Mercurial > repos > iuc > jbrowse
annotate jbrowse.xml @ 32:6b774e9d6387 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit df0ef2f7aaf34e585edbf88654fec9dd9e6acff1
author | iuc |
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date | Tue, 16 Jul 2019 05:08:10 -0400 |
parents | 2bb2e07a7a21 |
children | 0ae74c70b267 |
rev | line source |
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19
8f33c9fbc119
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
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1 <tool id="jbrowse" name="JBrowse" version="@TOOL_VERSION@+@WRAPPER_VERSION@"> |
0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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2 <description>genome browser</description> |
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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3 <macros> |
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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4 <import>macros.xml</import> |
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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5 </macros> |
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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6 <expand macro="requirements"/> |
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836d1aa3e89a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
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7 <version_command>python '${__tool_directory__}/jbrowse.py' --version</version_command> |
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1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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8 <command detect_errors="aggressive"><![CDATA[ |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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9 #if $action.action_select == "create": |
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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10 mkdir -p $output.files_path && |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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11 #else: |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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12 cp -R $action.update_jbrowse.extra_files_path $output.files_path && |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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13 #end if |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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14 |
3 | 15 ## Copy the XML file into the directory, mostly for debugging |
16 ## but nice if users want to reproduce locally | |
17 cp $trackxml $output.files_path/galaxy.xml && | |
18 | |
19 ## Once that's done, we run the python script to handle the real work | |
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836d1aa3e89a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
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20 python '$__tool_directory__/jbrowse.py' |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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21 |
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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22 --jbrowse \${JBROWSE_SOURCE_DIR} |
3 | 23 #if str($standalone) == "Complete": |
24 --standalone | |
25 #end if | |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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26 |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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27 --outdir $output.files_path |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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28 $trackxml && |
3 | 29 |
30 #if str($standalone) == "Complete": | |
31 mv $output.files_path/index.html $output; | |
32 #else: | |
33 mv $dummyIndex $output; | |
34 #end if | |
35 | |
36 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph. | |
37 #if str($uglyTestingHack) == "enabled": | |
38 mv $trackxml $output | |
39 #end if | |
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5f70e7fe6077
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
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40 ]]></command> |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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41 <configfiles> |
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5f70e7fe6077
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
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42 <configfile name="dummyIndex"><![CDATA[ |
3 | 43 <html> |
44 <head> | |
45 </head> | |
46 <body> | |
47 <h1>JBrowse Data Directory</h1> | |
48 <p> | |
49 Hi! This is not a full JBrowse instance. JBrowse v0.4(+?) | |
50 started shipping with the ability to produce just the | |
51 "data" directory from a JBrowse instance, rather than a | |
52 complete, standalone instance. This was intended to be used | |
53 with the in-development Apollo integration, but may have other | |
54 uses as well. | |
55 </p> | |
56 <p> | |
57 <u>This is not usable on its own</u>. The output dataset may be | |
58 used with Apollo, or may be passed through the "JBrowse - | |
59 Convert to Standalone" tool in Galaxy to "upgrade" to a full | |
60 JBrowse instance. | |
61 </p> | |
62 </body> | |
63 </html> | |
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5f70e7fe6077
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
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64 ]]></configfile> |
3 | 65 <configfile name="trackxml"><![CDATA[<?xml version="1.0"?> |
66 <root> | |
67 <metadata> | |
68 <gencode>$gencode</gencode> | |
69 <genomes> | |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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70 #if str($reference_genome.genome_type_select) == "indexed": |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
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71 <genome path="${reference_genome.genomes.fields.path}"> |
836d1aa3e89a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
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72 <metadata /> |
836d1aa3e89a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
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73 </genome>s |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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74 #else |
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1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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75 <genome path="$reference_genome.genome"> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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76 <metadata> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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77 <dataset id="${__app__.security.encode_id($reference_genome.genome.id)}" hid="${reference_genome.genome.hid}" |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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78 size="${reference_genome.genome.get_size(nice_size=True)}" |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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79 edam_format="${reference_genome.genome.datatype.edam_format}" |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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80 file_ext="${reference_genome.genome.ext}" /> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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81 <history id="${__app__.security.encode_id($reference_genome.genome.history_id)}" |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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82 user_email="${reference_genome.genome.history.user.email}" |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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83 user_id="${reference_genome.genome.history.user_id}" |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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84 display_name="${reference_genome.genome.history.get_display_name()}"/> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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85 <metadata |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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86 #for (key, value) in $reference_genome.genome.get_metadata().items(): |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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87 #if "_types" not in $key: |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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88 ${key}="${value}" |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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89 #end if |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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90 #end for |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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91 /> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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92 <tool |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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93 tool_id="${reference_genome.genome.creating_job.tool_id}" |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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94 tool_version="${reference_genome.genome.creating_job.tool_version}" |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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95 /> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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96 </metadata> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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97 </genome> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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98 #end if |
3 | 99 </genomes> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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100 <general> |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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101 <defaultLocation>${jbgen.defaultLocation}</defaultLocation> |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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102 <trackPadding>${jbgen.trackPadding}</trackPadding> |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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103 |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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104 <shareLink>${jbgen.shareLink}</shareLink> |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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105 <aboutDescription>${jbgen.aboutDescription}</aboutDescription> |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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106 <show_tracklist>${jbgen.show_tracklist}</show_tracklist> |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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107 <show_nav>${jbgen.show_nav}</show_nav> |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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108 <show_overview>${jbgen.show_overview}</show_overview> |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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109 <show_menu>${jbgen.show_menu}</show_menu> |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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110 <hideGenomeOptions>${jbgen.hideGenomeOptions}</hideGenomeOptions> |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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111 </general> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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112 <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl> |
3 | 113 </metadata> |
114 <tracks> | |
115 #for $tg in $track_groups: | |
116 #for $track in $tg.data_tracks: | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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117 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}"> |
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118 #if $track.data_format.data_format_select != "rest" and $track.data_format.data_format_select != "sparql": |
3 | 119 <files> |
120 #for $dataset in $track.data_format.annotation: | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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121 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}"> |
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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122 <metadata> |
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123 <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}" |
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124 size="${dataset.get_size(nice_size=True)}" |
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125 edam_format="${dataset.datatype.edam_format}" |
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126 file_ext="${dataset.ext}" /> |
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127 <history id="${__app__.security.encode_id($dataset.history_id)}" |
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128 user_email="${dataset.history.user.email}" |
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129 user_id="${dataset.history.user_id}" |
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130 display_name="${dataset.history.get_display_name()}"/> |
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131 <metadata |
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132 #for (key, value) in $dataset.get_metadata().items(): |
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133 #if "_types" not in $key and $value is not None and len(str($value)) < 5000: |
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134 ${key}="${value}" |
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135 #end if |
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136 #end for |
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137 /> |
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138 <tool |
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139 tool_id="${dataset.creating_job.tool_id}" |
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140 tool_version="${dataset.creating_job.tool_version}" |
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141 /> |
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142 </metadata> |
