jbrowse: jbrowse.xml annotate

annotate jbrowse.xml @ 39:fd5dbf0f732e draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 145eb8fdc1460af572d90991d048432f8e9582da"

author	iuc
date	Tue, 28 Apr 2020 10:01:04 -0400
parents	7ed0827da5a8
children	17359b808b01

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 $output.files_path/galaxy.xml &&
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	18
35 3235aeb45c22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 22ed9cb1e65cff5239df7ad4c76eaf0e981cf279" iuc parents: 34 diff changeset	19 export JBROWSE_SOURCE_DIR=\$(dirname \$(which prepare-refseqs.pl))/../opt/jbrowse &&
3235aeb45c22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 22ed9cb1e65cff5239df7ad4c76eaf0e981cf279" iuc parents: 34 diff changeset	20
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	21 ## Once that's done, we run the python script to handle the real work
18 836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e iuc parents: 17 diff changeset	22 python '$__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	23
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	24 --jbrowse \${JBROWSE_SOURCE_DIR}
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	25 #if str($standalone) == "Complete":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	26 --standalone
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	27 #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	28
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	29 --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	30 $trackxml &&
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	31
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	32 #if str($standalone) == "Complete":
35 3235aeb45c22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 22ed9cb1e65cff5239df7ad4c76eaf0e981cf279" iuc parents: 34 diff changeset	33 cp $output.files_path/index.html $output;
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	34 #else:
35 3235aeb45c22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 22ed9cb1e65cff5239df7ad4c76eaf0e981cf279" iuc parents: 34 diff changeset	35 cp $dummyIndex $output;
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	36 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	37
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	38 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	39 #if str($uglyTestingHack) == "enabled":
35 3235aeb45c22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 22ed9cb1e65cff5239df7ad4c76eaf0e981cf279" iuc parents: 34 diff changeset	40 cp $trackxml $output
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	41 #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	42 ]]></command>
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	43 <configfiles>
22 5f70e7fe6077 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 21 diff changeset	44 <configfile name="dummyIndex"><![CDATA[
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	45 <html>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	46 <head>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	47 </head>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	48 <body>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	49 <h1>JBrowse Data Directory</h1>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	50 <p>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	51 Hi! This is not a full JBrowse instance. JBrowse v0.4(+?)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	52 started shipping with the ability to produce just the
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	53 "data" directory from a JBrowse instance, rather than a
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	54 complete, standalone instance. This was intended to be used
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	55 with the in-development Apollo integration, but may have other
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	56 uses as well.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	57 </p>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	58 <p>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	59 <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	60 used with Apollo, or may be passed through the "JBrowse -
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	61 Convert to Standalone" tool in Galaxy to "upgrade" to a full
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	62 JBrowse instance.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	63 </p>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	64 </body>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	65 </html>
22 5f70e7fe6077 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 21 diff changeset	66 ]]></configfile>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	67 <configfile name="trackxml"><![CDATA[<?xml version="1.0"?>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	68 <root>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	69 <metadata>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	70 <gencode>$gencode</gencode>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	71 <genomes>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	72 #if str($reference_genome.genome_type_select) == "indexed":
18 836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e iuc parents: 17 diff changeset	73 <genome path="${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	74 <metadata />
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e iuc parents: 17 diff changeset	75 </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	76 #else
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	77 <genome path="$reference_genome.genome">
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	78 <metadata>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	79 <dataset id="${__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	80 size="${reference_genome.genome.get_size(nice_size=True)}"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	81 edam_format="${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	82 file_ext="${reference_genome.genome.ext}" />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	83 <history id="${__app__.security.encode_id($reference_genome.genome.history_id)}"
39 fd5dbf0f732e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 145eb8fdc1460af572d90991d048432f8e9582da" iuc parents: 36 diff changeset	84 #if $reference_genome.genome.history.user:
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	85 user_email="${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	86 user_id="${reference_genome.genome.history.user_id}"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	87 display_name="${reference_genome.genome.history.get_display_name()}"/>
39 fd5dbf0f732e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 145eb8fdc1460af572d90991d048432f8e9582da" iuc parents: 36 diff changeset	88 #else
fd5dbf0f732e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 145eb8fdc1460af572d90991d048432f8e9582da" iuc parents: 36 diff changeset	89 user_email="anonymous"
fd5dbf0f732e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 145eb8fdc1460af572d90991d048432f8e9582da" iuc parents: 36 diff changeset	90 user_id="-1"
fd5dbf0f732e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 145eb8fdc1460af572d90991d048432f8e9582da" iuc parents: 36 diff changeset	91 display_name="Unnamed History"/>
fd5dbf0f732e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 145eb8fdc1460af572d90991d048432f8e9582da" iuc parents: 36 diff changeset	92 #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	93 <metadata
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	94 #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	95 #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	96 ${key}="${value}"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	97 #end if
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	98 #end for
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	99 />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	100 <tool
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	101 tool_id="${reference_genome.genome.creating_job.tool_id}"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	102 tool_version="${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	103 />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	104 </metadata>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	105 </genome>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	106 #end if
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	107 </genomes>
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	108 <general>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	109 <defaultLocation>${jbgen.defaultLocation}</defaultLocation>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	110 <trackPadding>${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	111
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	112 <shareLink>${jbgen.shareLink}</shareLink>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	113 <aboutDescription>${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	114 <show_tracklist>${jbgen.show_tracklist}</show_tracklist>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	115 <show_nav>${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	116 <show_overview>${jbgen.show_overview}</show_overview>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	117 <show_menu>${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	118 <hideGenomeOptions>${jbgen.hideGenomeOptions}</hideGenomeOptions>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	119 </general>
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	120 <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	121 </metadata>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	122 <tracks>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	123 #for $tg in $track_groups:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	124 #for $track in $tg.data_tracks:
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	125 <track cat="${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	126 #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	127 <files>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	128 #for $dataset in $track.data_format.annotation:
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	129 <trackFile path="${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	130 <metadata>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	131 <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	132 size="${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	133 edam_format="${dataset.datatype.edam_format}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	134 file_ext="${dataset.ext}" />
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	135 <history id="${__app__.security.encode_id($dataset.history_id)}"
39 fd5dbf0f732e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 145eb8fdc1460af572d90991d048432f8e9582da" iuc parents: 36 diff changeset	136 #if $dataset.history.user:
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	137 user_email="${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	138 user_id="${dataset.history.user_id}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	139 display_name="${dataset.history.get_display_name()}"/>
39 fd5dbf0f732e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 145eb8fdc1460af572d90991d048432f8e9582da" iuc parents: 36 diff changeset	140 #else
fd5dbf0f732e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 145eb8fdc1460af572d90991d048432f8e9582da" iuc parents: 36 diff changeset	141 user_email="anonymous"
fd5dbf0f732e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 145eb8fdc1460af572d90991d048432f8e9582da" iuc parents: 36 diff changeset	142 user_id="-1"
fd5dbf0f732e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 145eb8fdc1460af572d90991d048432f8e9582da" iuc parents: 36 diff changeset	143 display_name="Unnamed History"/>
fd5dbf0f732e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 145eb8fdc1460af572d90991d048432f8e9582da" iuc parents: 36 diff changeset	144 #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	145 <metadata
