Mercurial > repos > fubar > jbrowse2

annotate jbrowse2.xml @ 91:6246925692cb draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
author fubar
date Thu, 18 Apr 2024 10:57:29 +0000
parents 51980e0dafd2
children 3c4db8203fad
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
90
51980e0dafd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11-dirty
fubar
parents: 89
diff changeset
1 <tool id="jbrowse2" name="JBrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_15" profile="22.05">
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
2 <description>genome browser</description>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
3 <macros>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
4 <import>macros.xml</import>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
5 </macros>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
6 <expand macro="edamInc"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
7 <xrefs>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
8 <xref type="bio.tools">jbrowse2</xref>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
9 </xrefs>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
10 <expand macro="requirements"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
11 <version_command>python '${__tool_directory__}/jbrowse2.py' --version</version_command>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
12 <command detect_errors="aggressive"><![CDATA[
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
13 mkdir -p '$output.files_path' &&
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
14 cp '$trackxml' '$output.files_path/galaxy.xml' &&
38
07849bf248e3 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a74e469a81b38c7142f63de510ae31d3754d1767
fubar
parents: 36
diff changeset
15 export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2 &&
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
16 #if $jbgen.ucol.formcoll=="collect":
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
17 python '$__tool_directory__/autogenJB2.py'
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
18 #for $key in $autoCollection.keys():
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
19 #if $autoCollection[$key].is_collection:
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
20 #set subCol=$autoCollection[$key]
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
21 #set pafs=[($subCol[x],$subcol[x].ext,x) for x in $subCol.keys() if $subCol[x].ext == 'paf']
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
22 #if len($pafs) > 0:
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
23 --pafmeta '$pafs[0]'
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
24 #set refs = [($pafs[0][2],$subCol[x],x) for x in $subCol.keys() if $subCol[x].ext == 'fasta']
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
25 #for $ref in $refs:
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
26 --pafreferencemeta '$ref'
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
27 #end for
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
28 #end if
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
29 #else if $autoCollection[$key].ext == 'fasta':
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
30 --referencemeta '$autoCollection[$key],$autoCollection[$key].ext,$key'
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
31 #else if $autoCollection[$key].ext in ['bed', 'bigwig', 'cool', 'gff', 'gff3', 'hic', 'maf', 'mcool', 'scool', 'vcf']
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
32 --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key'
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
33 #else if $autoCollection[$key].ext in ['bam',]
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
34 --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key,$autoCollection[$key].metadata.bam_index'
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
35 #else if $autoCollection[$key].ext in ['cram',]
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
36 --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key,$autoCollection[$key].metadata.cram_index'
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
37 #end if
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
38 #end for
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
39 --outdir '$output.files_path'
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
40 --jbrowse2path \${JBROWSE2_PATH}
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
41 --sessName "Autogen JBrowse" &&
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
42 #if $jbgen.zipOut == "true":
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
43 (cd '$output.files_path' && zip -r - . ) > '$output'
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
44 #else
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
45 cp '$output.files_path/index.html' '$output'
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
46 #end if
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
47 #else:
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
48 python '$__tool_directory__/jbrowse2.py'
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
49 --jbrowse2path \${JBROWSE2_PATH}
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
50 --outdir '$output.files_path'
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
51 --xml '$trackxml' &&
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
52 #if $jbgen.zipOut == "true":
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
53 (cd '$output.files_path' && zip -r - . ) > '$output'
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
54 #else
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
55 cp '$output.files_path/index.html' '$output'
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
56 #end if
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
57 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph.
