name="font_size" type="integer" value="10" label="Font size"/> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
142 </section> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
143 </xml> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
144 <xml name="color_selection_minmax"> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
145 <section name="jbcolor" title="JBrowse Color Options [Advanced]" expanded="false"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
146 <!-- Abuse auto/manual for bicolor pivot. Means we'll have to handle the |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
147 auto case as well, but may be safe to just say "brewer colors? Pff, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
148 red/blue" --> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
149 <expand macro="auto_manual_tk" token_cond_label="Color" token_cond_name="color" token_select_label="Color Selection" token_select_name="color_select" token_automatic_label="Automatically selected" token_manual_label="Manual Color Selection"> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
150 <expand macro="jb_color" label="JBrowse style.pos_color" name="style_pos_color" value="blue" help="CSS color, default 'blue'. When drawing bicolor plots, the fill color to use for values that are above the pivot point."/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
151 <expand macro="jb_color" label="JBrowse style.neg_color" name="style_neg_color" value="red" help=" CSS color, default 'red'. When drawing bicolor plots, the fill color to use for values that are below the pivot point."/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
152 </expand> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
153 <conditional name="bicolor_pivot" label="Bicolor Pivot"> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
154 <param name="bicolor_pivot_select" type="select" label="Bicolor Pivot"> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
155 <option value="zero" selected="true">Zero</option> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
156 <option value="mean">Mean</option> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
157 <option value="custom">Custom Value</option> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
158 </param> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
159 <when value="zero"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
160 <when value="mean"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
161 <when value="custom"> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
162 <param name="pivot_point" type="float" value="0.0" label="JBrowse style.bicolor_pivot" help="Where to change from pos_color to neg_color when drawing bicolor plots."/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
163 </when> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
164 </conditional> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
165 </section> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
166 </xml> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
167 <xml name="color_selection" token_scaling_lin_select="true" token_scaling_log_select="false"> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
168 <section name="jbcolor_scale" title="JBrowse Feature Score Scaling & Coloring Options [Advanced]" expanded="false"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
169 <conditional name="color_score" label="JBrowse style.color & Score relationship"> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
170 <param name="color_score_select" type="select" label="Color Score Algorithm" help="How to color the features. If it is based on score, then features with a score attribute anywhere in their hierachy will have their color affected by the score. If you choose to ignore the score, then you'll be able to select a single solid color for every feature in the track"> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
171 <option value="score">Based on score</option> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
172 <option value="none" selected="true">Ignore score</option> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
173 </param> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
174 <when value="none"> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
175 <!-- When no scaling is done, no scores available, then just let the |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
176 user choose a base color for the track --> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
177 <expand macro="auto_color"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
178 </when> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
179 <when value="score"> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
180 <!-- Scaling --> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
181 <param name="score_scaling" type="select" label="JBrowse style.color function's score scaling" help="How should the colors be distributed across the values? For blast results which distributes scores on the scale of approximately [1e-500, 10], it makes sense to request a logarithmic scaling of the color values. Logarithmic is indeed the default for blast. However other analysis methods may produce scores on ranges such as [0, 100] where a linear scale would be more appropriate for color distribution."> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
182 <option value="linear" selected="@SCALING_LIN_SELECT@">Linear scaling</option> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
183 <option value="logarithmic" selected="false">Logarithmic scaling</option> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
184 <option value="blast" selected="@SCALING_LOG_SELECT@">Blast scaling</option> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
185 </param> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
186 <!-- Scaling Bounds --> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
187 <conditional name="score_scales" label="Minimum/Maximum values for track scores"> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
188 <param name="scale_select" type="select" label="How should minimum and maximum values be determined for the scores of the features"> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
189 <option value="automatic" selected="true">Automatically determined</option> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
190 <option value="manual">Manually specify minimum and maximum expected scores for the feature track</option> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
191 </param> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
192 <when value="automatic"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
193 <when value="manual"> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
194 <param name="minimum" type="integer" value="0" label="Minimum expected score"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
195 <param name="maximum" type="integer" value="100" label="Maximum expected score"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
196 </when> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
197 </conditional> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
198 <!-- Scale color --> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
199 <conditional name="color_scheme" label="Color Scheme for scored features"> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
200 <param name="score_scheme" type="select" label="JBrowse style.color function's color scheme for scored values"> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
201 <option value="opacity">Opacity (high scores = 1.0 opacity)</option> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