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	146 #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	147 #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	148 ${key}="${value}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	149 #end if
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	150 #end for
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	151 />
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	152 <tool
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	153 tool_id="${dataset.creating_job.tool_id}"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	154 tool_version="${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	155 />
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	156 </metadata>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	157 </trackFile>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	158 #end for
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	159 </files>
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	160 #end if
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	161
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	162 <options>
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	163 #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	164 <style>
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	165 <overridePlugins>${track.data_format.override_apollo_plugins}</overridePlugins>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	166 <overrideDraggable>${track.data_format.override_apollo_drag}</overrideDraggable>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	167 <className>${track.data_format.jbstyle.style_classname}</className>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	168 <description>${track.data_format.jbstyle.style_description}</description>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	169 <label>${track.data_format.jbstyle.style_label}</label>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	170 <height>${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	171 <maxHeight>${track.data_format.jbstyle.max_height}</maxHeight>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	172 </style>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	173 <scaling>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	174 #if str($track.data_format.jbcolor_scale.color_score.color_score_select) == "none":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	175 <method>ignore</method>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	176 <scheme>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	177 #if str($track.data_format.jbcolor_scale.color_score.color.color_select) == "automatic":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	178 <color>__auto__</color>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	179 #else
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	180 <color>${track.data_format.jbcolor_scale.color_score.color.style_color}</color>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	181 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	182 </scheme>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	183 #else
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	184 <method>score</method>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	185 <algo>${track.data_format.jbcolor_scale.color_score.score_scaling}</algo>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	186 <scales>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	187 <type>${track.data_format.jbcolor_scale.color_score.score_scales.scale_select}</type>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	188
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	189 #if str($track.data_format.jbcolor_scale.color_score.score_scales.scale_select) == "manual":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	190 <min>${track.data_format.jbcolor_scale.color_score.score_scales.minimum}</min>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	191 <max>${track.data_format.jbcolor_scale.color_score.score_scales.maximum}</max>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	192 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	193 </scales>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	194 <scheme>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	195 <type>${track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme}</type>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	196 ## auto_color
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	197 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme) == "opacity":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	198 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.color.color_select) == "automatic":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	199 <color>__auto__</color>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	200 #else
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	201 <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	202 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	203 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	204 </scheme>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	205 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	206 </scaling>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	207 <menus>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	208 #for $menu_item in $track.data_format.jbmenu.track_menu:
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	209 <menu>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	210 <action>${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	211 #if str($menu_item.menu_label) != "":
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	212 <label>${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	213 #end if
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	214 #if str($menu_item.menu_title) != "":
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	215 <title>${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	216 #end if
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	217 #if str($menu_item.menu_url) != "":
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	218 <url>${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	219 #end if
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	220 #if str($menu_item.menu_icon) != "":
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	221 <iconClass>${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	222 #end if
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	223 </menu>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	224 #end for
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	225 </menus>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	226 #end if
31 2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	227 #if str($track.data_format.data_format_select) in ["gene_calls", "pileup", "blast", "wiggle", "vcf"]:
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	228 <custom_config>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	229 #for $custom_option in $track.data_format.jb_custom_config.option:
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	230 <${custom_option.opt_key}>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	231 <${custom_option.opt_value.val_type}>${$custom_option.opt_value.val}</${custom_option.opt_value.val_type}>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	232 </${custom_option.opt_key}>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	233 #end for
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	234 </custom_config>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	235 #end if
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	236
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	237 #if str($track.data_format.data_format_select) == "wiggle":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	238 <wiggle>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	239 <type>${track.data_format.xyplot}</type>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	240 <variance_band>${track.data_format.var_band}</variance_band>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	241 #if str($track.data_format.scaling.scale_select) == "auto_local":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	242 <autoscale>local</autoscale>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	243 #else if str($track.data_format.scaling.scale_select) == "auto_global":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	244 <autoscale>global</autoscale>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	245 #else:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	246 <min>${track.data_format.scaling.minimum}</min>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	247 <max>${track.data_format.scaling.maximum}</max>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	248 #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	249 <scale>${track.data_format.scale_select2}</scale>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	250
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	251 ## Wiggle tracks need special color config
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	252 #if str($track.data_format.jbcolor.color.color_select) != "automatic":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	253 <color_pos>${track.data_format.jbcolor.color.style_pos_color}</color_pos>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	254 <color_neg>${track.data_format.jbcolor.color.style_neg_color}</color_neg>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	255 #else:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	256 <color_pos>__auto__</color_pos>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	257 <color_neg>__auto__</color_neg>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	258 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	259
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	260 ## Bicolor pivot config
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	261 #if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "zero":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	262 <bicolor_pivot>zero</bicolor_pivot>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	263 #else if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "mean":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	264 <bicolor_pivot>mean</bicolor_pivot>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	265 #else:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	266 <bicolor_pivot>${track.data_format.jbcolor.bicolor_pivot.pivot_point}</bicolor_pivot>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	267 #end if
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	268 <multibigwig>${track.data_format.MultiBigWig}</multibigwig>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	269 </wiggle>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	270 #else if str($track.data_format.data_format_select) == "pileup":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	271 <pileup>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	272 <auto_snp>${track.data_format.auto_snp}</auto_snp>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	273 <bam_indices>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	274 #for $dataset in $track.data_format.annotation:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	275 <bam_index>${dataset.metadata.bam_index}</bam_index>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	276 #end for
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	277 </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	278 <chunkSizeLimit>${track.data_format.chunkSizeLimit}</chunkSizeLimit>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	279 </pileup>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	280 #else if str($track.data_format.data_format_select) == "blast":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	281 <blast>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	282 #if str($track.data_format.blast_parent) != "":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	283 <parent>${track.data_format.blast_parent}</parent>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	284 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	285 <protein>${track.data_format.is_protein}</protein>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	286 <min_gap>${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	287 <index>${track.data_format.index}</index>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	288 </blast>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	289 #else if str($track.data_format.data_format_select) == "gene_calls":