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143 </trackFile> |
3 | 144 #end for |
145 </files> | |
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146 #end if |
3 | 147 |
148 <options> | |
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149 #if str($track.data_format.data_format_select) == "gene_calls" or str($track.data_format.data_format_select) == "blast" or str($track.data_format.data_format_select) == "rest" or str($track.data_format.data_format_select) == "sparql": |
3 | 150 <style> |
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151 <overridePlugins>${track.data_format.override_apollo_plugins}</overridePlugins> |
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152 <overrideDraggable>${track.data_format.override_apollo_drag}</overrideDraggable> |
3 | 153 <className>${track.data_format.jbstyle.style_classname}</className> |
154 <description>${track.data_format.jbstyle.style_description}</description> | |
155 <label>${track.data_format.jbstyle.style_label}</label> | |
156 <height>${track.data_format.jbstyle.style_height}</height> | |
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157 <maxHeight>${track.data_format.jbstyle.max_height}</maxHeight> |
3 | 158 </style> |
159 <scaling> | |
160 #if str($track.data_format.jbcolor_scale.color_score.color_score_select) == "none": | |
161 <method>ignore</method> | |
162 <scheme> | |
163 #if str($track.data_format.jbcolor_scale.color_score.color.color_select) == "automatic": | |
164 <color>__auto__</color> | |
165 #else | |
166 <color>${track.data_format.jbcolor_scale.color_score.color.style_color}</color> | |
167 #end if | |
168 </scheme> | |
169 #else | |
170 <method>score</method> | |
171 <algo>${track.data_format.jbcolor_scale.color_score.score_scaling}</algo> | |
172 <scales> | |
173 <type>${track.data_format.jbcolor_scale.color_score.score_scales.scale_select}</type> | |
174 | |
175 #if str($track.data_format.jbcolor_scale.color_score.score_scales.scale_select) == "manual": | |
176 <min>${track.data_format.jbcolor_scale.color_score.score_scales.minimum}</min> | |
177 <max>${track.data_format.jbcolor_scale.color_score.score_scales.maximum}</max> | |
178 #end if | |
179 </scales> | |
180 <scheme> | |
181 <type>${track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme}</type> | |
182 ## auto_color | |
183 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme) == "opacity": | |
184 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.color.color_select) == "automatic": | |
185 <color>__auto__</color> | |
186 #else | |
187 <color>${track.data_format.jbcolor_scale.color_score.color_scheme.color.style_color}</color> | |
188 #end if | |
189 #end if | |
190 </scheme> | |
191 #end if | |
192 </scaling> | |
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193 <menus> |
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194 #for $menu_item in $track.data_format.jbmenu.track_menu: |
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195 <menu> |
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196 <action>${menu_item.menu_action}</action> |
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197 #if str($menu_item.menu_label) != "": |
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198 <label>${menu_item.menu_label}</label> |
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199 #end if |
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200 #if str($menu_item.menu_title) != "": |
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201 <title>${menu_item.menu_title}</title> |
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202 #end if |
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203 #if str($menu_item.menu_url) != "": |
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204 <url>${menu_item.menu_url.replace("&", "&").replace("\"", """)}</url> |
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205 #end if |
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206 #if str($menu_item.menu_icon) != "": |
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207 <iconClass>${menu_item.menu_icon}</iconClass> |
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208 #end if |
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209 </menu> |
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210 #end for |
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211 </menus> |
3 | 212 #end if |
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213 #if str($track.data_format.data_format_select) in ["gene_calls", "pileup", "blast", "wiggle", "vcf"]: |
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214 <custom_config> |
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215 #for $custom_option in $track.data_format.jb_custom_config.option: |
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216 <${custom_option.opt_key}> |
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217 <${custom_option.opt_value.val_type}>${$custom_option.opt_value.val}</${custom_option.opt_value.val_type}> |
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218 </${custom_option.opt_key}> |
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219 #end for |
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220 </custom_config> |
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221 #end if |
3 | 222 |
223 #if str($track.data_format.data_format_select) == "wiggle": | |
224 <wiggle> | |
225 <type>${track.data_format.xyplot}</type> | |
226 <variance_band>${track.data_format.var_band}</variance_band> | |
227 #if str($track.data_format.scaling.scale_select) == "auto_local": | |
228 <autoscale>local</autoscale> | |
229 #else if str($track.data_format.scaling.scale_select) == "auto_global": | |
230 <autoscale>global</autoscale> | |
231 #else: | |
232 <min>${track.data_format.scaling.minimum}</min> | |
233 <max>${track.data_format.scaling.maximum}</max> | |
234 #end if | |
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235 <scale>${track.data_format.scale_select2}</scale> |
3 | 236 |
237 ## Wiggle tracks need special color config | |
238 #if str($track.data_format.jbcolor.color.color_select) != "automatic": | |
239 <color_pos>${track.data_format.jbcolor.color.style_pos_color}</color_pos> | |
240 <color_neg>${track.data_format.jbcolor.color.style_neg_color}</color_neg> | |
241 #else: | |
242 <color_pos>__auto__</color_pos> | |
243 <color_neg>__auto__</color_neg> | |
244 #end if | |
245 | |
246 ## Bicolor pivot config | |
247 #if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "zero": | |
248 <bicolor_pivot>zero</bicolor_pivot> | |
249 #else if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "mean": | |
250 <bicolor_pivot>mean</bicolor_pivot> | |
251 #else: | |
252 <bicolor_pivot>${track.data_format.jbcolor.bicolor_pivot.pivot_point}</bicolor_pivot> | |
253 #end if | |
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254 <multibigwig>${track.data_format.MultiBigWig}</multibigwig> |
3 | 255 </wiggle> |
256 #else if str($track.data_format.data_format_select) == "pileup": | |
257 <pileup> | |
258 <auto_snp>${track.data_format.auto_snp}</auto_snp> | |
259 <bam_indices> | |
260 #for $dataset in $track.data_format.annotation: | |
261 <bam_index>${dataset.metadata.bam_index}</bam_index> | |
262 #end for | |
263 </bam_indices> | |
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264 <chunkSizeLimit>${track.data_format.chunkSizeLimit}</chunkSizeLimit> |
3 | 265 </pileup> |
266 #else if str($track.data_format.data_format_select) == "blast": | |
267 <blast> | |
268 #if str($track.data_format.blast_parent) != "": | |
269 <parent>${track.data_format.blast_parent}</parent> | |
270 #end if | |
271 <protein>${track.data_format.is_protein}</protein> | |
272 <min_gap>${track.data_format.min_gap}</min_gap> | |
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273 <index>${track.data_format.index}</index> |
3 | 274 </blast> |
275 #else if str($track.data_format.data_format_select) == "gene_calls": | |
276 <gff> | |
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277 <trackType>${track.data_format.track_config.track_class}</trackType> |
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278 #if $track.data_format.track_config.track_class in ['JBrowse/View/Track/CanvasFeatures', 'NeatCanvasFeatures/View/Track/NeatFeatures']: |
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279 #if str($track.data_format.track_config.canvas_options.transcriptType) != "": |
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280 <transcriptType>${track.data_format.track_config.canvas_options.transcriptType}</transcriptType> |
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281 #end if |
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282 #if str($track.data_format.track_config.canvas_options.subParts) != "": |
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283 <subParts>${track.data_format.track_config.canvas_options.subParts}</subParts> |
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284 #end if |
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285 #if str($track.data_format.track_config.canvas_options.impliedUTRs) != "false": |
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286 <impliedUTRs>${track.data_format.track_config.canvas_options.impliedUTRs}</impliedUTRs> |
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287 #end if |
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288 #else if $track.data_format.track_config.track_class in ['JBrowse/View/Track/HTMLFeatures', 'NeatHTMLFeatures/View/Track/NeatFeatures']: |
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289 #if str($track.data_format.track_config.html_options.topLevelFeatures) != "": |
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290 <topLevelFeatures>${track.data_format.track_config.html_options.topLevelFeatures}</topLevelFeatures> |
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291 #end if |
10
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292 #end if |
3 | 293 #if $track.data_format.match_part.match_part_select: |
294 <match>${track.data_format.match_part.name}</match> | |
295 #end if | |
8
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296 <index>${track.data_format.index}</index> |
3 | 297 </gff> |
25
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298 #else if str($track.data_format.data_format_select) == "rest": |
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299 <label>${track.data_format.label}</label> |
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300 <rest> |
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301 <url>${track.data_format.url}</url> |
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302 </rest> |
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303 #else if str($track.data_format.data_format_select) == "sparql": |
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304 <label>${track.data_format.label}</label> |
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305 <sparql> |
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306 <url>${track.data_format.url}</url> |
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307 <query>${track.data_format.query}</query> |
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308 </sparql> |
3 | 309 #end if |
310 </options> | |
311 </track> | |
312 #end for | |
313 #end for | |
314 </tracks> | |
25
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315 ## Disable plugins until https://github.com/GMOD/jbrowse/issues/1288 is fixed |
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316 ## <plugins |
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317 ## ComboTrackSelector="${plugins.ComboTrackSelector}" |
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318 ## Bookmarks="${plugins.Bookmarks}" |
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319 ## GCContent="${plugins.GCContent}" |
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320 ## BlastView="${plugins.BlastView}" |
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321 ## theme="${plugins.theme}" |
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322 ## /> |
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323 <plugins |
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324 ComboTrackSelector="${plugins.ComboTrackSelector}" |
25
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325 Bookmarks="" |
17
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326 GCContent="${plugins.GCContent}" |
25
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327 BlastView="${plugins.BlastView}" |
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328 theme="" |
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329 /> |
31
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330 </root> |
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331 ]]></configfile> |
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332 </configfiles> |
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333 <inputs> |
8
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334 <conditional name="reference_genome"> |
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335 <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select"> |
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336 <option selected="True" value="indexed">Use a built-in genome</option> |
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337 <option value="history">Use a genome from history</option> |
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338 </param> |
8
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339 <when value="indexed"> |
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340 <param |
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341 help="If your genome of interest is not listed, contact the Galaxy team" |
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342 label="Select a reference genome" |
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343 name="genomes" |
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344 type="select" |
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345 > |
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346 <options from_data_table="all_fasta"> |
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347 <filter column="2" type="sort_by" /> |
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348 <validator message="No genomes are available for the selected input dataset" type="no_options" /> |
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349 </options> |
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350 </param> |
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351 </when> |
