jbrowse: jbrowse.xml annotate

annotate jbrowse.xml @ 30:ca2def38369c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 74554507efb46fb40ce6e12f0b73425e52ec0977

author	iuc
date	Thu, 11 Apr 2019 09:35:00 -0400
parents	112eb40ba6cf
children	2bb2e07a7a21

rev	line source
19 8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47 iuc parents: 18 diff changeset	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 parents: diff changeset	2 <description>genome browser</description>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	3 <macros>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	4 <import>macros.xml</import>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	5 </macros>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	6 <expand macro="requirements"/>
18 836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e iuc parents: 17 diff changeset	7 <version_command>python '${__tool_directory__}/jbrowse.py' --version</version_command>
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	8 <command detect_errors="aggressive"><![CDATA[
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	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 parents: 6 diff changeset	10 mkdir -p $output.files_path &&
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	11 #else:
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	12 cp -R $action.update_jbrowse.extra_files_path $output.files_path &&
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	13 #end if
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	14
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	15 ## Copy the XML file into the directory, mostly for debugging
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	16 ## but nice if users want to reproduce locally
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	17 cp $trackxml $output.files_path/galaxy.xml &&
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	18
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	19 ## Once that's done, we run the python script to handle the real work
18 836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e iuc parents: 17 diff changeset	20 python '$__tool_directory__/jbrowse.py'
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	21
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	22 --jbrowse \${JBROWSE_SOURCE_DIR}
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	23 #if str($standalone) == "Complete":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	24 --standalone
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	25 #end if
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	26
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	27 --outdir $output.files_path
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	28 $trackxml &&
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	29
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	30 #if str($standalone) == "Complete":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	31 mv $output.files_path/index.html $output;
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	32 #else:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	33 mv $dummyIndex $output;
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	34 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	35
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	36 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	37 #if str($uglyTestingHack) == "enabled":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	38 mv $trackxml $output
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	39 #end if
22 5f70e7fe6077 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 21 diff changeset	40 ]]></command>
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	41 <configfiles>
22 5f70e7fe6077 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 21 diff changeset	42 <configfile name="dummyIndex"><![CDATA[
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	43 <html>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	44 <head>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	45 </head>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	46 <body>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	47 <h1>JBrowse Data Directory</h1>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	48 <p>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	49 Hi! This is not a full JBrowse instance. JBrowse v0.4(+?)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	50 started shipping with the ability to produce just the
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	51 "data" directory from a JBrowse instance, rather than a
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	52 complete, standalone instance. This was intended to be used
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	53 with the in-development Apollo integration, but may have other
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	54 uses as well.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	55 </p>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	56 <p>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	57 <u>This is not usable on its own</u>. The output dataset may be
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	58 used with Apollo, or may be passed through the "JBrowse -
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	59 Convert to Standalone" tool in Galaxy to "upgrade" to a full
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	60 JBrowse instance.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	61 </p>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	62 </body>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	63 </html>
22 5f70e7fe6077 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 21 diff changeset	64 ]]></configfile>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	65 <configfile name="trackxml"><![CDATA[<?xml version="1.0"?>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	66 <root>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	67 <metadata>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	68 <gencode>$gencode</gencode>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	69 <genomes>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	70 #if str($reference_genome.genome_type_select) == "indexed":
18 836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e iuc parents: 17 diff changeset	71 <genome path="${reference_genome.genomes.fields.path}">
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e iuc parents: 17 diff changeset	72 <metadata />
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e iuc parents: 17 diff changeset	73 </genome>s
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	74 #else
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	75 <genome path="$reference_genome.genome">
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	76 <metadata>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	77 <dataset id="${__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 iuc parents: 23 diff changeset	78 size="${reference_genome.genome.get_size(nice_size=True)}"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	79 edam_format="${reference_genome.genome.datatype.edam_format}"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	80 file_ext="${reference_genome.genome.ext}" />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	81 <history id="${__app__.security.encode_id($reference_genome.genome.history_id)}"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	82 user_email="${reference_genome.genome.history.user.email}"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	83 user_id="${reference_genome.genome.history.user_id}"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	84 display_name="${reference_genome.genome.history.get_display_name()}"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	85 <metadata
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	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 iuc parents: 23 diff changeset	87 #if "_types" not in $key:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	88 ${key}="${value}"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	89 #end if
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	90 #end for
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	91 />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	92 <tool
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	93 tool_id="${reference_genome.genome.creating_job.tool_id}"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	94 tool_version="${reference_genome.genome.creating_job.tool_version}"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	95 />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	96 </metadata>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	97 </genome>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	98 #end if
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	99 </genomes>
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	100 <general>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	101 <defaultLocation>${jbgen.defaultLocation}</defaultLocation>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	102 <trackPadding>${jbgen.trackPadding}</trackPadding>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	103
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	104 <shareLink>${jbgen.shareLink}</shareLink>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	105 <aboutDescription>${jbgen.aboutDescription}</aboutDescription>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	106 <show_tracklist>${jbgen.show_tracklist}</show_tracklist>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	107 <show_nav>${jbgen.show_nav}</show_nav>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	108 <show_overview>${jbgen.show_overview}</show_overview>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	109 <show_menu>${jbgen.show_menu}</show_menu>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	110 <hideGenomeOptions>${jbgen.hideGenomeOptions}</hideGenomeOptions>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	111 </general>
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	112 <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	113 </metadata>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	114 <tracks>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	115 #for $tg in $track_groups:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	116 #for $track in $tg.data_tracks:
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	117 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	118 #if $track.data_format.data_format_select != "rest" and $track.data_format.data_format_select != "sparql":
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	119 <files>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	120 #for $dataset in $track.data_format.annotation:
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	121 <trackFile path="${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 iuc parents: 16 diff changeset	122 <metadata>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	123 <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	124 size="${dataset.get_size(nice_size=True)}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	125 edam_format="${dataset.datatype.edam_format}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	126 file_ext="${dataset.ext}" />
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	127 <history id="${__app__.security.encode_id($dataset.history_id)}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	128 user_email="${dataset.history.user.email}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	129 user_id="${dataset.history.user_id}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	130 display_name="${dataset.history.get_display_name()}"/>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	131 <metadata
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	132 #for (key, value) in $dataset.get_metadata().items():
30 ca2def38369c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 74554507efb46fb40ce6e12f0b73425e52ec0977 iuc parents: 29 diff changeset	133 #if "_types" not in $key and $value is not None and len(str($value)) < 5000:
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	134 ${key}="${value}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	135 #end if
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	136 #end for
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	137 />
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	138 <tool
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	139 tool_id="${dataset.creating_job.tool_id}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	140 tool_version="${dataset.creating_job.tool_version}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	141 />
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	142 </metadata>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	143 </trackFile>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	144 #end for
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	145 </files>
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	146 #end if
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	147
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	148 <options>
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	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 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	150 <style>