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	290 <gff>
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	291 <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	292 #if $track.data_format.track_config.track_class in ['JBrowse/View/Track/CanvasFeatures', 'NeatCanvasFeatures/View/Track/NeatFeatures']:
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	293 #if str($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	294 <transcriptType>${track.data_format.track_config.canvas_options.transcriptType}</transcriptType>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	295 #end if
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	296 #if str($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	297 <subParts>${track.data_format.track_config.canvas_options.subParts}</subParts>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	298 #end if
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	299 #if str($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	300 <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	301 #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	302 #else if $track.data_format.track_config.track_class in ['JBrowse/View/Track/HTMLFeatures', 'NeatHTMLFeatures/View/Track/NeatFeatures']:
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	303 #if str($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	304 <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	305 #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	306 #end if
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	307 #if $track.data_format.match_part.match_part_select:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	308 <match>${track.data_format.match_part.name}</match>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	309 #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	310 <index>${track.data_format.index}</index>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	311 </gff>
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	312 #else if str($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	313 <label>${track.data_format.label}</label>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	314 <rest>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	315 <url>${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	316 </rest>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	317 #else if str($track.data_format.data_format_select) == "sparql":
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	318 <label>${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	319 <sparql>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	320 <url>${track.data_format.url}</url>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	321 <query>${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	322 </sparql>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	323 #end if
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	324 </options>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	325 </track>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	326 #end for
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	327 #end for
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	328 </tracks>
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	329 ## 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	330 ## <plugins
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	331 ## ComboTrackSelector="${plugins.ComboTrackSelector}"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	332 ## Bookmarks="${plugins.Bookmarks}"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	333 ## GCContent="${plugins.GCContent}"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	334 ## BlastView="${plugins.BlastView}"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	335 ## theme="${plugins.theme}"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	336 ## />
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	337 <plugins
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	338 ComboTrackSelector="${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	339 Bookmarks=""
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	340 GCContent="${plugins.GCContent}"
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	341 BlastView="${plugins.BlastView}"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	342 theme=""
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	343 />
31 2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	344 </root>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	345 ]]></configfile>
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	346 </configfiles>
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	347 <inputs>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	348 <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	349 <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	350 <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	351 <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	352 </param>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	353 <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	354 <param
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	355 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	356 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	357 name="genomes"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	358 type="select"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	359 >
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	360 <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	361 <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	362 <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	363 </options>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	364 </param>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	365 </when>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	366 <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	367 <param
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	368 format="fasta"
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	369 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	370 name="genome"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	371 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	372 </when>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	373 </conditional>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	374
22 5f70e7fe6077 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 21 diff changeset	375 <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	376
22 5f70e7fe6077 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 21 diff changeset	377 <param name="gencode" type="select" label="Genetic Code">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	378 <option value="1">1. The Standard Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	379 <option value="2">2. The Vertebrate Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	380 <option value="3">3. The Yeast Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	381 <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	382 <option value="5">5. The Invertebrate Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	383 <option value="6">6. The Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	384 <option value="9">9. The Echinoderm and Flatworm Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	385 <option value="10">10. The Euplotid Nuclear Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	386 <option value="11">11. The Bacterial, Archaeal and Plant Plastid Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	387 <option value="12">12. The Alternative Yeast Nuclear Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	388 <option value="13">13. The Ascidian Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	389 <option value="14">14. The Alternative Flatworm Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	390 <option value="16">16. Chlorophycean Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	391 <option value="21">21. Trematode Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	392 <option value="22">22. Scenedesmus obliquus Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	393 <option value="23">23. Thraustochytrium Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	394 <option value="24">24. Pterobranchia Mitochondrial Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	395 <option value="25">25. Candidate Division SR1 and Gracilibacteria Code</option>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	396 </param>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	397
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	398 <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	399 <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	400 <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	401 <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	402 </param>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	403 <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	404 <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	405 <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	406 </when>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	407 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	408
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	409 <repeat name="track_groups" title="Track Group">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	410 <param label="Track Category"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	411 name="category"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	412 type="text"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	413 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	414 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	415 <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	416 <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	417 <param type="select" label="Track Type" name="data_format_select">
33 0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	418 <option value="gene_calls">GFF/GFF3/BED 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	419 <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	420 <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	421 <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	422 <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	423 <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	424 <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	425 </param>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	426 <when value="blast">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	427 <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	428
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	429 <param label="Features used in Blast Search"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	430 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	431 format="gff3"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	432 name="blast_parent"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	433 optional="true"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	434 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	435
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	436 <param label="Minimum Gap Size"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	437 help="before a new match_part feature is created"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	438 name="min_gap"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	439 type="integer"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	440 value="10"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	441 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	442 <param label="Is this a protein blast search?"