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352 <when value="history"> |
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353 <param |
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354 format="fasta" |
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355 label="Select the reference genome" |
25
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356 name="genome" |
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357 type="data" /> |
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358 </when> |
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359 </conditional> |
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360 |
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361 <param name="standalone" type="boolean" truevalue="Complete" falsevalue="Data Directory" checked="true" label="Produce Standalone Instance" help="Produce a full, working JBrowse instance or just the data directory. Data dir mode is experimental and intended to be used with Apollo"/> |
3 | 362 |
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363 <param name="gencode" type="select" label="Genetic Code"> |
3 | 364 <option value="1">1. The Standard Code</option> |
365 <option value="2">2. The Vertebrate Mitochondrial Code</option> | |
366 <option value="3">3. The Yeast Mitochondrial Code</option> | |
367 <option value="4">4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> | |
368 <option value="5">5. The Invertebrate Mitochondrial Code</option> | |
369 <option value="6">6. The Ciliate, Dasycladacean and Hexamita Nuclear Code</option> | |
370 <option value="9">9. The Echinoderm and Flatworm Mitochondrial Code</option> | |
371 <option value="10">10. The Euplotid Nuclear Code</option> | |
372 <option value="11">11. The Bacterial, Archaeal and Plant Plastid Code</option> | |
373 <option value="12">12. The Alternative Yeast Nuclear Code</option> | |
374 <option value="13">13. The Ascidian Mitochondrial Code</option> | |
375 <option value="14">14. The Alternative Flatworm Mitochondrial Code</option> | |
376 <option value="16">16. Chlorophycean Mitochondrial Code</option> | |
377 <option value="21">21. Trematode Mitochondrial Code</option> | |
378 <option value="22">22. Scenedesmus obliquus Mitochondrial Code</option> | |
379 <option value="23">23. Thraustochytrium Mitochondrial Code</option> | |
380 <option value="24">24. Pterobranchia Mitochondrial Code</option> | |
381 <option value="25">25. Candidate Division SR1 and Gracilibacteria Code</option> | |
382 </param> | |
383 | |
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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384 <conditional name="action"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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385 <param type="select" label="JBrowse-in-Galaxy Action" name="action_select"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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386 <option value="create">New JBrowse Instance</option> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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387 <option value="update">Update exising JBrowse Instance</option> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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388 </param> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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changeset
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389 <when value="create" /> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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390 <when value="update"> |
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5f70e7fe6077
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
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391 <param name="update_jbrowse" type="data" format="html" label="Previous JBrowse Instance" /> |
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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392 </when> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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393 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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394 |
3 | 395 <repeat name="track_groups" title="Track Group"> |
396 <param label="Track Category" | |
397 name="category" | |
398 type="text" | |
399 value="Default" | |
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400 help="Organise your tracks into Categories for a nicer end-user experience. You can use #date# and it will be replaced with the current date in 'yyyy-mm-dd' format, which is very useful for repeatedly updating a JBrowse instance when member databases / underlying tool versions are updated." optional="False"/> |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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401 <repeat name="data_tracks" title="Annotation Track"> |
17
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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402 <conditional name="data_format" label="Track Options"> |
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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403 <param type="select" label="Track Type" name="data_format_select"> |
3 | 404 <option value="gene_calls">GFF/GFF3/BED/GBK Features</option> |
1
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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405 <option value="pileup">BAM Pileups</option> |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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406 <option value="blast">Blast XML</option> |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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407 <option value="wiggle">BigWig XY</option> |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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408 <option value="vcf">VCF SNPs</option> |
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409 <option value="rest">REST Endpoint</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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410 <option value="sparql">SPARQL</option> |
1
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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411 </param> |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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412 <when value="blast"> |
3 | 413 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" /> |
1
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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414 |
3 | 415 <param label="Features used in Blast Search" |
416 help="in GFF3. This is used so we know where to map features. E.g. where results of which CDS Protein32 match up to. The query IDs in your blast results should MATCH some feature IDs in your GFF3 file. This is an optional field and is most useful if using JBrowse to display protein blast results on a DNA genome. blastn results don't need this, blastp results on a protein sequence don't need this." | |
417 format="gff3" | |
418 name="blast_parent" | |
419 optional="true" | |
420 type="data"/> | |
1
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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421 |
3 | 422 <param label="Minimum Gap Size" |
423 help="before a new match_part feature is created" | |
424 name="min_gap" | |
425 type="integer" | |
426 value="10" | |
427 min="2" /> | |
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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428 <param label="Is this a protein blast search?" |
3 | 429 type="boolean" |
430 name="is_protein" | |
431 truevalue="true" | |
432 falsevalue="false" /> | |
433 | |
8
ad4b9d7eae6a
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434 <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" /> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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435 |
3 | 436 <expand macro="track_styling" |
437 classname="feature" | |
438 label="description" | |
439 description="Hit_titles" | |
440 height="600px"/> | |
441 <expand macro="color_selection" | |
442 token_scaling_lin_select="false" | |
443 token_scaling_log_select="true" /> | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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444 <expand macro="track_custom_config" /> |
8
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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445 <expand macro="track_menu" /> |
5
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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446 <expand macro="track_display" /> |
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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447 </when> |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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448 <when value="vcf"> |
3 | 449 <expand macro="input_conditional" label="SNP Track Data" format="vcf" /> |
31
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450 <expand macro="track_custom_config" /> |
5
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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451 <expand macro="track_display" /> |
1
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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452 </when> |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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453 <when value="gene_calls"> |
3 | 454 <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" /> |
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455 <conditional name="match_part" label="match/match_part data"> |
3 | 456 <param label="This is match/match_part data" |
457 type="boolean" | |
458 name="match_part_select" | |
459 truevalue="true" | |
460 falsevalue="false" /> | |
461 <when value="true"> | |
462 <param label="Match Part Feature Type" | |
463 name="name" | |
464 type="text" | |
465 value="match" | |
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466 help="Match_parts have several options for the parent feature type, such as cDNA_match, match, translated_nucleotide_match, etc. Please select the appropriate one here. You can leave empty to try autodetection (only works with CanvasFeatures track type)." |
1c718d8b3532
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9cac72c004cc7ef57be997e2fdafb3b1839a300f
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467 optional="True"/> |
3 | 468 </when> |
469 <when value="false" /> | |
470 </conditional> | |
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471 |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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472 <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" /> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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473 |
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474 <conditional name="track_config"> |
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
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475 <param type="select" label="JBrowse Track Type [Advanced]" name="track_class"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 75f6e483debb4c0d388bf4a54df81ee89af598d5
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476 <option value="NeatHTMLFeatures/View/Track/NeatFeatures" selected="true">Neat HTML Features</option> |
08776ba76cf5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 75f6e483debb4c0d388bf4a54df81ee89af598d5
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477 <option value="NeatCanvasFeatures/View/Track/NeatFeatures">Neat Canvas Features</option> |
10
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
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478 <option value="JBrowse/View/Track/HTMLFeatures">HTML Features</option> |
26
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 75f6e483debb4c0d388bf4a54df81ee89af598d5
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479 <option value="JBrowse/View/Track/CanvasFeatures">Canvas Features</option> |
25
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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480 <option value="BlastView/View/Track/CanvasFeatures">Blast Features</option><!-- Disable plugins until https://github.com/GMOD/jbrowse/issues/1288 is fixed --> |
10
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481 </param> |
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
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482 <when value="JBrowse/View/Track/CanvasFeatures"> |
27
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483 <expand macro="canvas_options" /> |
61ce21e36cb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
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484 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
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485 <when value="JBrowse/View/Track/HTMLFeatures"> |
61ce21e36cb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
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486 <expand macro="html_options" /> |
61ce21e36cb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
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487 </when> |
61ce21e36cb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
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488 <when value="BlastView/View/Track/CanvasFeatures" /> |
61ce21e36cb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
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489 <when value="NeatHTMLFeatures/View/Track/NeatFeatures"> |
61ce21e36cb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
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490 <expand macro="html_options" /> |
26
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491 </when> |
27
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
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492 <when value="NeatCanvasFeatures/View/Track/NeatFeatures"> |
61ce21e36cb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
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493 <expand macro="canvas_options" /> |
61ce21e36cb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
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494 </when> |
10
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495 </conditional> |
27
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
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496 <expand macro="track_styling" |