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	151 <overridePlugins>${track.data_format.override_apollo_plugins}</overridePlugins>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	152 <overrideDraggable>${track.data_format.override_apollo_drag}</overrideDraggable>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	153 <className>${track.data_format.jbstyle.style_classname}</className>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	154 <description>${track.data_format.jbstyle.style_description}</description>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	155 <label>${track.data_format.jbstyle.style_label}</label>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	156 <height>${track.data_format.jbstyle.style_height}</height>
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	157 <maxHeight>${track.data_format.jbstyle.max_height}</maxHeight>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	158 </style>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	159 <scaling>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	160 #if str($track.data_format.jbcolor_scale.color_score.color_score_select) == "none":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	161 <method>ignore</method>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	162 <scheme>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	163 #if str($track.data_format.jbcolor_scale.color_score.color.color_select) == "automatic":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	164 <color>__auto__</color>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	165 #else
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	166 <color>${track.data_format.jbcolor_scale.color_score.color.style_color}</color>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	167 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	168 </scheme>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	169 #else
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	170 <method>score</method>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	171 <algo>${track.data_format.jbcolor_scale.color_score.score_scaling}</algo>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	172 <scales>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	173 <type>${track.data_format.jbcolor_scale.color_score.score_scales.scale_select}</type>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	174
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	175 #if str($track.data_format.jbcolor_scale.color_score.score_scales.scale_select) == "manual":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	176 <min>${track.data_format.jbcolor_scale.color_score.score_scales.minimum}</min>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	177 <max>${track.data_format.jbcolor_scale.color_score.score_scales.maximum}</max>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	178 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	179 </scales>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	180 <scheme>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	181 <type>${track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme}</type>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	182 ## auto_color
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	183 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme) == "opacity":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	184 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.color.color_select) == "automatic":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	185 <color>__auto__</color>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	186 #else
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	187 <color>${track.data_format.jbcolor_scale.color_score.color_scheme.color.style_color}</color>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	188 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	189 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	190 </scheme>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	191 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	192 </scaling>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	193 <menus>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	194 #for $menu_item in $track.data_format.jbmenu.track_menu:
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	195 <menu>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	196 <action>${menu_item.menu_action}</action>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	197 #if str($menu_item.menu_label) != "":
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	198 <label>${menu_item.menu_label}</label>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	199 #end if
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	200 #if str($menu_item.menu_title) != "":
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	201 <title>${menu_item.menu_title}</title>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	202 #end if
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	203 #if str($menu_item.menu_url) != "":
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	204 <url>${menu_item.menu_url.replace("&", "&").replace("\"", """)}</url>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	205 #end if
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	206 #if str($menu_item.menu_icon) != "":
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	207 <iconClass>${menu_item.menu_icon}</iconClass>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	208 #end if
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	209 </menu>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	210 #end for
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	211 </menus>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	212 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	213
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	214 #if str($track.data_format.data_format_select) == "wiggle":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	215 <wiggle>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	216 <type>${track.data_format.xyplot}</type>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	217 <variance_band>${track.data_format.var_band}</variance_band>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	218 #if str($track.data_format.scaling.scale_select) == "auto_local":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	219 <autoscale>local</autoscale>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	220 #else if str($track.data_format.scaling.scale_select) == "auto_global":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	221 <autoscale>global</autoscale>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	222 #else:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	223 <min>${track.data_format.scaling.minimum}</min>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	224 <max>${track.data_format.scaling.maximum}</max>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	225 #end if
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	226 <scale>${track.data_format.scale_select2}</scale>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	227
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	228 ## Wiggle tracks need special color config
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	229 #if str($track.data_format.jbcolor.color.color_select) != "automatic":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	230 <color_pos>${track.data_format.jbcolor.color.style_pos_color}</color_pos>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	231 <color_neg>${track.data_format.jbcolor.color.style_neg_color}</color_neg>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	232 #else:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	233 <color_pos>__auto__</color_pos>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	234 <color_neg>__auto__</color_neg>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	235 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	236
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	237 ## Bicolor pivot config
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	238 #if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "zero":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	239 <bicolor_pivot>zero</bicolor_pivot>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	240 #else if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "mean":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	241 <bicolor_pivot>mean</bicolor_pivot>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	242 #else:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	243 <bicolor_pivot>${track.data_format.jbcolor.bicolor_pivot.pivot_point}</bicolor_pivot>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	244 #end if
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	245 <multibigwig>${track.data_format.MultiBigWig}</multibigwig>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	246 </wiggle>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	247 #else if str($track.data_format.data_format_select) == "pileup":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	248 <pileup>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	249 <auto_snp>${track.data_format.auto_snp}</auto_snp>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	250 <bam_indices>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	251 #for $dataset in $track.data_format.annotation:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	252 <bam_index>${dataset.metadata.bam_index}</bam_index>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	253 #end for
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	254 </bam_indices>
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	255 <chunkSizeLimit>${track.data_format.chunkSizeLimit}</chunkSizeLimit>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	256 </pileup>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	257 #else if str($track.data_format.data_format_select) == "blast":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	258 <blast>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	259 #if str($track.data_format.blast_parent) != "":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	260 <parent>${track.data_format.blast_parent}</parent>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	261 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	262 <protein>${track.data_format.is_protein}</protein>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	263 <min_gap>${track.data_format.min_gap}</min_gap>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	264 <index>${track.data_format.index}</index>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	265 </blast>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	266 #else if str($track.data_format.data_format_select) == "gene_calls":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	267 <gff>
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	268 <trackType>${track.data_format.track_config.track_class}</trackType>
27 61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	269 #if $track.data_format.track_config.track_class in ['JBrowse/View/Track/CanvasFeatures', 'NeatCanvasFeatures/View/Track/NeatFeatures']:
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	270 #if str($track.data_format.track_config.canvas_options.transcriptType) != "":
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	271 <transcriptType>${track.data_format.track_config.canvas_options.transcriptType}</transcriptType>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	272 #end if
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	273 #if str($track.data_format.track_config.canvas_options.subParts) != "":
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	274 <subParts>${track.data_format.track_config.canvas_options.subParts}</subParts>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	275 #end if
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	276 #if str($track.data_format.track_config.canvas_options.impliedUTRs) != "false":
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	277 <impliedUTRs>${track.data_format.track_config.canvas_options.impliedUTRs}</impliedUTRs>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	278 #end if
27 61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	279 #else if $track.data_format.track_config.track_class in ['JBrowse/View/Track/HTMLFeatures', 'NeatHTMLFeatures/View/Track/NeatFeatures']:
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	280 #if str($track.data_format.track_config.html_options.topLevelFeatures) != "":
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	281 <topLevelFeatures>${track.data_format.track_config.html_options.topLevelFeatures}</topLevelFeatures>
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	282 #end if
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	283 #end if
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	284 #if $track.data_format.match_part.match_part_select:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	285 <match>${track.data_format.match_part.name}</match>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	286 #end if
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	287 <index>${track.data_format.index}</index>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	288 </gff>
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	289 #else if str($track.data_format.data_format_select) == "rest":