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	443 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	444 name="is_protein"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	445 truevalue="true"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	446 falsevalue="false" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	447
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	448 <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	449
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	450 <expand macro="track_styling"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	451 classname="feature"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	452 label="description"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	453 description="Hit_titles"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	454 height="600px"/>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	455 <expand macro="color_selection"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	456 token_scaling_lin_select="false"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	457 token_scaling_log_select="true" />
31 2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	458 <expand macro="track_custom_config" />
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	459 <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	460 <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	461 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	462 <when value="vcf">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	463 <expand macro="input_conditional" label="SNP Track Data" format="vcf" />
31 2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	464 <expand macro="track_custom_config" />
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	465 <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	466 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	467 <when value="gene_calls">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	468 <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	469 <conditional name="match_part" label="match/match_part data">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	470 <param label="This is match/match_part data"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	471 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	472 name="match_part_select"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	473 truevalue="true"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	474 falsevalue="false" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	475 <when value="true">
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	476 <param label="Match Part Feature Type"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	477 name="name"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	478 type="text"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	479 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	480 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	481 optional="True"/>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	482 </when>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	483 <when value="false" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	484 </conditional>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	485
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	486 <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	487
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	488 <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	489 <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	490 <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	491 <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	492 <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	493 <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	494 <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	495 </param>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	496 <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	497 <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	498 </when>
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	499 <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	500 <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	501 </when>
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	502 <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	503 <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	504 <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	505 </when>
27 61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	506 <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	507 <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	508 </when>
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	509 </conditional>
27 61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 26 diff changeset	510 <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	511 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	512 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	513 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	514 height="10px"/>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	515 <expand macro="color_selection" />
31 2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	516 <expand macro="track_custom_config" />
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	517 <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	518 <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	519 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	520 <when value="pileup">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	521 <expand macro="input_conditional" label="BAM Track Data" format="bam" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	522 <param label="Autogenerate SNP Track"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	523 help="Not recommended for deep coverage BAM files"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	524 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	525 name="auto_snp"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	526 truevalue="true"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	527 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	528 <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	529 name="chunkSizeLimit"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	530 type="integer"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	531 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	532 value="5000000" />
31 2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	533 <expand macro="track_custom_config" />
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	534 <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	535 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	536 <when value="wiggle">
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	537 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	538
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	539 <param label="Use XYPlot"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	540 help="instead of continuous colored band"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	541 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	542 name="xyplot"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	543 truevalue="JBrowse/View/Track/Wiggle/XYPlot"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	544 falsevalue="JBrowse/View/Track/Wiggle/Density" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	545 <param label="Show variance band"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	546 help="Only for XYPlots"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	547 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	548 name="var_band"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	549 truevalue="true"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	550 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	551
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	552 <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	553 <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	554 <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	555 <option value="auto_global">Autoscale (global)</option>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	556 <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	557 </param>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	558 <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	559 <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	560 <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	561 <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	562 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	563 <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	564 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	565 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	566 </conditional>
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	567 <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	568 <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	569 <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	570 </param>
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	571
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	572 <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	573 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	574
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	575 <expand macro="color_selection_minmax" />
31 2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	576 <expand macro="track_custom_config" />
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	577 <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	578 </when>
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	579 <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	580 <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	581 <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	582 <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	583 classname="feature"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	584 label="description"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	585 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	586 height="600px"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	587 <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	588 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	589 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	590 <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	591 <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	592 </when>
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	593
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	594 <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	595 <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	596 <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	597 <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	598 <sanitizer>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	599 <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	600 <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	601 <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	602 <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	603 </mapping>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	604 <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	605 <add value="\|" />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	606 <add value="#" />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	607 <add value="{"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	608 <add value="}"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	609 <add value="!"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	610 <add value="?"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	611 <add value="&"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	612 <add value="+"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	613 <add value="="/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	614 <add value="'"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	615 <add value='"'/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	616 </valid>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	617 </sanitizer>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	618 </param>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	619 <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	620 classname="feature"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	621 label="description"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	622 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	623 height="600px"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	624 <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	625 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	626 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	627 <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	628 <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	629 </when>
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	630 </conditional>
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	631 </repeat>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	632 </repeat>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	633
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	634 <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	635 <!-- 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	636 <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	637
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	638 <param
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	639 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	640 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	641