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
58 #if str($uglyTestingHack) == "enabled":
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
59 && cp '$trackxml' '$output'
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
60 #end if
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
61 #end if
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
62 ]]></command>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
63 <configfiles>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
64 <configfile name="trackxml"><![CDATA[<?xml version="1.0"?>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
65 <root>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
66 <metadata>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
67 <general>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
68 <defaultLocation>${jbgen.defaultLocation}</defaultLocation>
31
cb4b32ca9968 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
fubar
parents: 30
diff changeset
69 <zipOut>${jbgen.zipOut}</zipOut>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
70 <analytics>${jbgen.enableAnalytics}</analytics>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
71 <primary_color>${jbgen.primary_color}</primary_color>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
72 <secondary_color>${jbgen.secondary_color}</secondary_color>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
73 <tertiary_color>${jbgen.tertiary_color}</tertiary_color>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
74 <quaternary_color>${jbgen.quaternary_color}</quaternary_color>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
75 <font_size>${jbgen.font_size}</font_size>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
76 <session_name>${jbgen.session_name}</session_name>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
77 </general>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
78 <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
79 </metadata>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
80 #if $jbgen.ucol.formcoll=="form":
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
81 #for $assembly in $assemblies:
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
82 <assembly>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
83 <metadata>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
84 <genomes>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
85 #if str($assembly.reference_genome.genome_type_select) == "uri":
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
86 <genome path="${assembly.reference_genome.uri}" label="${assembly.reference_genome.refname}" useuri="yes">
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
87 <metadata>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
88 <dataset
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
89 dname = "${assembly.reference_genome.refname}" />
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
90 </metadata>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
91 </genome>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
92 #else if str($assembly.reference_genome.genome_type_select) == "indexed":
87
de8fb46bc3ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93-dirty
fubar
parents: 86
diff changeset
93 <genome path="${assembly.reference_genome.genome.fields.path}" label="${assembly.reference_genome.genome.fields.dbkey}" useuri="no">
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
94 <metadata>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
95 <dataset
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
96 dname = "${assembly.reference_genome.genome.fields.name}" />
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
97 </metadata>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
98 </genome>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
99 #else
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
100 <genome path="$assembly.reference_genome.genome" label="${assembly.reference_genome.genome.name}" useuri="no">
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
101 <metadata>
88
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
102
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
103 <dataset id="${__app__.security.encode_id($assembly.reference_genome.genome.id)}"
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
104 hid="${assembly.reference_genome.genome.hid}"
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
105 size="${assembly.reference_genome.genome.get_size(nice_size=True)}"
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
106 edam_format="${assembly.reference_genome.genome.datatype.edam_format}"
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
107 file_ext="${assembly.reference_genome.genome.ext}"
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
108 dname = "${assembly.reference_genome.genome.name}"
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
109 />
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
110 <history
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
111 #if $assembly.reference_genome.genome.history.user:
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
112 user_email="${assembly.reference_genome.genome.history.user.email}"
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
113 user_id="${assembly.reference_genome.genome.history.user_id}"
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
114 display_name="${assembly.reference_genome.genome.history.get_display_name()}"/>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
115 #else
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
116 user_email="anonymous"
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
117 user_id="-1"
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
118 display_name="Unnamed History"
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
119 #end if
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
120 id="${__app__.security.encode_id($assembly.reference_genome.genome.history_id)}"
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
121 />
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
122 <metadata
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
123 #for (key, value) in $assembly.reference_genome.genome.get_metadata().items():
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
124 #if "_types" not in $key:
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
125 #if isinstance($value, list):
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
126 #set value_str = "[%s]" % ','.join([str(val) for val in value])
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
127 ${key}="$value_str"
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
128 #else
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
129 ${key}="${value}"
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
130 #end if
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
131 #end if
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
132 #end for
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
133 />
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
134 <tool
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
135 tool_id="${assembly.reference_genome.genome.creating_job.tool_id}"
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
136 tool_version="${assembly.reference_genome.genome.creating_job.tool_version}"
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
137 />
88
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
138
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
139 </metadata>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
140 </genome>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
141 #end if
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
142 </genomes>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
143 </metadata>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
144 <tracks>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
145 #for $tg in $assembly.track_groups:
31
cb4b32ca9968 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
fubar
parents: 30
diff changeset
146 #for $track in $tg.data_tracks:
88
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
147 #set input_exists = "False"
48
460d5b6c5d98 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a-dirty
fubar
parents: 46
diff changeset
148 #if $track.data_format.useuri.insource == "uri":
88
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
149 #if $track.data_format.useuri.annouri:
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
150 #set input_exists = "True"
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
151 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
152 <files>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
153 <trackFile path="${track.data_format.useuri.annouri}" ext="${track.data_format.data_format_select}"
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
154 label="${track.data_format.useuri.annoname}" useuri="yes">
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
155 <metadata>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
156 <dataset id = "${track.data_format.useuri.annouri}" />
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
157 </metadata>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