202 <!--<option value="brewer">Brewer Color Schemes</option>--> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
203 </param> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
204 <when value="opacity"> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
205 <!-- Single color selection mode --> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
206 <expand macro="auto_color"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
207 </when> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
208 <!--<when value="brewer">--> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
209 <!--[> Brewer continuum selection <]--> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
210 <!--<expand macro="brewer_scheme" />--> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
211 <!--</when>--> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
212 </conditional> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
213 </when> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
214 </conditional> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
215 </section> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
216 </xml> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
217 <xml name="track_visibility"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
218 <param name="track_visibility" type="select" label="Track Visibility"> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
219 <option value="default_off">Off when browser opens</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
220 <option value="default_on" selected="true">On when browser opens</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
221 </param> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
222 </xml> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
223 <xml name="track_styling_linear"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
224 <param name="show_labels" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show labels"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
225 <param name="show_descriptions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show descriptions"/> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
226 <param name="display_mode" type="select" label="Display mode"> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
227 <option value="normal" selected="true">normal</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
228 <option value="compact">compact</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
229 <option value="reducedRepresentation">reducedRepresentation</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
230 <option value="collapse">collapse</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
231 </param> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
232 <param name="max_height" type="integer" value="600" label="Max height" help="Maximum height that the track is permitted to reach in pixels."/> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
233 </xml> |
85
3b2ff9864995
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty
fubar
parents:
80
diff
changeset
|
234 <xml name="track_styling_vgp"> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
235 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
236 <param name="show_labels" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show labels"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
237 <param name="show_descriptions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show descriptions"/> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
238 <param name="display" type="select" label="Display style" help="How the track will be displayed by default"> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
239 <option value="LinearBasicDisplay" selected="true">LinearBasicDisplay</option> |
5
efc64d8f4b72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9
fubar
parents:
3
diff
changeset
|
240 <option value="LinearPileupDisplay">LinearPileupDisplay - good for dense tracks at scale</option> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
241 <option value="LinearArcDisplay">LinearArcDisplay</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
242 </param> |
112
56f9a6e0fe80
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 566509061b742b73c8dd1a1db6813fbf6a7a3792
bgruening
parents:
108
diff
changeset
|
243 <param name="usebedscore" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use column 5 as a score for the display if bed format" |
56f9a6e0fe80
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 566509061b742b73c8dd1a1db6813fbf6a7a3792
bgruening
parents:
108
diff
changeset
|
244 help="The *Bigwig extremes to bed features* tool generates bed files with scores 1 or -1. This option renders them red and blue"/> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
245 </section> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
246 </xml> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
247 <xml name="track_styling_feature"> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
248 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false"> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
249 <conditional name="track_style"> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
250 <param name="display" type="select" label="Display style" help="How the track will be displayed by default"> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
251 <option value="LinearBasicDisplay" selected="true">LinearBasicDisplay</option> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
252 <option value="LinearPileupDisplay">LinearPileupDisplay - good for dense tracks at scale</option> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
253 <option value="LinearArcDisplay">LinearArcDisplay</option> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
254 </param> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
255 <when value="LinearPileupDisplay"> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
256 <expand macro="track_styling_linear"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
257 </when> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
258 <when value="LinearBasicDisplay"> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
259 <expand macro="track_styling_linear"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
260 <!-- examples: https://github.com/GMOD/jbrowse-components/discussions/2729 |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
261 and https://github.com/GMOD/jbrowse-components/blob/main/plugins/svg/src/SvgFeatureRenderer/configSchema.ts#L41 --> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
262 <param name="label" type="text" value="jexl:get(feature,'name') || get(feature,'id')" label="Features label" help="See https://jbrowse.org/jb2/docs/config_guide/#configuration-callbacks for syntax"> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
263 <sanitizer> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
264 <valid initial="default"> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
265 <add value="|"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
266 <add value="{"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
267 <add value="}"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
268 <add value="!"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
269 <add value="?"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
270 <add value="+"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
271 <add value="="/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
272 <add value="'"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