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	290 <label>${track.data_format.label}</label>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	291 <rest>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	292 <url>${track.data_format.url}</url>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	293 </rest>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	294 #else if str($track.data_format.data_format_select) == "sparql":
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	295 <label>${track.data_format.label}</label>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	296 <sparql>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	297 <url>${track.data_format.url}</url>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	298 <query>${track.data_format.query}</query>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	299 </sparql>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	300 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	301 </options>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	302 </track>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	303 #end for
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	304 #end for
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	305 </tracks>
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	306 ## Disable plugins until https://github.com/GMOD/jbrowse/issues/1288 is fixed
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	307 ## <plugins
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	308 ## ComboTrackSelector="${plugins.ComboTrackSelector}"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	309 ## Bookmarks="${plugins.Bookmarks}"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	310 ## GCContent="${plugins.GCContent}"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	311 ## BlastView="${plugins.BlastView}"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	312 ## theme="${plugins.theme}"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	313 ## />
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	314 <plugins
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	315 ComboTrackSelector="${plugins.ComboTrackSelector}"
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	316 Bookmarks=""
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	317 GCContent="${plugins.GCContent}"
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	318 BlastView="${plugins.BlastView}"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	319 theme=""
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	320 />
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	321 </root>]]></configfile>
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	322 </configfiles>
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	323 <inputs>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	324 <conditional name="reference_genome">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	325 <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	326 <option selected="True" value="indexed">Use a built-in genome</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	327 <option value="history">Use a genome from history</option>
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	328 </param>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	329 <when value="indexed">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	330 <param
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	331 help="If your genome of interest is not listed, contact the Galaxy team"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	332 label="Select a reference genome"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	333 name="genomes"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	334 type="select"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	335 >
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	336 <options from_data_table="all_fasta">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	337 <filter column="2" type="sort_by" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	338 <validator message="No genomes are available for the selected input dataset" type="no_options" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	339 </options>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	340 </param>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	341 </when>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	342 <when value="history">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	343 <param
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	344 format="fasta"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	345 label="Select the reference genome"
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	346 name="genome"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	347 type="data" />
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	348 </when>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	349 </conditional>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	350
22 5f70e7fe6077 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 21 diff changeset	351 <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 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	352
22 5f70e7fe6077 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 21 diff changeset	353 <param name="gencode" type="select" label="Genetic Code">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	354 <option value="1">1. The Standard Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	355 <option value="2">2. The Vertebrate Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	356 <option value="3">3. The Yeast Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	357 <option value="4">4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	358 <option value="5">5. The Invertebrate Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	359 <option value="6">6. The Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	360 <option value="9">9. The Echinoderm and Flatworm Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	361 <option value="10">10. The Euplotid Nuclear Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	362 <option value="11">11. The Bacterial, Archaeal and Plant Plastid Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	363 <option value="12">12. The Alternative Yeast Nuclear Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	364 <option value="13">13. The Ascidian Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	365 <option value="14">14. The Alternative Flatworm Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	366 <option value="16">16. Chlorophycean Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	367 <option value="21">21. Trematode Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	368 <option value="22">22. Scenedesmus obliquus Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	369 <option value="23">23. Thraustochytrium Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	370 <option value="24">24. Pterobranchia Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	371 <option value="25">25. Candidate Division SR1 and Gracilibacteria Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	372 </param>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	373
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	374 <conditional name="action">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	375 <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 iuc parents: 6 diff changeset	376 <option value="create">New JBrowse Instance</option>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	377 <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 iuc parents: 6 diff changeset	378 </param>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	379 <when value="create" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	380 <when value="update">
22 5f70e7fe6077 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 21 diff changeset	381 <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 iuc parents: 6 diff changeset	382 </when>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	383 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	384
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	385 <repeat name="track_groups" title="Track Group">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	386 <param label="Track Category"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	387 name="category"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	388 type="text"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	389 value="Default"
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	390 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 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	391 <repeat name="data_tracks" title="Annotation Track">
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	392 <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 iuc parents: 0 diff changeset	393 <param type="select" label="Track Type" name="data_format_select">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	394 <option value="gene_calls">GFF/GFF3/BED/GBK Features</option>
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	395 <option value="pileup">BAM Pileups</option>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	396 <option value="blast">Blast XML</option>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	397 <option value="wiggle">BigWig XY</option>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	398 <option value="vcf">VCF SNPs</option>
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	399 <option value="rest">REST Endpoint</option>
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	400 <option value="sparql">SPARQL</option>
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	401 </param>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	402 <when value="blast">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	403 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" />
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	404
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	405 <param label="Features used in Blast Search"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	406 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."
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	407 format="gff3"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	408 name="blast_parent"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	409 optional="true"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	410 type="data"/>
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	411
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	412 <param label="Minimum Gap Size"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	413 help="before a new match_part feature is created"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	414 name="min_gap"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	415 type="integer"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	416 value="10"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	417 min="2" />
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	418 <param label="Is this a protein blast search?"
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	419 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	420 name="is_protein"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	421 truevalue="true"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	422 falsevalue="false" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	423
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	424 <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 iuc parents: 6 diff changeset	425
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	426 <expand macro="track_styling"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	427 classname="feature"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	428 label="description"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	429 description="Hit_titles"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	430 height="600px"/>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	431 <expand macro="color_selection"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	432 token_scaling_lin_select="false"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	433 token_scaling_log_select="true" />
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	434 <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	435 <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	436 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	437 <when value="vcf">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	438 <expand macro="input_conditional" label="SNP Track Data" format="vcf" />
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	439 <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	440 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	441 <when value="gene_calls">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	442 <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" />
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	443 <conditional name="match_part" label="match/match_part data">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	444 <param label="This is match/match_part data"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	445 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	446 name="match_part_select"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	447 truevalue="true"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	448 falsevalue="false" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	449 <when value="true">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	450 <param label="Match Part Feature Type"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	451 name="name"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	452 type="text"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	453 value="match"