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497 classname="feature" |
27
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
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498 label="product,name,id" |
61ce21e36cb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
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499 description="note,description" |
61ce21e36cb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
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500 height="10px"/> |
3 | 501 <expand macro="color_selection" /> |
31
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
502 <expand macro="track_custom_config" /> |
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
503 <expand macro="track_menu" /> |
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
504 <expand macro="track_display" /> |
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
505 </when> |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
506 <when value="pileup"> |
3 | 507 <expand macro="input_conditional" label="BAM Track Data" format="bam" /> |
508 <param label="Autogenerate SNP Track" | |
509 help="Not recommended for deep coverage BAM files" | |
510 type="boolean" | |
511 name="auto_snp" | |
512 truevalue="true" | |
513 falsevalue="false" /> | |
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
514 <param label="Maximum size of BAM chunks" |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
515 name="chunkSizeLimit" |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
516 type="integer" |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
517 help="Maximum size in bytes of BAM chunks that the browser will try to deal with. When this is exceeded, most tracks will display 'Too much data' message." |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
518 value="5000000" /> |
31
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
519 <expand macro="track_custom_config" /> |
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
520 <expand macro="track_display" /> |
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
521 </when> |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
522 <when value="wiggle"> |
3 | 523 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" /> |
524 | |
525 <param label="Use XYPlot" | |
526 help="instead of continuous colored band" | |
527 type="boolean" | |
528 name="xyplot" | |
529 truevalue="JBrowse/View/Track/Wiggle/XYPlot" | |
530 falsevalue="JBrowse/View/Track/Wiggle/Density" /> | |
531 <param label="Show variance band" | |
532 help="Only for XYPlots" | |
533 type="boolean" | |
534 name="var_band" | |
535 truevalue="true" | |
536 falsevalue="false" /> | |
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
537 |
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
538 <conditional name="scaling" label="Scaling"> |
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
539 <param type="select" label="Track Scaling" name="scale_select"> |
23
dba3c47e1798
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit cf2c8f3039021b645ac45980a02ffe1f69a3f958
iuc
parents:
22
diff
changeset
|
540 <option value="auto_local" selected="true">Autoscale (local)</option> |
dba3c47e1798
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit cf2c8f3039021b645ac45980a02ffe1f69a3f958
iuc
parents:
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diff
changeset
|
541 <option value="auto_global">Autoscale (global)</option> |
3 | 542 <option value="fixed">Specify Min/Max</option> |
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
543 </param> |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
544 <when value="auto_local"></when> |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
545 <when value="auto_global"></when> |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
546 <when value="fixed"> |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
547 <param label="Track minimum" name="minimum" |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
548 type="integer" value="0" /> |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
549 <param label="Track maximum" name="maximum" |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
550 type="integer" value="100" /> |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
551 </when> |
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
552 </conditional> |
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
553 <param type="select" label="Visual Scaling" name="scale_select2"> |
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
554 <option value="linear" selected="true">Linear</option> |
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
555 <option value="log">Logarithmic (Dynamically Calculated)</option> |
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
556 </param> |
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
557 |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
558 <param label="Use MultiBigWig Plugin" name="MultiBigWig" truevalue="True" falsevalue="" type="boolean" |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
559 help="MultiBigWig is a plugin to group multiple big-wig tracks in a more aesthetically pleasing format and to show data in a higher density display." /> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
560 |
3 | 561 <expand macro="color_selection_minmax" /> |
31
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
562 <expand macro="track_custom_config" /> |
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
563 <expand macro="track_display" /> |
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
564 </when> |
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
565 <when value="rest"> |
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
566 <param type="text" label="REST Endpoint" name="url" /> |
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
567 <param type="text" label="Track Label" name="label" value="REST Genes" /> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
568 <expand macro="track_styling" |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
569 classname="feature" |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
570 label="description" |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
571 description="Hit_titles" |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
572 height="600px"/> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
573 <expand macro="color_selection" |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
574 token_scaling_lin_select="false" |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
575 token_scaling_log_select="true" /> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
576 <expand macro="track_menu" /> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
577 <expand macro="track_display" /> |
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
578 </when> |
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
579 |
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
580 <when value="sparql"> |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
581 <param type="text" label="SPARQL Server URL" name="url" /> |
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
582 <param type="text" label="Track Label" name="label" value="SPARQL Genes" /> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
583 <param type="text" label="SPARQL Query" name="query" area="true"> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
584 <sanitizer> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
585 <mapping initial="galaxy.util.mapped_chars"> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
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diff
changeset
|
586 <add source=" " target=" " /> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
587 <add source=">" target="__gt__" /> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
588 <add source="<" target="__lt__" /> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
589 </mapping> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
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diff
changeset
|
590 <valid initial="default"> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
591 <add value="|" /> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
592 <add value="#" /> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
593 <add value="{"/> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
594 <add value="}"/> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
595 <add value="!"/> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
596 <add value="?"/> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
597 <add value="&"/> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
598 <add value="+"/> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
599 <add value="="/> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
600 <add value="'"/> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
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601 <add value='"'/> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
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changeset
|
602 </valid> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
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changeset
|
603 </sanitizer> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
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changeset
|
604 </param> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
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changeset
|
605 <expand macro="track_styling" |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
|
606 classname="feature" |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
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607 label="description" |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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608 description="Hit_titles" |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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609 height="600px"/> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
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changeset
|
610 <expand macro="color_selection" |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
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611 token_scaling_lin_select="false" |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
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612 token_scaling_log_select="true" /> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
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changeset
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613 <expand macro="track_menu" /> |
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
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diff
changeset
|
614 <expand macro="track_display" /> |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
|
615 </when> |
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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diff
changeset
|
616 </conditional> |
0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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changeset
|
617 </repeat> |
3 | 618 </repeat> |
619 | |
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
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diff
changeset
|
620 <expand macro="general_options" /> |
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
|
621 <!-- Disable plugins until https://github.com/GMOD/jbrowse/issues/1288 is fixed --> |
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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changeset
|
622 <section name="plugins" title="Plugins" expanded="false"> |
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
|
623 |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents:
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changeset
|
624 <param |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents:
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changeset
|
625 label="BlastView" name="BlastView" truevalue="True" falsevalue="" type="boolean" checked="true" |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
|
626 help="A JBrowse plugin for viewing blast alignments. This plugin makes MANY assumptions about the format of your data, and may not work without those assumptions: 1) you use protein_match / match_part 2) your features have a Blast_qseq, Blast_mseq, and Blast_sseq attribute in their GFF3 representation." /> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
|
627 |
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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diff
changeset
|
628 <param |
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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diff
changeset
|
629 label="Combo Track Selector" name="ComboTrackSelector" truevalue="True" falsevalue="" type="boolean" |
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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diff
changeset
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630 help="ComboTrackSelector is a plugin to allow the co-existence of the Hierarchical and Faceted Track selectors in JBrowse, built for/by the Arabidopsis Information Portal (Araport) project" /> |
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents:
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changeset
|
631 <!-- No way to disable now that it's built in jbrowse conda package --> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
|
632 <!--param |
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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parents:
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diff
changeset
|
633 label="Bookmarks" name="Bookmarks" truevalue="True" falsevalue="" type="boolean" |
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
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634 help="JBrowse plugin allowing users to manage a persistent list of bookmarks kept in localstorage" /--> |
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
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diff
changeset
|
635 |
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
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diff
changeset
|
636 <param |
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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diff
changeset
|
637 label="GC Content" name="GCContent" truevalue="True" falsevalue="" type="boolean" |
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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diff
changeset