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	642 <param
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	643 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	644 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	645 <!-- 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	646 <!--param
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	647 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	648 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	649
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	650 <param
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	651 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	652 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	653
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	654 <!--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	655 <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	656 <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	657 <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	658 </param-->
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	659 </section>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	660
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	661 <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	662 </inputs>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	663 <outputs>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	664 <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	665 </outputs>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	666 <tests>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	667 <test>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	668 <!-- gencode -->
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	669 <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	670 <param name="reference_genome\|genome" value="merlin.fa"/>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	671 <param name="gencode" value="1" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	672 <param name="standalone" value="Data Directory" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	673 <param name="uglyTestingHack" value="enabled" />
31 2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	674 <output name="output" file="gencode/test-1.xml" lines_diff="16"/>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	675 </test>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	676 <test>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	677 <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	678 <param name="reference_genome\|genome" value="merlin.fa"/>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	679 <param name="gencode" value="11" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	680 <param name="standalone" value="Data Directory" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	681 <param name="uglyTestingHack" value="enabled" />
31 2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	682 <output name="output" file="gencode/test.xml" lines_diff="16"/>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	683 </test>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	684 <test>
8 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="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	686 <param name="reference_genome\|genome" value="merlin.fa"/>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	687 <param name="gencode" value="11" />
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	688 <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	689 <repeat name="track_groups">
34 9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908" iuc parents: 33 diff changeset	690 <param name="category" value="Default" />
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908" iuc parents: 33 diff changeset	691 <repeat name="data_tracks">
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908" iuc parents: 33 diff changeset	692 <conditional name="data_format">
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908" iuc parents: 33 diff changeset	693 <param name="data_format_select" value="gene_calls"/>
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908" iuc parents: 33 diff changeset	694 <param name="annotation" value="bed/test-3.bed,bed/test-6.bed"/>
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908" iuc parents: 33 diff changeset	695 </conditional>
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908" iuc parents: 33 diff changeset	696 </repeat>
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908" iuc parents: 33 diff changeset	697 </repeat>
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908" iuc parents: 33 diff changeset	698 <param name="uglyTestingHack" value="enabled" />
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908" iuc parents: 33 diff changeset	699 <output name="output" file="bed/test.xml" lines_diff="32"/>
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908" iuc parents: 33 diff changeset	700 </test>
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908" iuc parents: 33 diff changeset	701 <test>
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908" iuc parents: 33 diff changeset	702 <param name="reference_genome\|genome_type_select" value="history"/>
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908" iuc parents: 33 diff changeset	703 <param name="reference_genome\|genome" value="merlin.fa"/>
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908" iuc parents: 33 diff changeset	704 <param name="gencode" value="11" />
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908" iuc parents: 33 diff changeset	705 <param name="standalone" value="Data Directory" />
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908" iuc parents: 33 diff changeset	706 <repeat name="track_groups">
8 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="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	708 <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	709 <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	710 <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	711 <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	712 <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	713 <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	714 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	715 <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	716 <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	717 <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	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">
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="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	721 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	722 </section>
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 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	725 </repeat>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	726
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	727 <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	728 <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	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="none"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	739 <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	740 <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	741 <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	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>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	744 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	745 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	746 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	747 </repeat>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	748
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	749 <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	750 <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	751 <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	752 <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	753 <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	754 <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	755 <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	756 <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	757 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	758 <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	759 <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	760 <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	761 <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	762 <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	763 <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	764 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	765 <conditional 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	766 <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	767 <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	768 <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	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>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	771 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	772 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	773 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	774 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	775 <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	776 <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	777 <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	778 <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	779 <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	780 <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	781 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	782 <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	783 <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	784 <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	785 <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	786 <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	787 <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	788 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	789 <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	790 <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	791 <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	792 <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	793 <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	794 </conditional>
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>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	797 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	798 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	799 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	800 <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	801 <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	802 <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	803 <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	804 <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	805 <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	806 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	807 <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	808 <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	809 <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	810 <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	811 <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	812 <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	813 <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	814 <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	815 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	816 <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	817 <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	818 <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	819 <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	820 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	821 </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>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	823 </section>
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 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	826 <repeat name="data_tracks">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	827 <conditional name="data_format">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	828 <param name="data_format_select" value="gene_calls"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	829 <param name="annotation" value="gff3/1.gff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	830 <conditional name="match_part">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	831 <param name="match_part_select" value="false"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	832 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	833 <section name="jbcolor_scale">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	834 <conditional name="color_score">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	835 <param name="color_score_select" value="score"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	836 <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	837 <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	838 <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	839 <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	840 <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	841 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	842 <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	843 <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	844 <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	845 <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	846 <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	847 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	848 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	849 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	850 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	851 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	852 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	853 </repeat>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	854