21 1c718d8b3532 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9cac72c004cc7ef57be997e2fdafb3b1839a300f iuc parents: 19 diff changeset	454 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 iuc parents: 19 diff changeset	455 optional="True"/>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	456 </when>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	457 <when value="false" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	458 </conditional>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	459
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	460 <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 iuc parents: 6 diff changeset	461
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	462 <conditional name="track_config">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	463 <param type="select" label="JBrowse Track Type [Advanced]" name="track_class">
26 08776ba76cf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 75f6e483debb4c0d388bf4a54df81ee89af598d5 iuc parents: 25 diff changeset	464 <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 iuc parents: 25 diff changeset	465 <option value="NeatCanvasFeatures/View/Track/NeatFeatures">Neat Canvas Features</option>
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	466 <option value="JBrowse/View/Track/HTMLFeatures">HTML Features</option>
26 08776ba76cf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 75f6e483debb4c0d388bf4a54df81ee89af598d5 iuc parents: 25 diff changeset	467 <option value="JBrowse/View/Track/CanvasFeatures">Canvas Features</option>
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	468 <option value="BlastView/View/Track/CanvasFeatures">Blast Features</option><!-- Disable plugins until https://github.com/GMOD/jbrowse/issues/1288 is fixed -->
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	469 </param>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	470 <when value="JBrowse/View/Track/CanvasFeatures">
27 61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	471 <expand macro="canvas_options" />
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	472 </when>
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	473 <when value="JBrowse/View/Track/HTMLFeatures">
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	474 <expand macro="html_options" />
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	475 </when>
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	476 <when value="BlastView/View/Track/CanvasFeatures" />
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	477 <when value="NeatHTMLFeatures/View/Track/NeatFeatures">
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	478 <expand macro="html_options" />
26 08776ba76cf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 75f6e483debb4c0d388bf4a54df81ee89af598d5 iuc parents: 25 diff changeset	479 </when>
27 61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	480 <when value="NeatCanvasFeatures/View/Track/NeatFeatures">
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	481 <expand macro="canvas_options" />
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	482 </when>
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	483 </conditional>
27 61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	484 <expand macro="track_styling"
30 ca2def38369c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 74554507efb46fb40ce6e12f0b73425e52ec0977 iuc parents: 29 diff changeset	485 classname="feature"
27 61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	486 label="product,name,id"
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	487 description="note,description"
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	488 height="10px"/>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	489 <expand macro="color_selection" />
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	490 <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	491 <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	492 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	493 <when value="pileup">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	494 <expand macro="input_conditional" label="BAM Track Data" format="bam" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	495 <param label="Autogenerate SNP Track"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	496 help="Not recommended for deep coverage BAM files"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	497 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	498 name="auto_snp"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	499 truevalue="true"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	500 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	501 <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	502 name="chunkSizeLimit"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	503 type="integer"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	504 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	505 value="5000000" />
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	506 <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	507 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	508 <when value="wiggle">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	509 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	510
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	511 <param label="Use XYPlot"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	512 help="instead of continuous colored band"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	513 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	514 name="xyplot"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	515 truevalue="JBrowse/View/Track/Wiggle/XYPlot"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	516 falsevalue="JBrowse/View/Track/Wiggle/Density" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	517 <param label="Show variance band"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	518 help="Only for XYPlots"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	519 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	520 name="var_band"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	521 truevalue="true"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	522 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	523
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	524 <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	525 <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	526 <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: 22 diff changeset	527 <option value="auto_global">Autoscale (global)</option>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	528 <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	529 </param>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	530 <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	531 <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	532 <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	533 <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	534 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	535 <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	536 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	537 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	538 </conditional>
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	539 <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	540 <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	541 <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	542 </param>
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	543
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	544 <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	545 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	546
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	547 <expand macro="color_selection_minmax" />
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	548 <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	549 </when>
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	550 <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	551 <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	552 <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	553 <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	554 classname="feature"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	555 label="description"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	556 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	557 height="600px"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	558 <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	559 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	560 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	561 <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	562 <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	563 </when>
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	564
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	565 <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	566 <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	567 <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	568 <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	569 <sanitizer>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	570 <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: 23 diff changeset	571 <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	572 <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	573 <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	574 </mapping>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	575 <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	576 <add value="\|" />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	577 <add value="#" />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	578 <add value="{"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	579 <add value="}"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	580 <add value="!"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	581 <add value="?"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	582 <add value="&"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	583 <add value="+"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	584 <add value="="/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	585 <add value="'"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	586 <add value='"'/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	587 </valid>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	588 </sanitizer>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	589 </param>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	590 <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	591 classname="feature"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	592 label="description"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	593 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	594 height="600px"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	595 <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	596 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	597 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	598 <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	599 <expand macro="track_display" />
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	600 </when>
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	601 </conditional>
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	602 </repeat>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	603 </repeat>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	604
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	605 <expand macro="general_options" />
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	606 <!-- 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 iuc parents: 16 diff changeset	607 <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 iuc parents: 23 diff changeset	608
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	609 <param
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	610 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 iuc parents: 23 diff changeset	611 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 iuc parents: 23 diff changeset	612
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	613 <param
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	614 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 iuc parents: 16 diff changeset	615 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 iuc parents: 23 diff changeset	616 <!-- 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 iuc parents: 23 diff changeset	617 <!--param
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	618 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 iuc parents: 23 diff changeset	619 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: 16 diff changeset	620
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	621 <param
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	622 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 iuc parents: 16 diff changeset	623 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 iuc parents: 16 diff changeset	624