273 </valid> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
274 </sanitizer> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
275 </param> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
276 <param name="description" type="text" value="jexl:get(feature,'note') || get(feature,'description')" label="Features description" help="See https://jbrowse.org/jb2/docs/config_guide/#configuration-callbacks for syntax"> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
277 <sanitizer> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
278 <valid initial="default"> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
279 <add value="|"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
280 <add value="{"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
281 <add value="}"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
282 <add value="!"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
283 <add value="?"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
284 <add value="+"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
285 <add value="="/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
286 <add value="'"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
287 </valid> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
288 </sanitizer> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
289 </param> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
290 </when> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
291 <when value="LinearArcDisplay"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
292 </conditional> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
293 </section> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
294 </xml> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
295 <xml name="track_styling_xam"> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
296 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false"> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
297 <conditional name="track_style"> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
298 <param name="display" type="select" label="Display style" help="How the track will be displayed by default"> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
299 <option value="LinearAlignmentsDisplay" selected="true">LinearAlignmentsDisplay</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
300 <option value="LinearPileupDisplay">LinearPileupDisplay</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
301 <option value="LinearSNPCoverageDisplay">LinearSNPCoverageDisplay</option> |
62
ab0d6782a95f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents:
60
diff
changeset
|
302 <option value="LinearReadArcsDisplay">LinearReadArcsDisplay</option> |
ab0d6782a95f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents:
60
diff
changeset
|
303 <option value="LinearReadCloudDisplay">LinearReadCloudDisplay</option> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
304 </param> |
62
ab0d6782a95f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents:
60
diff
changeset
|
305 <!-- TODO check if possible to handle more options than just the display style--> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
306 <when value="LinearAlignmentsDisplay"/> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
307 <when value="LinearPileupDisplay"/> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
308 <when value="LinearSNPCoverageDisplay"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
309 <param name="displayCrossHatches" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Draw cross hatches"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
310 <param name="minScore" type="integer" value="" optional="true" label="Min score"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
311 <param name="maxScore" type="integer" value="" optional="true" label="Max score"/> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
312 </when> |
62
ab0d6782a95f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents:
60
diff
changeset
|
313 <when value="LinearReadArcsDisplay"/> |
ab0d6782a95f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents:
60
diff
changeset
|
314 <when value="LinearReadCloudDisplay"/> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
315 </conditional> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
316 </section> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
317 </xml> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
318 <xml name="track_styling_vcf"> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
319 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false"> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
320 <conditional name="track_style"> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
321 <param name="display" type="select" label="Display style" help="How the track will be displayed by default"> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
322 <option value="LinearVariantDisplay" selected="true">LinearVariantDisplay</option> |
62
ab0d6782a95f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents:
60
diff
changeset
|
323 <option value="LinearPairedArcDisplay">LinearPairedArcDisplay</option> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
324 </param> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
325 <when value="LinearVariantDisplay"> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
326 <expand macro="track_styling_linear"/> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
327 </when> |
62
ab0d6782a95f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents:
60
diff
changeset
|
328 <when value="LinearPairedArcDisplay"/> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
329 </conditional> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
330 </section> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
331 </xml> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
332 <xml name="track_styling_bigwig"> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
333 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false"> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
334 <conditional name="track_style"> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
335 <param name="display" type="select" label="Display style" help="How the track will be displayed by default"> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
336 <option value="LinearWiggleDisplay" selected="true">LinearWiggleDisplay</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
337 </param> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
338 <when value="LinearWiggleDisplay"> |
99
990291e918c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
fubar
parents:
98
diff
changeset
|
339 <param name="color" type="color" value="#135560" label="Wiggle colour"> |
990291e918c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
fubar
parents:
98
diff
changeset
|
340 <sanitizer> |
990291e918c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
fubar
parents:
98
diff
changeset
|
341 <valid initial="string.ascii_letters,string.digits"> |
990291e918c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
fubar
parents:
98
diff
changeset
|
342 <add value="#"/> |
990291e918c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
fubar
parents:
98
diff
changeset
|
343 </valid> |
990291e918c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
fubar
parents:
98
diff
changeset
|
344 </sanitizer> |
990291e918c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
fubar
parents:
98
diff
changeset
|
345 </param> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
346 <param name="autoscale" type="select" label="Autoscale type"> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