158 </trackFile>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
159 </files>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
160 #end if
48
460d5b6c5d98 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a-dirty
fubar
parents: 46
diff changeset
161 #else if $track.data_format.useuri.insource == "history":
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
162 #if $track.data_format.useuri.annotation:
88
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
163 #set input_exists = "True"
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
164 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
43
7e14b3f1f8e1 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 2feb3d2616ba482d4204463309aa0cc7f8081a15-dirty
fubar
parents: 42
diff changeset
165 <files>
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
166 #for $dataset in $track.data_format.useuri.annotation:
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
167 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.name}" useuri="no">
35
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 34
diff changeset
168 <metadata>
88
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
169
35
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 34
diff changeset
170 <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}"
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 34
diff changeset
171 size="${dataset.get_size(nice_size=True)}"
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 34
diff changeset
172 edam_format="${dataset.datatype.edam_format}"
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 34
diff changeset
173 file_ext="${dataset.ext}" />
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 34
diff changeset
174 <history id="${__app__.security.encode_id($dataset.history_id)}"
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 34
diff changeset
175 #if $dataset.history.user:
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 34
diff changeset
176 user_email="${dataset.history.user.email}"
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 34
diff changeset
177 user_id="${dataset.history.user_id}"
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 34
diff changeset
178 display_name="${dataset.history.get_display_name()}"/>
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 34
diff changeset
179 #else
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 34
diff changeset
180 user_email="anonymous"
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 34
diff changeset
181 user_id="-1"
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 34
diff changeset
182 display_name="Unnamed History"/>
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 34
diff changeset
183 #end if
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
184
35
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 34
diff changeset
185 <metadata
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 34
diff changeset
186 #for (key, value) in $dataset.get_metadata().items():
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 34
diff changeset
187 #if "_types" not in $key and $value is not None and len(str($value)) < 5000:
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 34
diff changeset
188 #if isinstance($value, list):
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 34
diff changeset
189 #set value_str = "[%s]" % ','.join([str(val) for val in value])
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 34
diff changeset
190 ${key}="$value_str"
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 34
diff changeset
191 #else
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 34
diff changeset
192 ${key}="${value}"
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 34
diff changeset
193 #end if
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 34
diff changeset
194 #end if
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 34
diff changeset
195 #end for
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 34
diff changeset
196 />
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 34
diff changeset
197 <tool
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 34
diff changeset
198 tool_id="${dataset.creating_job.tool_id}"
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 34
diff changeset
199 tool_version="${dataset.creating_job.tool_version}"
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 34
diff changeset
200 />
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 34
diff changeset
201 </metadata>
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 34
diff changeset
202 </trackFile>
88
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
203 #end for
43
7e14b3f1f8e1 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 2feb3d2616ba482d4204463309aa0cc7f8081a15-dirty
fubar
parents: 42
diff changeset
204 </files>
60
81d535970196 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 403a35e1245fa5e62f4be6116a725b9e4d9c353a
fubar
parents: 59
diff changeset
205 #end if
88
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
206 #end if
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
207 #if $input_exists == "True":
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
208 <options>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
209 <style>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
210 #if str($track.data_format.data_format_select) in ["gff", "bed", "maf", "blastxml"]:
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
211 <type>${track.data_format.jbstyle.display}</type>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
212 #if str($track.data_format.jbstyle.display) in ["LinearBasicDisplay", "LinearVariantDisplay"]:
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
213 <trackShowLabels>${track.data_format.jbstyle.show_labels}</trackShowLabels>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
214 <trackShowDescriptions>${track.data_format.jbstyle.show_descriptions}</trackShowDescriptions>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
215 #end if
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
216 #else if str($track.data_format.data_format_select) == "vcf":
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
217 <type>${track.data_format.jbstyle.track_style.display}</type>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
218 #if str($track.data_format.jbstyle.track_style.display) in ["LinearBasicDisplay", "LinearVariantDisplay"]:
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
219 <trackShowLabels>${track.data_format.jbstyle.track_style.show_labels}</trackShowLabels>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
220 <trackShowDescriptions>${track.data_format.jbstyle.track_style.show_descriptions}</trackShowDescriptions>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
221 #end if
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
222
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
223 #end if
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
224 #if str($track.data_format.data_format_select) in ["bam", "cram"]:
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
225 <type>LinearAlignmentsDisplay</type>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
226 #end if
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
227 #if str($track.data_format.data_format_select) in ["hic", "cool", "mcool", "scool"]:
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
228 <type>LinearHicDisplay</type>
85
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty
fubar
parents: 82
diff changeset
229 #end if
88
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
230 </style>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
231 #if str($track.data_format.data_format_select) == "bam":
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
232 <bam>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
233 <bam_index>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
234 #for $dataset in $track.data_format.useuri.annotation:
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
235 ${dataset.name},${dataset.metadata.bam_index}
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
236 #end for
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
237 </bam_index>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
238 </bam>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
239 #else if str($track.data_format.data_format_select) == "cram":
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
240 <cram>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
241 <cram_index>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
242 #for $dataset in $track.data_format.useuri.annotation:
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
243 ${dataset.name},${dataset.metadata.cram_index}
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
244 #end for
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
245 </cram_index>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
246 </cram>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
247 #else if str($track.data_format.data_format_select) == "blastxml":
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
248 <blast>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