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	625 <!--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 iuc parents: 16 diff changeset	626 <option value="" selected="True">Default</option>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	627 <option value="Minimalist">Minimalist</option>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	628 <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: 23 diff changeset	629 </param-->
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	630 </section>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	631
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	632 <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	633 </inputs>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	634 <outputs>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	635 <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 iuc parents: diff changeset	636 </outputs>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	637 <tests>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	638 <test>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	639 <!-- gencode -->
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	640 <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	641 <param name="reference_genome\|genome" value="merlin.fa"/>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	642 <param name="gencode" value="1" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	643 <param name="standalone" value="Data Directory" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	644 <param name="uglyTestingHack" value="enabled" />
19 8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47 iuc parents: 18 diff changeset	645 <output name="output" file="gencode/test-1.xml" lines_diff="14"/>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	646 </test>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	647 <test>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	648 <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	649 <param name="reference_genome\|genome" value="merlin.fa"/>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	650 <param name="gencode" value="11" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	651 <param name="standalone" value="Data Directory" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	652 <param name="uglyTestingHack" value="enabled" />
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	653 <output name="output" file="gencode/test.xml" lines_diff="14"/>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	654 </test>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	655 <test>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	656 <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	657 <param name="reference_genome\|genome" value="merlin.fa"/>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	658 <param name="gencode" value="11" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	659 <param name="standalone" value="Data Directory" />
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	660 <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	661 <param name="category" value="Auto Coloured" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	662 <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	663 <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	664 <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	665 <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: 6 diff changeset	666 <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	667 <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	668 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	669 <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	670 <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	671 <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	672 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	673 <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	674 <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	675 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	676 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	677 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	678 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	679 </repeat>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	680
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	681 <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	682 <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	683 <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	684 <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	685 <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	686 <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	687 <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	688 <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	689 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	690 <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	691 <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	692 <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	693 <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	694 <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	695 <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	696 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	697 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	698 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	699 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	700 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	701 </repeat>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	702
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	703 <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	704 <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	705 <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	706 <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	707 <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	708 <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	709 <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	710 <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	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 <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	713 <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	714 <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	715 <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	716 <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	717 <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	718 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	719 <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	720 <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	721 <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	722 <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	723 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	724 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	725 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	726 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	727 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	728 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	729 <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	730 <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	731 <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	732 <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	733 <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	734 <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	735 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	736 <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	737 <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	738 <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	739 <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	740 <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	741 <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	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 <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	744 <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	745 <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	746 <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	747 <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	748 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	749 </conditional>
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>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	752 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	753 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	754 <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	755 <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	756 <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	757 <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	758 <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	759 <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	760 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	761 <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	762 <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	763 <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	764 <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	765 <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	766 <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	767 <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	768 <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	769 </conditional>
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="color_scheme">
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="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	772 <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	773 <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	774 </conditional>
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 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	777 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	778 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	779 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	780 <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	781 <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	782 <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	783 <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	784 <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	785 <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	786 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	787 <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	788 <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	789 <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	790 <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	791 <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	792 <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	793 <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	794 <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	795 </conditional>
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="color_scheme">
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="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	798 <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	799 <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	800 <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	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 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	803 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	804 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	805 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	806 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	807 </repeat>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	808
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	809 <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	810 <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	811 <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	812 <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	813 <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	814 <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	815 <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	816 <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	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 <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	819 <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	820 <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	821 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	822 <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	823 <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	824 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	825 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	826 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	827 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	828 <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	829 <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	830 <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	831 <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	832 <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	833 <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	834 <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	835 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	836 <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	837 <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	838 <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	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 <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	841 <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	842 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	843 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	844 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	845 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	846 </repeat>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	847