347 <option value="local" selected="true">Local</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
348 <option value="global">Global</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
349 <option value="globalsd">Global ± 3σ</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
350 <option value="localsd">Local ± 3σ</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
351 </param> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
352 <param name="resolution" type="integer" value="1" label="Resolution"/> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
353 <param name="summaryScoreMode" type="select" label="Autoscale type"> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
354 <option value="max">Max</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
355 <option value="min">Min</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
356 <option value="avg">Avg</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
357 <option value="whiskers" selected="true">Whiskers (combines all three)</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
358 </param> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
359 <param name="filled" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Fill in histogram"/> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
360 <param name="scaleType" type="select" label="Autoscale type"> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
361 <option value="linear" selected="true">Linear</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
362 <option value="log">Log</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
363 </param> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
364 <param name="displayCrossHatches" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Draw cross hatches"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
365 <param name="minScore" type="integer" value="" optional="true" label="Min score"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
366 <param name="maxScore" type="integer" value="" optional="true" label="Max score"/> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
367 </when> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
368 </conditional> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
369 </section> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
370 </xml> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
371 <xml name="track_menu"> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
372 <section name="jbmenu" title="JBrowse Contextual Menu options [Advanced]" expanded="false"> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
373 <repeat name="track_menu" title="Track Menu"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
374 <param name="menu_action" type="select" label="Menu action" help="Action performed when user clicks on the menu"> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
375 <option value="iframeDialog" selected="true">iframeDialog: causes the given url to be opened in a popup dialog box within JBrowse, in an iframe element.</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
376 <option value="newWindow">newWindow: causes the given url to be opened in a new browser window.</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
377 <option value="navigateTo">navigateTo: opens the given url in the same browser window, navigating the user away from JBrowse.</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
378 </param> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
379 <param name="menu_label" type="text" label="Menu label" help="Will be displayed in the contextual menu on each feature ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)"> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
380 <expand macro="menu_sanitize"/> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
381 </param> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
382 <param name="menu_title" type="text" label="Menu title" help="Will be displayed in the popup title bar if displayed ({id}, {type}, {start}, {end}, {strand} variables will be interpreted)"> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
383 <expand macro="menu_sanitize"/> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
384 </param> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
385 <param name="menu_url" type="text" label="Menu url" help="Destination URL ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)"> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
386 <expand macro="menu_sanitize"/> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
387 </param> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
388 <param name="menu_icon" type="select" label="Menu icon" help="Icon to display next to menu label"> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
389 <option value="dijitIconBookmark" selected="true">Bookmark</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
390 <option value="dijitIconSave">Save</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
391 <option value="dijitIconPrint">Print</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
392 <option value="dijitIconCut">Cut</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
393 <option value="dijitIconCopy">Copy</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
394 <option value="dijitIconClear">Clear</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
395 <option value="dijitIconDelete">Delete</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
396 <option value="dijitIconUndo">Undo</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
397 <option value="dijitIconEdit">Edit</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
398 <option value="dijitIconNewTask">New Task</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
399 <option value="dijitIconEditTask">Edit Task</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
400 <option value="dijitIconEditProperty">Edit Property</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
401 <option value="dijitIconTask">Task</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
402 <option value="dijitIconFilter">Filter</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
403 <option value="dijitIconConfigure">Configure</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
404 <option value="dijitIconSearch">Search</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
405 <option value="dijitIconApplication">Application</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
406 <option value="dijitIconChart">Chart</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
407 <option value="dijitIconConnector">Connector</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
408 <option value="dijitIconDatabase">Database</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
409 <option value="dijitIconDocuments">Documents</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
410 <option value="dijitIconMail">Mail</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
411 <option value="dijitLeaf">Leaf</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
412 <option value="dijitIconFile">File</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
413 <option value="dijitIconFunction">Function</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
414 <option value="dijitIconKey">Key</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
415 <option value="dijitIconPackage">Package</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
416 <option value="dijitIconSample">Sample</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
417 <option value="dijitIconTable">Table</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