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	855 <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	856 <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	857 <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	858 <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	859 <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	860 <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	861 <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	862 <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	863 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	864 <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	865 <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	866 <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	867 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	868 <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	869 <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	870 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	871 </section>
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 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	874 <repeat name="data_tracks">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	875 <conditional name="data_format">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	876 <param name="data_format_select" value="gene_calls"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	877 <param name="annotation" value="gff3/2.gff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	878 <conditional name="match_part">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	879 <param name="match_part_select" value="true"/>
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="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	881 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	882 <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	883 <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	884 <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	885 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	886 <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	887 <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	888 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	889 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	890 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	891 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	892 </repeat>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	893
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	894 <param name="uglyTestingHack" value="enabled" />
36 7ed0827da5a8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit e846227dfeed6e58ab8e2ee528e8fbc7c3938f86" iuc parents: 35 diff changeset	895 <output name="output" file="gff3/test.xml" lines_diff="260" />
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	896 </test>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	897 <test>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	898 <param name="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	899 <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	900 <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	901 <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	902
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	903 <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	904 <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	905 <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	906 <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	907 <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	908 <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	909 <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	910 <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	911 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	912 <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	913 <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	914 <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	915 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	916 <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	917 <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	918 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	919 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	920 <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	921 <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	922 <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	923 <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	924 <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	925 <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	926 <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	927 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	928 <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	929 <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	930 <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	931 <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	932 <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	933 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	934 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	935 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	936 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	937 <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	938 <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	939 <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	940 <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	941 <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	942 <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	943 <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	944 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	945 <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	946 <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	947 <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	948 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	949 <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	950 <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	951 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	952 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	953 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	954 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	955 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	956
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	957 <param name="uglyTestingHack" value="enabled" />
31 2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	958 <output name="output" file="menus/test.xml" lines_diff="44"/>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	959 </test>
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	960 <test>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	961 <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	962 <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	963 <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	964 <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	965
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	966 <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	967 <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	968 <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	969 <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	970 <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	971 <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	972 <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	973 <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	974 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	975 <conditional name="track_config">
31 2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	976 <param name="track_class" value="JBrowse/View/Track/CanvasFeatures"/>
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	977 <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	978 <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	979 <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	980 <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	981 </section>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	982 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	983 <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	984 <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	985 <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	986 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	987 <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	988 <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	989 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	990 </section>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	991 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	992 </repeat>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	993 </repeat>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	994
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	995 <param name="uglyTestingHack" value="enabled" />
31 2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	996 <output name="output" file="track_config/test.xml" lines_diff="30"/>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	997 </test>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	998 <test>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	999 <param name="reference_genome\|genome_type_select" value="history"/>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1000 <param name="reference_genome\|genome" value="merlin.fa"/>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1001 <param name="gencode" value="11" />
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1002 <param name="standalone" value="Data Directory" />
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1003
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1004 <repeat name="track_groups">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1005 <param name="category" value="With custom track config" />
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1006 <repeat name="data_tracks">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1007 <conditional name="data_format">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1008 <param name="data_format_select" value="gene_calls"/>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1009 <param name="annotation" value="gff3/1.gff"/>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1010 <conditional name="match_part">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1011 <param name="match_part_select" value="false"/>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1012 </conditional>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1013 <section name="jb_custom_config">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1014 <repeat name="option">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1015 <param name="opt_key" value="displayMode"/>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1016 <conditional name="opt_value">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1017 <param name="val_type" value="text"/>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1018 <param name="val" value="collapsed"/>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1019 </conditional>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1020 </repeat>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1021 <repeat name="option">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1022 <param name="opt_key" value="histograms.height"/>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1023 <conditional name="opt_value">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1024 <param name="val_type" value="integer"/>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1025 <param name="val" value="150"/>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1026 </conditional>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1027 </repeat>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1028 <repeat name="option">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1029 <param name="opt_key" value="maxFeatureScreenDensity"/>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1030 <conditional name="opt_value">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1031 <param name="val_type" value="float"/>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1032 <param name="val" value="0.1"/>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1033 </conditional>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1034 </repeat>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1035 <repeat name="option">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1036 <param name="opt_key" value="style.strandArrow"/>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1037 <conditional name="opt_value">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1038 <param name="val_type" value="boolean"/>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1039 <param name="val" value="false"/>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1040 </conditional>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1041 </repeat>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1042 </section>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1043 </conditional>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1044 </repeat>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1045 </repeat>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1046