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	848 <param name="uglyTestingHack" value="enabled" />
19 8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47 iuc parents: 18 diff changeset	849 <output name="output" file="gff3/test.xml" lines_diff="256" />
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	850 </test>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	851 <test>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	852 <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	853 <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	854 <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	855 <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	856
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	857 <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	858 <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	859 <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	860 <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	861 <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	862 <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	863 <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	864 <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	865 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	866 <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	867 <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	868 <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	869 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	870 <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	871 <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	872 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	873 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	874 <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	875 <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	876 <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	877 <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	878 <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	879 <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	880 <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	881 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	882 <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	883 <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	884 <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	885 <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	886 <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	887 </repeat>
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 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	890 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	891 <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	892 <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	893 <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	894 <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	895 <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	896 <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	897 <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	898 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	899 <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	900 <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	901 <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	902 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	903 <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	904 <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	905 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	906 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	907 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	908 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	909 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	910
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	911 <param name="uglyTestingHack" value="enabled" />
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	912 <output name="output" file="menus/test.xml" lines_diff="24"/>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	913 </test>
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	914 <test>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	915 <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	916 <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	917 <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	918 <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	919
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	920 <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	921 <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	922 <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	923 <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	924 <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	925 <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	926 <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	927 <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	928 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	929 <conditional name="track_config">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	930 <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	931 <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	932 <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	933 <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	934 </section>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	935 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	936 <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	937 <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	938 <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	939 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	940 <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	941 <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	942 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	943 </section>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	944 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	945 </repeat>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	946 </repeat>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	947
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="uglyTestingHack" value="enabled" />
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	949 <output name="output" file="track_config/test.xml" lines_diff="26"/>
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	950 </test>
18 836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e iuc parents: 17 diff changeset	951 <test>
19 8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47 iuc parents: 18 diff changeset	952 <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	953 <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	954 <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	955 <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	956
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47 iuc parents: 18 diff changeset	957 <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	958 <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	959 <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	960 <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	961 <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	962 <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	963 </conditional>
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47 iuc parents: 18 diff changeset	964 </repeat>
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47 iuc parents: 18 diff changeset	965 </repeat>
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47 iuc parents: 18 diff changeset	966
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47 iuc parents: 18 diff changeset	967 <param name="uglyTestingHack" value="enabled" />
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47 iuc parents: 18 diff changeset	968 <output name="output" file="bam/test.xml" lines_diff="48"/>
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47 iuc parents: 18 diff changeset	969 </test>
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47 iuc parents: 18 diff changeset	970
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47 iuc parents: 18 diff changeset	971 <test>
18 836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e iuc parents: 17 diff changeset	972 <!-- data_table -->
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e iuc parents: 17 diff changeset	973 <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	974 <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	975 <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	976 <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	977 <param name="uglyTestingHack" value="enabled" />
19 8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47 iuc parents: 18 diff changeset	978 <output name="output" file="gencode/test-data_table.xml" lines_diff="6" />
18 836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e iuc parents: 17 diff changeset	979 </test>
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	980
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	981 <test>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	982 <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	983 <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	984 <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	985 <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	986
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	987 <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	988 <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	989 <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	990 <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	991 <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	992 <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	993 <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	994 </conditional>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	995 </repeat>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	996 <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	997 <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	998 <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	999 <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	1000 <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	1001 <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	1002 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	1003 select ?start,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1004 ?end,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1005 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	1006 1,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1007 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	1008 -1,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1009 0
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1010 )
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1011 ) as ?strand,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1012 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	1013 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	1014 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	1015 ?obj as ?uniqueID,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1016 ?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	1017 where {
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1018 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	1019 }"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1020 </conditional>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1021 </repeat>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1022 </repeat>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1023
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1024 <param name="uglyTestingHack" value="enabled" />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1025 <output name="output" file="endpoints/test.xml" lines_diff="48"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1026 </test>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1027 </tests>
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	1028 <help><![CDATA[
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1029 JBrowse-in-Galaxy
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1030 =================
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1031
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1032 JBrowse-in-Galaxy offers a highly configurable, workflow-compatible
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1033 alternative to Trackster.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1034
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1035 Overview
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1036 --------
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1037
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1038 JBrowse is a fast, embeddable genome browser built completely with
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1039 JavaScript and HTML5.