418 <option value="dijitIconUsers">Users</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
419 <option value="dijitIconFolderClosed">Folder Closed</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
420 <option value="dijitIconFolderOpen">Folder Open</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
421 <option value="dijitIconError">Error</option> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
422 </param> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
423 </repeat> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
424 </section> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
425 </xml> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
426 <xml name="menu_sanitize"> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
427 <sanitizer> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
428 <valid> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
429 <add value="{"/> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
430 <add value="}"/> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
431 <add value="!"/> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
432 <add value="?"/> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
433 <add value="&"/> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
434 <add value="+"/> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
435 <add value="="/> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
436 <add value="'"/> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
437 <add value="""/> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
438 </valid> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
439 </sanitizer> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
440 </xml> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
441 <xml name="input_conditional" token_label="Track Data" token_format="data"> |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
45
diff
changeset
|
442 <conditional name="useuri"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
443 <param name="insource" type="select" label="Define track data as a history file or an internet URI" help="A public URI implies that all the associated tabix files are also in place. They are created for history files"> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
89
diff
changeset
|
444 <option value="history" selected="true">Track data from a history file</option> |
99
990291e918c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
fubar
parents:
98
diff
changeset
|
445 <option value="uri">Tabix data URI: Internet connection required to view. Tabix index files must be available</option> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
89
diff
changeset
|
446 </param> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
89
diff
changeset
|
447 <when value="history"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
448 <param name="annotation" type="data" format="@FORMAT@" optional="true" label="@LABEL@" multiple="True"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
89
diff
changeset
|
449 </when> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
89
diff
changeset
|
450 <when value="uri"> |
99
990291e918c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
fubar
parents:
98
diff
changeset
|
451 <param name="annouri" type="text" label="@LABEL@" help="Requires internet. Will show an error if not online. Saves all the tabix file disk storage"/> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
452 <param name="annoname" type="text" label="Short name for track display"> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
89
diff
changeset
|
453 <sanitizer invalid_char="_"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
454 <valid initial="string.printable"> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
455 <remove value="'"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
456 </valid> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
89
diff
changeset
|
457 </sanitizer> |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
45
diff
changeset
|
458 </param> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
89
diff
changeset
|
459 </when> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
89
diff
changeset
|
460 </conditional> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
89
diff
changeset
|
461 </xml> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
89
diff
changeset
|
462 <xml name="pafref_conditional" token_label="Track Data" token_format="data"> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
89
diff
changeset
|
463 <conditional name="pafuseuri"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
464 <param name="insource" type="select" label="PAF reference data from a history file or an internet URI?" help="Multiple references can be used for mashmap PAF. A URI source requires all the associated tabix index files to be in place."> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
89
diff
changeset
|
465 <option value="history" selected="true">PAF reference comparison genome from a history file</option> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
89
diff
changeset
|
466 <option value="uri">PAF reference comparison genome tabix .gz URI with index files at the corresponding URIs</option> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
89
diff
changeset
|
467 </param> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
89
diff
changeset
|
468 <when value="history"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
469 <param name="annotation" type="data" format="@FORMAT@" label="@LABEL@" help="Add all PAF reference comparison genomes used to make the PAF" multiple="true"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
89
diff
changeset
|
470 </when> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
89
diff
changeset
|
471 <when value="uri"> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
89
diff
changeset
|
472 <repeat name="refuri" title="PAF reference comparison genome URI" min="1"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
473 <param name="annotation" type="text" label="@LABEL@"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
474 <param name="annoname" type="text" label="Short name for this reference" help="Short names take less track space"> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
475 <sanitizer invalid_char="_"> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
476 <valid initial="string.printable"> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
477 <remove value="'"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
478 </valid> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
479 </sanitizer> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
89
diff
changeset
|
480 </param> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
89
diff
changeset
|
481 </repeat> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
89
diff
changeset
|
482 </when> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
89
diff
changeset
|
483 </conditional> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
89
diff
changeset
|
484 </xml> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
485 <xml name="citations"> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
486 <citations> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
487 <citation type="doi">10.1186/s13059-016-0924-1</citation> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
488 <citation type="doi">10.1101/gr.094607.109</citation> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
489 </citations> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
490 </xml> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
491 </macros> |