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1047 <param name="uglyTestingHack" value="enabled" />
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1048 <output name="output" file="custom_config/test.xml" lines_diff="30"/>
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	1049 </test>
18 836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e iuc parents: 17 diff changeset	1050 <test>
19 8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47 iuc parents: 18 diff changeset	1051 <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	1052 <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	1053 <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	1054 <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	1055
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47 iuc parents: 18 diff changeset	1056 <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	1057 <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	1058 <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	1059 <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	1060 <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	1061 <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	1062 </conditional>
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47 iuc parents: 18 diff changeset	1063 </repeat>
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47 iuc parents: 18 diff changeset	1064 </repeat>
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47 iuc parents: 18 diff changeset	1065
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47 iuc parents: 18 diff changeset	1066 <param name="uglyTestingHack" value="enabled" />
31 2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1067 <output name="output" file="bam/test.xml" lines_diff="42"/>
19 8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47 iuc parents: 18 diff changeset	1068 </test>
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47 iuc parents: 18 diff changeset	1069
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47 iuc parents: 18 diff changeset	1070 <test>
18 836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e iuc parents: 17 diff changeset	1071 <!-- data_table -->
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e iuc parents: 17 diff changeset	1072 <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	1073 <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	1074 <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	1075 <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	1076 <param name="uglyTestingHack" value="enabled" />
31 2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1077 <output name="output" file="gencode/test-data_table.xml" lines_diff="4" />
18 836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e iuc parents: 17 diff changeset	1078 </test>
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1079
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1080 <test>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1081 <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	1082 <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	1083 <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	1084 <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	1085
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1086 <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	1087 <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	1088 <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	1089 <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	1090 <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	1091 <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	1092 <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	1093 </conditional>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1094 </repeat>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1095 <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	1096 <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	1097 <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	1098 <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	1099 <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	1100 <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	1101 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	1102 select ?start,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1103 ?end,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1104 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	1105 1,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1106 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	1107 -1,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1108 0
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1109 )
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1110 ) as ?strand,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1111 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	1112 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	1113 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	1114 ?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	1115 ?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	1116 where {
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1117 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	1118 }"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1119 </conditional>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1120 </repeat>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1121 </repeat>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1122
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1123 <param name="uglyTestingHack" value="enabled" />
31 2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 30 diff changeset	1124 <output name="output" file="endpoints/test.xml" lines_diff="16"/>
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1125 </test>
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1126 </tests>
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	1127 <help><![CDATA[
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1128 JBrowse-in-Galaxy
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1129 =================
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1130
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1131 JBrowse-in-Galaxy offers a highly configurable, workflow-compatible
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1132 alternative to Trackster.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1133
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1134 Overview
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1135 --------
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1136
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1137 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	1138 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	1139
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1140 The JBrowse-in-Galaxy (JiG) tool was written to help build complex
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1141 JBrowse installations straight from Galaxy, taking advantage of the
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1142 latest Galaxy features such as dataset collections, sections, and colour
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1143 pickers. It allows you to build up a JBrowse instance without worrying
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1144 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	1145 options need to be supplied and where. Additionally it comes with many
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1146 javascript functions to handle colouring of features which would be
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1147 nearly impossible to write without the assistance of this tool.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1148
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1149 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	1150 <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	1151 with missing features or bugs in the tool.
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1152
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1153 Options
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1154 -------
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1155
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1156 The first option you encounter is the Fasta Sequence(s). This option
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1157 now accepts multiple fasta files, allowing you to build JBrowse
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1158 instances that contain data for multiple genomes or chrosomomes
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1159 (generally known as "landmark features" in gff3 terminology.) Up to 30
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1160 will be shown from the dropdown selector within JBrowse, this is a known
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1161 issue.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1162
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 23 diff changeset	1163 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	1164 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	1165 Currently Galaxy copies the entire JBrowse directory in order to have a
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1166 complete, downloadable file that contains a ready-to-go JBrowse
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1167 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	1168 complete copy of JBrowse (12Mb) that's duplicated for every JBrowse
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1169 dataset in their history, and admins don't want useless copies of
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1170 JBrowse on disk. Unfortunately we have not come up with the perfect
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1171 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	1172 been given the option to produce just the ``data/`` directory. For those
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1173 unfamiliar with JBrowse, the ``data/`` directory contains processed data
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1174 files, but no way to view them. This feature is additionally implemented
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1175 for upcoming `Apollo <https://github.com/gmod/apollo>`__ integration.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1176
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1177 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	1178 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	1179 JBrowse highlight the correct start and stop codons.
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1180
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1181 Track Groups represent a set of tracks in a single category. These
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1182 can be used to let your users understand relationships between large
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1183 groups of tracks.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1184
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1185 .. image:: sections.png
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1186
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1187 Annotation Tracks
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1188 -----------------
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1189
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1190 Within Track Groups, you have one or more Annotation Tracks. Each
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1191 Annotation Track is a groups of datasets which have similar styling.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1192 This allows you to rapidly build up JBrowse instances without having to
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1193 configure tracks individually. A massive improvement over previous
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1194 versions. For example, if you have five different GFF3 files from
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1195 various gene callers that you wish to display, you can take advantage of
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1196 this feature to style all of them similarly.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1197
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1198 There are a few different types of tracks supported, each with their own
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1199 set of options:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1200
33 0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	1201 GFF3/BED
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	1202 ~~~~~~~~
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1203
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1204 These are your standard feature tracks. They usually highlight genes,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1205 mRNAs and other features of interest along a genomic region. The
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1206 underlying tool and this help documentation focus primarily on GFF3
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1207 data, and have not been tested extensively with other formats. Automatic
33 0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	1208 min/max detection will fail under BED datasets.