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1040
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1041 The JBrowse-in-Galaxy (JiG) tool was written to help build complex
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1042 JBrowse installations straight from Galaxy, taking advantage of the
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1043 latest Galaxy features such as dataset collections, sections, and colour
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1044 pickers. It allows you to build up a JBrowse instance without worrying
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1045 about how to run the command line tools to format your data, and which
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1046 options need to be supplied and where. Additionally it comes with many
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1047 javascript functions to handle colouring of features which would be
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1048 nearly impossible to write without the assistance of this tool.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1049
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1050 The JBrowse-in-Galaxy tool is maintained by `the Galaxy IUC
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1051 <https://github.com/galaxyproject/tools-iuc/issues>`__, who you can help you
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1052 with missing features or bugs in the tool.
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1053
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1054 Options
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1055 -------
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1056
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1057 The first option you encounter is the Fasta Sequence(s). This option
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1058 now accepts multiple fasta files, allowing you to build JBrowse
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1059 instances that contain data for multiple genomes or chrosomomes
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1060 (generally known as "landmark features" in gff3 terminology.) Up to 30
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1061 will be shown from the dropdown selector within JBrowse, this is a known
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1062 issue.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1063
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1064 Standalone Instances enable you to have either a complete JBrowse instance
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1065 in a dataset, or just the data directory without JBrowse (e.g. for Apollo).
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1066 Currently Galaxy copies the entire JBrowse directory in order to have a
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1067 complete, downloadable file that contains a ready-to-go JBrowse
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1068 instance. This is obviously an anti-feature because users don't want a
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1069 complete copy of JBrowse (12Mb) that's duplicated for every JBrowse
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1070 dataset in their history, and admins don't want useless copies of
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1071 JBrowse on disk. Unfortunately we have not come up with the perfect
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1072 solution just yet, but we're working on it! In the meantime, users have
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1073 been given the option to produce just the ``data/`` directory. For those
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1074 unfamiliar with JBrowse, the ``data/`` directory contains processed data
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1075 files, but no way to view them. This feature is additionally implemented
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1076 for upcoming `Apollo <https://github.com/gmod/apollo>`__ integration.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1077
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1078 Genetic Code is a new feature in v0.4 of JiG / v1.12.0 of JBrowse,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1079 which allows users to specify a non standard genetic code, and have
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1080 JBrowse highlight the correct start and stop codons.
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1081
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1082 Track Groups represent a set of tracks in a single category. These
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1083 can be used to let your users understand relationships between large
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1084 groups of tracks.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1085
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1086 .. image:: sections.png
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1087
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1088 Annotation Tracks
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1089 -----------------
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1090
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1091 Within Track Groups, you have one or more Annotation Tracks. Each
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1092 Annotation Track is a groups of datasets which have similar styling.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1093 This allows you to rapidly build up JBrowse instances without having to
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1094 configure tracks individually. A massive improvement over previous
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1095 versions. For example, if you have five different GFF3 files from
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1096 various gene callers that you wish to display, you can take advantage of
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1097 this feature to style all of them similarly.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1098
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1099 There are a few different types of tracks supported, each with their own
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1100 set of options:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1101
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1102 GFF3/BED/GBK
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1103 ~~~~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1104
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1105 These are your standard feature tracks. They usually highlight genes,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1106 mRNAs and other features of interest along a genomic region. The
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1107 underlying tool and this help documentation focus primarily on GFF3
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1108 data, and have not been tested extensively with other formats. Automatic
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1109 min/max detection will likely fail under BED and GBK datasets.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1110
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1111 The data may be of a subclass we call match/match part data. This
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1112 consists of top level ``match`` features, with a child ``match_part``
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1113 feature, and is often used in displaying alignments. (See "Alignments"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1114 section on the `GFF3
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	1115 specification <https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md>`__ for more
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1116 information). If the data is match/match part, you will need to specify
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1117 the top level match feature name, as it can be one of a few different SO
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1118 terms, and JiG does not yet have the ability to understand SO terms.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1119
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1120 Next up is the Styling Options section, which lets you control a few
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1121 properties on how the track is styled. Most of these you will not need
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1122 to configure and can safely leave on defaults. Occasionally you will
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1123 want to change what information is shown in the end product.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1124
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1125 .. image:: styling.png
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1126
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1127 In the above image you can see some black text, and some blue text. The
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1128 source of the black text is configured with the style.label option,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1129 and the source of the blue text is configured with the
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1130 style.description option.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1131
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1132 Feature Score Scaling & Colouring Options
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1133 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1134
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1135 First, you need to choose between ignoring the score attribute of GFF3
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1136 files, or using it. If you choose to ignore it, all features will be
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1137 coloured with a solid colour. If you choose to use it, features will
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1138 have slightly different colours based on their scores.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1139
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1140 .. image:: opacity.png
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1141
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1142 If you choose Ignore score, you may choose between automatically
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1143 choosing a colour, or manually specifying one. The automatically chosen
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1144 colours vary along a brewer palette and generally look quite nice with
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1145 no human intervention required. The manual colour choice is somewhat
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1146 self explanatory. Clicking on the small coloured square will bring up a
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1147 colour palette.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1148
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1149 If you choose Base on score, you're faced with a dizzying array of
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1150 options. First is the function to map the colour choices to colour
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1151 values. JiG comes with a few functions built in such as linear scaling,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1152 logarithmic scaling, and blast scaling.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1153
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1154 The linear scaling method says "take these values, and they map
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1155 directly to a range of output values". Logarithmic scaling says
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1156 "please take the log of the score before mapping", and Blast scaling
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1157 is further specialised to handle blast data more nicely. These are
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1158 convenience functions to help transform the wide array of possible
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1159 values in the GFF3 score attribute to more meaningful numbers. If you
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1160 need more comprehensive score scaling, it is recommended that you
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1161 pre-process your GFF3 files somehow.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1162
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1163 Once you've selected a scaling method, you can choose to manually
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1164 specify the minimum and maximum expected values, or you can let JiG
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1165 determine them for you automatically.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1166
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1167 Finally, opacity is the only mapping we currently provide. Future
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1168 iterations will attempt to improve upon this and provide more colour
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1169 scales. The Opacity option maps the highest scoring features to full
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1170 opacity, and everything else to lower ones.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1171
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1172 BAM Pileups
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1173 ~~~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1174
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1175 We support BAM files and can automatically generate SNP tracks based on
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1176 that bam data.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1177
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1178 .. image:: bam.png
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1179
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1180 This is strongly discouraged for high coverage density datasets.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1181 Unfortunately there are no other configuration options exposed for bam
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1182 files.