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638 help="A JBrowse plugin for plotting GC Content and GC Skew. The plugin consists of a storeClass that automatically calculates the percentage of G/C bases in a region, a track type that derives from the Wiggle XY or density types, and a dialog box to adjust the sliding window size, window step size, and the calculation mode (content or skew)." /> |
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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changeset
|
639 |
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
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diff
changeset
|
640 <!--param type="select" label="JBrowse Theme" name="theme"> |
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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parents:
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diff
changeset
|
641 <option value="" selected="True">Default</option> |
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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changeset
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642 <option value="Minimalist">Minimalist</option> |
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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643 <option value="Dark">Dark</option> |
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
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changeset
|
644 </param--> |
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
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diff
changeset
|
645 </section> |
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
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diff
changeset
|
646 |
3 | 647 <param type="hidden" name="uglyTestingHack" value="" /> |
0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
648 </inputs> |
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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diff
changeset
|
649 <outputs> |
3 | 650 <data format="html" name="output" label="JBrowse on $on_string - $standalone"/> |
0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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diff
changeset
|
651 </outputs> |
3 | 652 <tests> |
653 <test> | |
654 <!-- gencode --> | |
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
655 <param name="reference_genome|genome_type_select" value="history"/> |
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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656 <param name="reference_genome|genome" value="merlin.fa"/> |
3 | 657 <param name="gencode" value="1" /> |
658 <param name="standalone" value="Data Directory" /> | |
659 <param name="uglyTestingHack" value="enabled" /> | |
31
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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660 <output name="output" file="gencode/test-1.xml" lines_diff="16"/> |
3 | 661 </test> |
662 <test> | |
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
663 <param name="reference_genome|genome_type_select" value="history"/> |
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
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664 <param name="reference_genome|genome" value="merlin.fa"/> |
3 | 665 <param name="gencode" value="11" /> |
666 <param name="standalone" value="Data Directory" /> | |
667 <param name="uglyTestingHack" value="enabled" /> | |
31
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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|
668 <output name="output" file="gencode/test.xml" lines_diff="16"/> |
3 | 669 </test> |
670 <test> | |
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
671 <param name="reference_genome|genome_type_select" value="history"/> |
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
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672 <param name="reference_genome|genome" value="merlin.fa"/> |
3 | 673 <param name="gencode" value="11" /> |
674 <param name="standalone" value="Data Directory" /> | |
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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diff
changeset
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675 <repeat name="track_groups"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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changeset
|
676 <param name="category" value="Auto Coloured" /> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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diff
changeset
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677 <repeat name="data_tracks"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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changeset
|
678 <conditional name="data_format"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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changeset
|
679 <param name="data_format_select" value="gene_calls"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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diff
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680 <param name="annotation" value="gff3/A.gff,gff3/B.gff,gff3/C.gff,gff3/D.gff"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
681 <conditional name="match_part"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
682 <param name="match_part_select" value="false"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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diff
changeset
|
683 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
684 <section name="jbcolor_scale"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
685 <conditional name="color_score"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
686 <param name="color_score_select" value="none"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
687 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
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688 <conditional name="color"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
689 <param name="color_select" value="automatic"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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changeset
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690 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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diff
changeset
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691 </section> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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diff
changeset
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692 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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diff
changeset
|
693 </repeat> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
694 </repeat> |
3 | 695 |
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
696 <repeat name="track_groups"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
697 <param name="category" value="Ignore Scale" /> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
698 <repeat name="data_tracks"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
699 <conditional name="data_format"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
700 <param name="data_format_select" value="gene_calls"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
701 <param name="annotation" value="gff3/1.gff"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
702 <conditional name="match_part"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
703 <param name="match_part_select" value="false"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
704 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
705 <section name="jbcolor_scale"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
706 <conditional name="color_score"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
707 <param name="color_score_select" value="none"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
708 <conditional name="color"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
709 <param name="color_select" value="manual"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
710 <param name="style_color" value="#ff00ff"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
711 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
712 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
713 </section> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
714 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
715 </repeat> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
716 </repeat> |
3 | 717 |
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
718 <repeat name="track_groups"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
719 <param name="category" value="Scaled Colour" /> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
720 <repeat name="data_tracks"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
721 <conditional name="data_format"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
722 <param name="data_format_select" value="gene_calls"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
723 <param name="annotation" value="gff3/1.gff"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
724 <conditional name="match_part"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
725 <param name="match_part_select" value="false"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
726 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
727 <section name="jbcolor_scale"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
728 <conditional name="color_score"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
729 <param name="color_score_select" value="score"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
730 <param name="score_scaling" value="linear"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
731 <conditional name="score_scales"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
732 <param name="scale_select" value="automatic"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
733 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
734 <conditional name="color_scheme"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
735 <param name="score_scheme" value="opacity"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
736 <conditional name="color"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
737 <param name="color_select" value="automatic"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
738 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
739 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
740 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
741 </section> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
742 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
743 </repeat> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
744 <repeat name="data_tracks"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
745 <conditional name="data_format"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
746 <param name="data_format_select" value="gene_calls"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
747 <param name="annotation" value="gff3/1.gff"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
748 <conditional name="match_part"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
749 <param name="match_part_select" value="false"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
750 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
751 <section name="jbcolor_scale"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
752 <conditional name="color_score"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
753 <param name="color_score_select" value="score"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
754 <param name="score_scaling" value="linear"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
755 <conditional name="score_scales"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
756 <param name="scale_select" value="automatic"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
757 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
758 <conditional name="color_scheme"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
759 <param name="score_scheme" value="opacity"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
760 <conditional name="color"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
761 <param name="color_select" value="manual"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
762 <param name="style_color" value="#0000ff"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
763 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
764 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
765 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
766 </section> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
767 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
768 </repeat> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
769 <repeat name="data_tracks"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
770 <conditional name="data_format"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
771 <param name="data_format_select" value="gene_calls"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
772 <param name="annotation" value="gff3/1.gff"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
773 <conditional name="match_part"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
774 <param name="match_part_select" value="false"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
775 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
776 <section name="jbcolor_scale"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
777 <conditional name="color_score"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
778 <param name="color_score_select" value="score"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
779 <param name="score_scaling" value="linear"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
780 <conditional name="score_scales"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
781 <param name="scale_select" value="manual"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
782 <param name="minimum" value="0"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
783 <param name="maximum" value="1000"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
784 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
785 <conditional name="color_scheme"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
786 <param name="score_scheme" value="opacity"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
787 <conditional name="color"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
788 <param name="color_select" value="automatic"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