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1209
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1210 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	1211 consists of top level ``match`` features, with a child ``match_part``
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1212 feature, and is often used in displaying alignments. (See "Alignments"
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1213 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	1214 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	1215 information). If the data is match/match part, you will need to specify
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1216 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	1217 terms, and JiG does not yet have the ability to understand SO terms.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1218
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1219 Next up is the Styling Options section, which lets you control a few
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1220 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	1221 to configure and can safely leave on defaults. Occasionally you will
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1222 want to change what information is shown in the end product.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1223
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1224 .. image:: styling.png
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1225
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1226 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	1227 source of the black text is configured with the style.label option,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1228 and the source of the blue text is configured with the
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1229 style.description option.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1230
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1231 Feature Score Scaling & Colouring Options
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1232 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1233
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1234 First, you need to choose between ignoring the score attribute of GFF3
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1235 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	1236 coloured with a solid colour. If you choose to use it, features will
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1237 have slightly different colours based on their scores.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1238
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1239 .. image:: opacity.png
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1240
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1241 If you choose Ignore score, you may choose between automatically
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1242 choosing a colour, or manually specifying one. The automatically chosen
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1243 colours vary along a brewer palette and generally look quite nice with
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1244 no human intervention required. The manual colour choice is somewhat
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1245 self explanatory. Clicking on the small coloured square will bring up a
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1246 colour palette.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1247
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1248 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	1249 options. First is the function to map the colour choices to colour
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1250 values. JiG comes with a few functions built in such as linear scaling,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1251 logarithmic scaling, and blast scaling.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1252
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1253 The linear scaling method says "take these values, and they map
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1254 directly to a range of output values". Logarithmic scaling says
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1255 "please take the log of the score before mapping", and Blast scaling
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1256 is further specialised to handle blast data more nicely. These are
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1257 convenience functions to help transform the wide array of possible
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1258 values in the GFF3 score attribute to more meaningful numbers. If you
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1259 need more comprehensive score scaling, it is recommended that you
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1260 pre-process your GFF3 files somehow.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1261
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1262 Once you've selected a scaling method, you can choose to manually
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1263 specify the minimum and maximum expected values, or you can let JiG
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1264 determine them for you automatically.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1265
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1266 Finally, opacity is the only mapping we currently provide. Future
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1267 iterations will attempt to improve upon this and provide more colour
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1268 scales. The Opacity option maps the highest scoring features to full
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1269 opacity, and everything else to lower ones.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1270
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1271 BAM Pileups
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1272 ~~~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1273
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1274 We support BAM files and can automatically generate SNP tracks based on
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1275 that bam data.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1276
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1277 .. image:: bam.png
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1278
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1279 This is strongly discouraged for high coverage density datasets.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1280 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	1281 files.
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1282
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1283 BlastXML
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1284 ~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1285
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1286 .. image:: blast.png
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1287
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1288 JiG now supports both blastn and blastp datasets. JiG internally uses a
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1289 blastXML to gapped GFF3 tool to convert your blastxml datasets into a
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1290 format amenable to visualization in JBrowse. This tool is also
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1291 available separately from the IUC on the toolshed.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1292
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1293 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	1294 real gap in the processed gff3 file. In the picture above, various sizes
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1295 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	1296 100nt, many of the smaller gaps would disappear, and the features on
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1297 both sides would be merged into one, longer feature. This setting is
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1298 inversely proportional to runtime and output file size. *Do not set this
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1299 to a low value for large datasets*. By setting this number lower, you
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1300 will have extremely large outputs and extremely long runtimes. The
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1301 default was configured based off of the author's experience, but the
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1302 author only works on small viruses. It is strongly recommended that
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1303 you filter your blast results before display, e.g. picking out the top
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1304 10 hits or so.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1305
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1306 Protein blast search option merely informs underlying tools that
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1307 they should adjust feature locations by 3x.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1308
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1309 Styling Options
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1310 ^^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1311
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1312 Please see the styling options for GFF3 datasets, they are identical.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1313
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1314 Feature Score Scaling & Coloring Options
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1315 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1316
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1317 Please see the score scaling and colouring options for GFF3 datasets,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1318 they are identical. Remember to set your score scaling to "blast" method
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1319 if you do use it.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1320
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1321 Bigwig XY
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1322 ~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1323
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1324 .. image:: bigwig.png
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1325
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1326 XYPlot
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1327
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1328 BigWig tracks can be displayed as a "density" plot which is continuous
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1329 line which varies in colour, or as an "XYplot." XYplots are preferable
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1330 for users to visually identify specific features in a bigwig track,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1331 however density tracks are more visually compact.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1332
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1333 Variance Band is an option available to XYPlots, and can be seen in
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1334 the third and fourth tracks in the above picture. This overlays a mean
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1335 line, and 1 and 2 standard deviation areas.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1336
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1337 Track Scaling is different from colour scaling, instead it
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1338 configures how the track behaves inside of JBrowse. **Autoscaling
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1339 globally** means that JBrowse will determine the minimum and maximum for
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1340 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	1341 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	1342 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	1343 good for global genomic context. However you may wish to consider
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1344 autoscaling locally instead. In the example of a region which varies
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1345 from 0-50, autoscaling locally would cause the individual track's
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1346 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	1347 options are palatable, you may manually hardcode the minimum and
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1348 maximums for the track to scale to.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1349
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1350 Colour Options
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1351 ^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1352
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1353 BigWig tracks have two colours in JBrowse, a positive and a negative
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1354 colour.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1355
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1356 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	1357
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1358 One of the more interesting options is the Bicolor pivot. This
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1359 option allows you to control the point at which JBrowse switches from
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1360 the positive colour to the negative. In the above graphic, you can see
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1361 this has been configured to "mean" for the first two (orange and blue)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1362 tracks.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1363
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1364 VCFs/SNPs
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1365 ~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1366
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1367 These tracks do not support any special configuration.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1368
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1369 Known Issues
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1370 ------------
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1371
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1372 - More than 30 landmark features cannot be listed in the manual
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1373 selector.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1374 - Non GFF3 likely has issue with automatically determined min/max
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1375 scores. Manually specify minimum and maximum score attributes, or do
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1376 not use varied colours based on scores to avoid this issue.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1377
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	1378 @ATTRIBUTION@
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	1379 ]]></help>
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 6 diff changeset	1380 <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	1381 </tool>

Mercurial > repos > iuc > jbrowse

annotate jbrowse.xml @ 39:fd5dbf0f732e draft