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1183
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1184 BlastXML
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1185 ~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1186
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1187 .. image:: blast.png
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1188
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1189 JiG now supports both blastn and blastp datasets. JiG internally uses a
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1190 blastXML to gapped GFF3 tool to convert your blastxml datasets into a
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1191 format amenable to visualization in JBrowse. This tool is also
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1192 available separately from the IUC on the toolshed.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1193
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1194 Minimum Gap Size reflects how long a gap must be before it becomes a
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1195 real gap in the processed gff3 file. In the picture above, various sizes
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1196 of gaps can be seen. If the minimum gap size was set much higher, say
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1197 100nt, many of the smaller gaps would disappear, and the features on
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1198 both sides would be merged into one, longer feature. This setting is
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1199 inversely proportional to runtime and output file size. *Do not set this
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1200 to a low value for large datasets*. By setting this number lower, you
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1201 will have extremely large outputs and extremely long runtimes. The
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1202 default was configured based off of the author's experience, but the
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1203 author only works on small viruses. It is strongly recommended that
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1204 you filter your blast results before display, e.g. picking out the top
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1205 10 hits or so.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1206
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1207 Protein blast search option merely informs underlying tools that
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1208 they should adjust feature locations by 3x.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1209
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1210 Styling Options
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1211 ^^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1212
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1213 Please see the styling options for GFF3 datasets, they are identical.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1214
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1215 Feature Score Scaling & Coloring Options
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1216 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1217
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1218 Please see the score scaling and colouring options for GFF3 datasets,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1219 they are identical. Remember to set your score scaling to "blast" method
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1220 if you do use it.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1221
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1222 Bigwig XY
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1223 ~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1224
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1225 .. image:: bigwig.png
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1226
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1227 XYPlot
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1228
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1229 BigWig tracks can be displayed as a "density" plot which is continuous
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1230 line which varies in colour, or as an "XYplot." XYplots are preferable
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1231 for users to visually identify specific features in a bigwig track,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1232 however density tracks are more visually compact.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1233
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1234 Variance Band is an option available to XYPlots, and can be seen in
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1235 the third and fourth tracks in the above picture. This overlays a mean
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1236 line, and 1 and 2 standard deviation areas.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1237
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1238 Track Scaling is different from colour scaling, instead it
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1239 configures how the track behaves inside of JBrowse. **Autoscaling
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1240 globally** means that JBrowse will determine the minimum and maximum for
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1241 the track, and fix the bounds of the viewport to that. E.g. if your
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1242 track ranges from 1-1000, and the region you're currently zoomed to only
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1243 goes from 0-50, then the viewport range will still show 1-1000. This is
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1244 good for global genomic context. However you may wish to consider
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1245 autoscaling locally instead. In the example of a region which varies
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1246 from 0-50, autoscaling locally would cause the individual track's
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1247 viewport to re-adjust and show just the 0-50 region. If neither of these
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1248 options are palatable, you may manually hardcode the minimum and
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1249 maximums for the track to scale to.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1250
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1251 Colour Options
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1252 ^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1253
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1254 BigWig tracks have two colours in JBrowse, a positive and a negative
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1255 colour.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1256
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1257 As always you may manually choose a colour, or let JiG choose for you.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1258
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1259 One of the more interesting options is the Bicolor pivot. This
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1260 option allows you to control the point at which JBrowse switches from
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1261 the positive colour to the negative. In the above graphic, you can see
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1262 this has been configured to "mean" for the first two (orange and blue)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1263 tracks.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1264
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1265 VCFs/SNPs
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1266 ~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1267
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1268 These tracks do not support any special configuration.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1269
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1270 Known Issues
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1271 ------------
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1272
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1273 - More than 30 landmark features cannot be listed in the manual
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1274 selector.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1275 - Non GFF3 likely has issue with automatically determined min/max
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1276 scores. Manually specify minimum and maximum score attributes, or do
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1277 not use varied colours based on scores to avoid this issue.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1278
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	1279 @ATTRIBUTION@
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	1280 ]]></help>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	1281 <expand macro="citations"/>
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	1282 </tool>

Mercurial > repos > iuc > jbrowse

annotate jbrowse.xml @ 30:ca2def38369c draft