789 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
790 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
791 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
792 </section> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
793 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
794 </repeat> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
795 <repeat name="data_tracks"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
796 <conditional name="data_format"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
797 <param name="data_format_select" value="gene_calls"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
798 <param name="annotation" value="gff3/1.gff"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
799 <conditional name="match_part"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
800 <param name="match_part_select" value="false"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
801 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
802 <section name="jbcolor_scale"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
803 <conditional name="color_score"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
804 <param name="color_score_select" value="score"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
805 <param name="score_scaling" value="linear"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
806 <conditional name="score_scales"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
807 <param name="scale_select" value="manual"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
808 <param name="minimum" value="0"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
809 <param name="maximum" value="1000"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
810 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
811 <conditional name="color_scheme"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
812 <param name="score_scheme" value="opacity"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
813 <conditional name="color"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
814 <param name="color_select" value="manual"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
815 <param name="style_color" value="#ff0000"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
816 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
817 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
818 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
819 </section> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
820 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
821 </repeat> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
822 </repeat> |
3 | 823 |
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
824 <repeat name="track_groups"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
825 <param name="category" value="Realistic" /> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
826 <repeat name="data_tracks"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
827 <conditional name="data_format"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
828 <param name="data_format_select" value="gene_calls"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
829 <param name="annotation" value="gff3/interpro.gff"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
830 <conditional name="match_part"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
831 <param name="match_part_select" value="false"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
832 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
833 <section name="jbcolor_scale"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
834 <conditional name="color_score"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
835 <param name="color_score_select" value="none"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
836 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
837 <conditional name="color"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
838 <param name="color_select" value="automatic"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
839 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
840 </section> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
841 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
842 </repeat> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
843 <repeat name="data_tracks"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
844 <conditional name="data_format"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
845 <param name="data_format_select" value="gene_calls"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
846 <param name="annotation" value="gff3/2.gff"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
847 <conditional name="match_part"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
848 <param name="match_part_select" value="true"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
849 <param name="name" value="cDNA_match"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
850 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
851 <section name="jbcolor_scale"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
852 <conditional name="color_score"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
853 <param name="color_score_select" value="none"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
854 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
855 <conditional name="color"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
856 <param name="color_select" value="automatic"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
857 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
858 </section> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
859 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
860 </repeat> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
861 </repeat> |
3 | 862 |
863 <param name="uglyTestingHack" value="enabled" /> | |
31
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
864 <output name="output" file="gff3/test.xml" lines_diff="170" /> |
3 | 865 </test> |
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
866 <test> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
867 <param name="reference_genome|genome_type_select" value="history"/> |
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
868 <param name="reference_genome|genome" value="merlin.fa"/> |
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
869 <param name="gencode" value="11" /> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
870 <param name="standalone" value="Data Directory" /> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
871 |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
872 <repeat name="track_groups"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
873 <param name="category" value="With menu or index" /> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
874 <repeat name="data_tracks"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
875 <conditional name="data_format"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
876 <param name="data_format_select" value="gene_calls"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
877 <param name="annotation" value="gff3/1.gff"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
878 <conditional name="match_part"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
879 <param name="match_part_select" value="false"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
880 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
881 <section name="jbcolor_scale"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
882 <conditional name="color_score"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
883 <param name="color_score_select" value="none"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
884 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
885 <conditional name="color"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
886 <param name="color_select" value="automatic"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
887 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
888 </section> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
889 <section name="jbmenu"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
890 <repeat name="track_menu"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
891 <param name="menu_action" value="iframeDialog"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
892 <param name="menu_label" value="Some menu item"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
893 <param name="menu_title" value="Frame title"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
894 <param name="menu_url" value="https://example.com/#!/?id={name}&q={type}&z="{end}""/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
895 <param name="menu_icon" value="dijitIconNewTask"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
896 </repeat> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
897 <repeat name="track_menu"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
898 <param name="menu_action" value="newWindow"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
899 <param name="menu_label" value="Another menu item"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
900 <param name="menu_title" value="Frame title 2"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
901 <param name="menu_url" value="https://example.com/#!/?id={name}&q={type}&z="{end}""/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
902 </repeat> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
903 </section> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
904 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
905 </repeat> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
906 <repeat name="data_tracks"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
907 <conditional name="data_format"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
908 <param name="data_format_select" value="gene_calls"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
909 <param name="annotation" value="gff3/1.gff"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
910 <param name="index" value="true"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
911 <conditional name="match_part"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
912 <param name="match_part_select" value="false"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
913 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
914 <section name="jbcolor_scale"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
915 <conditional name="color_score"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
916 <param name="color_score_select" value="none"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
917 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
918 <conditional name="color"> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
919 <param name="color_select" value="automatic"/> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
920 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
921 </section> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
922 </conditional> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
923 </repeat> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
924 </repeat> |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
925 |
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
926 <param name="uglyTestingHack" value="enabled" /> |
31
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
927 <output name="output" file="menus/test.xml" lines_diff="44"/> |
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
928 </test> |
10
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
929 <test> |
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
930 <param name="reference_genome|genome_type_select" value="history"/> |
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
931 <param name="reference_genome|genome" value="merlin.fa"/> |
10
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
932 <param name="gencode" value="11" /> |
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
933 <param name="standalone" value="Data Directory" /> |
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
934 |
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
935 <repeat name="track_groups"> |
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
936 <param name="category" value="With canvas config" /> |
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
937 <repeat name="data_tracks"> |
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
938 <conditional name="data_format"> |
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
939 <param name="data_format_select" value="gene_calls"/> |
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
940 <param name="annotation" value="gff3/1.gff"/> |
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
941 <conditional name="match_part"> |
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
942 <param name="match_part_select" value="false"/> |
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
943 </conditional> |
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
944 <conditional name="track_config"> |
31
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
945 <param name="track_class" value="JBrowse/View/Track/CanvasFeatures"/> |
10
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
946 <section name="canvas_options"> |
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
947 <param name="transcriptType" value="transcript"/> |
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
948 <param name="subParts" value="exon"/> |
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
949 <param name="impliedUTRs" value="true"/> |
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
950 </section> |
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
951 </conditional> |
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
952 <section name="jbcolor_scale"> |
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
953 <conditional name="color_score"> |
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
954 <param name="color_score_select" value="none"/> |
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
955 </conditional> |
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
956 <conditional name="color"> |
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
957 <param name="color_select" value="automatic"/> |
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
958 </conditional> |
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
959 </section> |
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
960 </conditional> |
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
961 </repeat> |
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
962 </repeat> |
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
963 |
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
964 <param name="uglyTestingHack" value="enabled" /> |
31
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
965 <output name="output" file="track_config/test.xml" lines_diff="30"/> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
966 </test> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
967 <test> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
968 <param name="reference_genome|genome_type_select" value="history"/> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
969 <param name="reference_genome|genome" value="merlin.fa"/> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
970 <param name="gencode" value="11" /> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
971 <param name="standalone" value="Data Directory" /> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
972 |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
973 <repeat name="track_groups"> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
974 <param name="category" value="With custom track config" /> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
975 <repeat name="data_tracks"> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
976 <conditional name="data_format"> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
977 <param name="data_format_select" value="gene_calls"/> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
978 <param name="annotation" value="gff3/1.gff"/> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
979 <conditional name="match_part"> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
980 <param name="match_part_select" value="false"/> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
981 </conditional> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
982 <section name="jb_custom_config"> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
983 <repeat name="option"> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
984 <param name="opt_key" value="displayMode"/> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
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diff
changeset
|
985 <conditional name="opt_value"> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
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diff
changeset
|
986 <param name="val_type" value="text"/> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
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diff
changeset
|
987 <param name="val" value="collapsed"/> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
988 </conditional> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
989 </repeat> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
990 <repeat name="option"> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
991 <param name="opt_key" value="histograms.height"/> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
992 <conditional name="opt_value"> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
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diff
changeset
|
993 <param name="val_type" value="integer"/> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
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diff
changeset
|
994 <param name="val" value="150"/> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
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diff
changeset
|
995 </conditional> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
996 </repeat> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
997 <repeat name="option"> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
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diff
changeset
|
998 <param name="opt_key" value="maxFeatureScreenDensity"/> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
999 <conditional name="opt_value"> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
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diff
changeset
|
1000 <param name="val_type" value="float"/> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1001 <param name="val" value="0.1"/> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1002 </conditional> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
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diff
changeset
|
1003 </repeat> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
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changeset
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1004 <repeat name="option"> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
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diff
changeset
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1005 <param name="opt_key" value="style.strandArrow"/> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
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diff
changeset
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1006 <conditional name="opt_value"> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
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changeset
|
1007 <param name="val_type" value="boolean"/> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
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changeset
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1008 <param name="val" value="false"/> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
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diff
changeset
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1009 </conditional> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
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diff
changeset
|
1010 </repeat> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
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diff
changeset
|
1011 </section> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
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diff
changeset
|
1012 </conditional> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
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diff
changeset
|
1013 </repeat> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
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diff
changeset
|
1014 </repeat> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
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diff
changeset
|
1015 |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
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diff
changeset
|
1016 <param name="uglyTestingHack" value="enabled" /> |
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
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diff
changeset
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1017 <output name="output" file="custom_config/test.xml" lines_diff="30"/> |
10
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
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diff
changeset
|
1018 </test> |
18
836d1aa3e89a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents:
17
diff
changeset
|
1019 <test> |
19
8f33c9fbc119
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents:
18
diff
changeset
|
1020 <param name="reference_genome|genome_type_select" value="history"/> |
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1021 <param name="reference_genome|genome" value="merlin.fa"/> |
19
8f33c9fbc119
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents:
18
diff
changeset
|
1022 <param name="gencode" value="11" /> |
8f33c9fbc119
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents:
18
diff
changeset
|
1023 <param name="standalone" value="Data Directory" /> |
8f33c9fbc119
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents:
18
diff
changeset
|
1024 |
8f33c9fbc119
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents:
18
diff
changeset
|
1025 <repeat name="track_groups"> |
8f33c9fbc119
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents:
18
diff
changeset
|
1026 <param name="category" value="Auto Coloured" /> |
8f33c9fbc119
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents:
18
diff
changeset
|
1027 <repeat name="data_tracks"> |
8f33c9fbc119
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents:
18
diff
changeset
|
1028 <conditional name="data_format"> |
8f33c9fbc119
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents:
18
diff
changeset
|
1029 <param name="data_format_select" value="pileup"/> |
8f33c9fbc119
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents:
18
diff
changeset
|
1030 <param name="annotation" value="bam/merlin-sample.bam"/> |
8f33c9fbc119
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents:
18
diff
changeset
|
1031 </conditional> |
8f33c9fbc119
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents:
18
diff
changeset
|
1032 </repeat> |
8f33c9fbc119
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents:
18
diff
changeset
|
1033 </repeat> |
8f33c9fbc119
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents:
18
diff
changeset
|
1034 |
8f33c9fbc119
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents:
18
diff
changeset
|
1035 <param name="uglyTestingHack" value="enabled" /> |
31
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1036 <output name="output" file="bam/test.xml" lines_diff="42"/> |
19
8f33c9fbc119
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents:
18
diff
changeset
|
1037 </test> |
8f33c9fbc119
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents:
18
diff
changeset
|
1038 |
8f33c9fbc119
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents:
18
diff
changeset
|
1039 <test> |
18
836d1aa3e89a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents:
17
diff
changeset
|
1040 <!-- data_table --> |
836d1aa3e89a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents:
17
diff
changeset
|
1041 <param name="reference_genome|genome_type_select" value="indexed"/> |
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1042 <param name="reference_genome|genome" value="merlin"/> |
18
836d1aa3e89a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents:
17
diff
changeset
|
1043 <param name="gencode" value="1" /> |
836d1aa3e89a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents:
17
diff
changeset
|
1044 <param name="standalone" value="Data Directory" /> |
836d1aa3e89a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents:
17
diff
changeset
|
1045 <param name="uglyTestingHack" value="enabled" /> |
31
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1046 <output name="output" file="gencode/test-data_table.xml" lines_diff="4" /> |
18
836d1aa3e89a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents:
17
diff
changeset
|
1047 </test> |
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1048 |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1049 <test> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1050 <param name="reference_genome|genome_type_select" value="history"/> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1051 <param name="reference_genome|genome" value="merlin.fa"/> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1052 <param name="gencode" value="11" /> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1053 <param name="standalone" value="Data Directory" /> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1054 |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1055 <repeat name="track_groups"> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1056 <param name="category" value="External endpoints" /> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1057 <repeat name="data_tracks"> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1058 <conditional name="data_format"> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1059 <param name="data_format_select" value="rest"/> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1060 <param name="url" value="http://example.org.external/rest_api/"/> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1061 <param name="label" value="Rest api"/> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1062 </conditional> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1063 </repeat> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1064 <repeat name="data_tracks"> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1065 <conditional name="data_format"> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1066 <param name="data_format_select" value="sparql"/> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1067 <param name="url" value="http://example.org.external/sparql/"/> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1068 <param name="label" value="Sparql endpoint"/> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1069 <param name="query" value=" DEFINE sql:select-option 'order' |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1070 prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1071 select ?start, |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1072 ?end, |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1073 IF( ?faldo_type = faldo:ForwardStrandPosition, |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1074 1, |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1075 IF( ?faldo_type = faldo:ReverseStrandPosition, |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1076 -1, |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1077 0 |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1078 ) |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1079 ) as ?strand, |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1080 str(?obj_type_name) as ?type, |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1081 str(?label) as ?name, |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1082 str(?obj_name) as ?description, |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1083 ?obj as ?uniqueID, |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
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diff
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|
1084 ?parent as ?parentUniqueID |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
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1085 where { |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1086 values ?faldo_type { faldo:ForwardStrandPosition faldo:ReverseStrandPosition faldo:BothStrandsPosition } |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1087 }"/> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
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diff
changeset
|
1088 </conditional> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1089 </repeat> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1090 </repeat> |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1091 |
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1092 <param name="uglyTestingHack" value="enabled" /> |
31
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
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diff
changeset
|
1093 <output name="output" file="endpoints/test.xml" lines_diff="16"/> |
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1094 </test> |
3 | 1095 </tests> |
0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
1096 <help><![CDATA[ |
3 | 1097 JBrowse-in-Galaxy |
1098 ================= | |
1099 | |
1100 JBrowse-in-Galaxy offers a highly configurable, workflow-compatible | |
1101 alternative to Trackster. | |
1102 | |
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
1103 Overview |
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1104 -------- |
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1105 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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1106 JBrowse is a fast, embeddable genome browser built completely with |
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1107 JavaScript and HTML5. |
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1108 |
3 | 1109 The JBrowse-in-Galaxy (JiG) tool was written to help build complex |
1110 JBrowse installations straight from Galaxy, taking advantage of the | |
1111 latest Galaxy features such as dataset collections, sections, and colour | |
1112 pickers. It allows you to build up a JBrowse instance without worrying | |
1113 about how to run the command line tools to format your data, and which | |
1114 options need to be supplied and where. Additionally it comes with many | |
1115 javascript functions to handle colouring of features which would be | |
1116 nearly impossible to write without the assistance of this tool. | |
1117 | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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1118 The JBrowse-in-Galaxy tool is maintained by `the Galaxy IUC |
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1119 <https://github.com/galaxyproject/tools-iuc/issues>`__, who you can help you |
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1120 with missing features or bugs in the tool. |
3 | 1121 |
1122 Options | |
1123 ------- | |
1124 | |
1125 The first option you encounter is the **Fasta Sequence(s)**. This option | |
1126 now accepts multiple fasta files, allowing you to build JBrowse | |
1127 instances that contain data for multiple genomes or chrosomomes | |
1128 (generally known as "landmark features" in gff3 terminology.) Up to 30 | |
1129 will be shown from the dropdown selector within JBrowse, this is a known | |
1130 issue. | |
1131 | |
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1132 **Standalone Instances** enable you to have either a complete JBrowse instance |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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1133 in a dataset, or just the data directory without JBrowse (e.g. for Apollo). |
3 | 1134 Currently Galaxy copies the entire JBrowse directory in order to have a |
1135 complete, downloadable file that contains a ready-to-go JBrowse | |
1136 instance. This is obviously an anti-feature because users don't want a | |
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1137 complete copy of JBrowse (12Mb) that's duplicated for every JBrowse |
3 | 1138 dataset in their history, and admins don't want useless copies of |
1139 JBrowse on disk. Unfortunately we have not come up with the perfect | |
1140 solution just yet, but we're working on it! In the meantime, users have | |
1141 been given the option to produce just the ``data/`` directory. For those | |
1142 unfamiliar with JBrowse, the ``data/`` directory contains processed data | |
1143 files, but no way to view them. This feature is additionally implemented | |
1144 for upcoming `Apollo <https://github.com/gmod/apollo>`__ integration. | |
1145 | |
1146 **Genetic Code** is a new feature in v0.4 of JiG / v1.12.0 of JBrowse, | |
1147 which allows users to specify a non standard genetic code, and have | |
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1148 JBrowse highlight the correct start and stop codons. |
3 | 1149 |
1150 **Track Groups** represent a set of tracks in a single category. These | |
1151 can be used to let your users understand relationships between large | |
1152 groups of tracks. | |
1153 | |
1154 .. image:: sections.png | |
1155 | |
1156 Annotation Tracks | |
1157 ----------------- | |
1158 | |
1159 Within Track Groups, you have one or more **Annotation Tracks**. Each | |
1160 Annotation Track is a groups of datasets which have similar styling. | |
1161 This allows you to rapidly build up JBrowse instances without having to | |
1162 configure tracks individually. A massive improvement over previous | |
1163 versions. For example, if you have five different GFF3 files from | |
1164 various gene callers that you wish to display, you can take advantage of | |
1165 this feature to style all of them similarly. | |
1166 | |
1167 There are a few different types of tracks supported, each with their own | |
1168 set of options: | |
1169 | |
1170 GFF3/BED/GBK | |
1171 ~~~~~~~~~~~~ | |
1172 | |
1173 These are your standard feature tracks. They usually highlight genes, | |
1174 mRNAs and other features of interest along a genomic region. The | |
1175 underlying tool and this help documentation focus primarily on GFF3 | |
1176 data, and have not been tested extensively with other formats. Automatic | |
1177 min/max detection will likely fail under BED and GBK datasets. | |
1178 | |
1179 The data may be of a subclass we call **match/match part** data. This | |
1180 consists of top level ``match`` features, with a child ``match_part`` | |
1181 feature, and is often used in displaying alignments. (See "Alignments" | |
1182 section on the `GFF3 | |
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1183 specification <https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md>`__ for more |
3 | 1184 information). If the data is match/match part, you will need to specify |
1185 the top level match feature name, as it can be one of a few different SO | |
1186 terms, and JiG does not yet have the ability to understand SO terms. | |
1187 | |
1188 Next up is the **Styling Options** section, which lets you control a few | |
1189 properties on how the track is styled. Most of these you will not need | |
1190 to configure and can safely leave on defaults. Occasionally you will | |
1191 want to change what information is shown in the end product. | |
1192 | |
1193 .. image:: styling.png | |
1194 | |
1195 In the above image you can see some black text, and some blue text. The | |
1196 source of the black text is configured with the **style.label** option, | |
1197 and the source of the blue text is configured with the | |
1198 **style.description** option. | |
1199 | |
1200 Feature Score Scaling & Colouring Options | |
1201 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
1202 | |
1203 First, you need to choose between ignoring the score attribute of GFF3 | |
1204 files, or using it. If you choose to ignore it, all features will be | |
1205 coloured with a solid colour. If you choose to use it, features will | |
1206 have slightly different colours based on their scores. | |
1207 | |
1208 .. image:: opacity.png | |
1209 | |
1210 If you choose **Ignore score**, you may choose between automatically | |
1211 choosing a colour, or manually specifying one. The automatically chosen | |
1212 colours vary along a brewer palette and generally look quite nice with | |
1213 no human intervention required. The manual colour choice is somewhat | |
1214 self explanatory. Clicking on the small coloured square will bring up a | |
1215 colour palette. | |
1216 | |
1217 If you choose **Base on score**, you're faced with a dizzying array of | |
1218 options. First is the function to map the colour choices to colour | |
1219 values. JiG comes with a few functions built in such as linear scaling, | |
1220 logarithmic scaling, and blast scaling. | |
1221 | |
1222 The **linear scaling** method says "take these values, and they map | |
1223 directly to a range of output values". **Logarithmic scaling** says | |
1224 "please take the log of the score before mapping", and **Blast scaling** | |
1225 is further specialised to handle blast data more nicely. These are | |
1226 convenience functions to help transform the wide array of possible | |
1227 values in the GFF3 score attribute to more meaningful numbers. If you | |
1228 need more comprehensive score scaling, it is recommended that you | |
1229 pre-process your GFF3 files somehow. | |
1230 | |
1231 Once you've selected a scaling method, you can choose to manually | |
1232 specify the minimum and maximum expected values, or you can let JiG | |
1233 determine them for you automatically. | |
1234 | |
1235 Finally, opacity is the only mapping we currently provide. Future | |
1236 iterations will attempt to improve upon this and provide more colour | |
1237 scales. The Opacity option maps the highest scoring features to full | |
1238 opacity, and everything else to lower ones. | |
1239 | |
1240 BAM Pileups | |
1241 ~~~~~~~~~~~ | |
1242 | |
1243 We support BAM files and can automatically generate SNP tracks based on | |
1244 that bam data. | |
1245 | |
1246 .. image:: bam.png | |
1247 | |
1248 This is *strongly discouraged* for high coverage density datasets. | |
1249 Unfortunately there are no other configuration options exposed for bam | |
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1250 files. |
3 | 1251 |
1252 BlastXML | |
1253 ~~~~~~~~ | |
1254 | |
1255 .. image:: blast.png | |
1256 | |
1257 JiG now supports both blastn and blastp datasets. JiG internally uses a | |
1258 blastXML to gapped GFF3 tool to convert your blastxml datasets into a | |
1259 format amenable to visualization in JBrowse. This tool is also | |
1260 available separately from the IUC on the toolshed. | |
1261 | |
1262 **Minimum Gap Size** reflects how long a gap must be before it becomes a | |
1263 real gap in the processed gff3 file. In the picture above, various sizes | |
1264 of gaps can be seen. If the minimum gap size was set much higher, say | |
1265 100nt, many of the smaller gaps would disappear, and the features on | |
1266 both sides would be merged into one, longer feature. This setting is | |
1267 inversely proportional to runtime and output file size. *Do not set this | |
1268 to a low value for large datasets*. By setting this number lower, you | |
1269 will have extremely large outputs and extremely long runtimes. The | |
1270 default was configured based off of the author's experience, but the | |
1271 author only works on small viruses. It is *strongly* recommended that | |
1272 you filter your blast results before display, e.g. picking out the top | |
1273 10 hits or so. | |
1274 | |
1275 **Protein blast search** option merely informs underlying tools that | |
1276 they should adjust feature locations by 3x. | |
1277 | |
1278 Styling Options | |
1279 ^^^^^^^^^^^^^^^ | |
1280 | |
1281 Please see the styling options for GFF3 datasets, they are identical. | |
1282 | |
1283 Feature Score Scaling & Coloring Options | |
1284 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
1285 | |
1286 Please see the score scaling and colouring options for GFF3 datasets, | |
1287 they are identical. Remember to set your score scaling to "blast" method | |
1288 if you do use it. | |
1289 | |
1290 Bigwig XY | |
1291 ~~~~~~~~~ | |
1292 | |
1293 .. image:: bigwig.png | |
1294 | |
1295 **XYPlot** | |
1296 | |
1297 BigWig tracks can be displayed as a "density" plot which is continuous | |
1298 line which varies in colour, or as an "XYplot." XYplots are preferable | |
1299 for users to visually identify specific features in a bigwig track, | |
1300 however density tracks are more visually compact. | |
1301 | |
1302 **Variance Band** is an option available to XYPlots, and can be seen in | |
1303 the third and fourth tracks in the above picture. This overlays a mean | |
1304 line, and 1 and 2 standard deviation areas. | |
1305 | |
1306 **Track Scaling** is different from colour scaling, instead it | |
1307 configures how the track behaves inside of JBrowse. **Autoscaling | |
1308 globally** means that JBrowse will determine the minimum and maximum for | |
1309 the track, and fix the bounds of the viewport to that. E.g. if your | |
1310 track ranges from 1-1000, and the region you're currently zoomed to only | |
1311 goes from 0-50, then the viewport range will still show 1-1000. This is | |
1312 good for global genomic context. However you may wish to consider | |
1313 **autoscaling locally** instead. In the example of a region which varies | |
1314 from 0-50, autoscaling locally would cause the individual track's | |
1315 viewport to re-adjust and show just the 0-50 region. If neither of these | |
1316 options are palatable, you may manually hardcode the minimum and | |
1317 maximums for the track to scale to. | |
1318 | |
1319 Colour Options | |
1320 ^^^^^^^^^^^^^^ | |
1321 | |
1322 BigWig tracks have two colours in JBrowse, a positive and a negative | |
1323 colour. | |
1324 | |
1325 As always you may manually choose a colour, or let JiG choose for you. | |
1326 | |
1327 One of the more interesting options is the **Bicolor pivot**. This | |
1328 option allows you to control the point at which JBrowse switches from | |
1329 the positive colour to the negative. In the above graphic, you can see | |
1330 this has been configured to "mean" for the first two (orange and blue) | |
1331 tracks. | |
1332 | |
1333 VCFs/SNPs | |
1334 ~~~~~~~~~ | |
1335 | |
1336 These tracks do not support any special configuration. | |
1337 | |
1338 Known Issues | |
1339 ------------ | |
1340 | |
1341 - More than 30 landmark features cannot be listed in the manual | |
1342 selector. | |
1343 - Non GFF3 likely has issue with automatically determined min/max | |
1344 scores. Manually specify minimum and maximum score attributes, or do | |
1345 not use varied colours based on scores to avoid this issue. | |
1346 | |
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1347 @ATTRIBUTION@ |
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1348 ]]></help> |
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1349 <expand macro="citations"/> |
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1350 </tool> |