249 #if str($track.data_format.blast_parent) != "":
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
250 <parent>${track.data_format.blast_parent}</parent>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
251 #end if
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
252 <protein>${track.data_format.is_protein}</protein>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
253 <min_gap>${track.data_format.min_gap}</min_gap>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
254 </blast>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
255 #else if str($track.data_format.data_format_select) == "gff":
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
256 <gff>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
257 #if $track.data_format.match_part.match_part_select == "true":
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
258 <match>${track.data_format.match_part.name}</match>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
259 #end if
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
260 </gff>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
261 #else if str($track.data_format.data_format_select) == "paf":
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
262 <paf>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
263 #if $track.data_format.pafuseuri.insource == "history":
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
264 <genome>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
265 #for $anno in $track.data_format.pafuseuri.annotation:
89
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11
fubar
parents: 88
diff changeset
266 ${anno}:${anno.name},
88
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
267 #end for
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
268 </genome>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
269 #else:
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
270 <genome>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
271 #for $refgenome in $track.data_format.pafuseuri.refuri:
89
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11
fubar
parents: 88
diff changeset
272 ${refgenome.annotation}:${refgenome.annoname},
88
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
273 #end for
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
274 </genome>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
275 #end if
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
276 </paf>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
277 #else if str($track.data_format.data_format_select) == "hic":
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
278 <hic>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
279 </hic>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
280 #else if str($track.data_format.data_format_select) == "cool":
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
281 <cool>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
282 </cool>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
283 #else if str($track.data_format.data_format_select) == "bed":
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
284 <bed>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
285 </bed>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
286 #else if str($track.data_format.data_format_select) == "sparql":
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
287 <label>${track.data_format.label}</label>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
288 <sparql>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
289 <url>${track.data_format.url}</url>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
290 <query>${track.data_format.query}</query>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
291 <query_refnames>${track.data_format.query_refnames}</query_refnames>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
292 </sparql>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
293 #end if
88
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
294 </options>
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
295 </track>
88
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
296 #end if
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
297 #end for
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
298 #end for
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
299 </tracks>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
300 </assembly>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
301 #end for
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
302 #end if
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
303 </root>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
304 ]]></configfile>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
305 </configfiles>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
306 <inputs>
88
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
307 <repeat name="assemblies" min="1" title="Genome reference to provide display coordinates for this set of tracks"
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
308 help="JBrowse2 can show a set of tracks for each of multiple genome reference fasta files">
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
309 <conditional name="reference_genome">
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
310 <param help="Select a built in, history or remote tabix URI for the reference track"
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
311 label="Reference genome source" name="genome_type_select" type="select">
88
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
312 <option selected="True" value="indexed">Use a Galaxy server built-in genome</option>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
313 <option value="history">Use a genome fasta file from the current history</option>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
314 <option value="uri">Provide a URI (e.g. "https://..." for a genome reference as tabix bgzip with predictable index file URI</option>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
315 </param>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
316 <when value="indexed">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
317 <param
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
318 help="If not listed, add a custom genome, use a history genome or a remote URI tabix genome"
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
319 label="Select a built in reference genome or custom genome"
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
320 name="genome"
53
bdfa6a7c4543 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4-dirty
fubar
parents: 48
diff changeset
321 type="select"
bdfa6a7c4543 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4-dirty
fubar
parents: 48
diff changeset
322 optional="true">
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
323 <options from_data_table="all_fasta">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
324 <filter column="2" type="sort_by"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
325 <validator message="No genomes are available for the selected input dataset" type="no_options">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
326 </validator>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
327 </options>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
328 </param>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
329 </when>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
330 <when value="history">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
331 <param
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
332 format="fasta"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
333 label="Select the reference genome"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
334 name="genome"
53
bdfa6a7c4543 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4-dirty
fubar
parents: 48
diff changeset
335 type="data"
bdfa6a7c4543 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4-dirty
fubar
parents: 48
diff changeset
336 optional="true">
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
337 </param>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
338 </when>
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
339 <when value="uri">
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
340 <param
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
341 label="URI pointing to tabix compressed fasta"
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
342 name="uri"
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
343 type="text">
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
344 </param>
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
345 <param
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
346 label="Reference dbkey for tracks with this genome, such as hg38 or SacCer4"
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
347 name="refname"
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
348 type="text">
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
349 </param>
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
350 </when>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
351 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
352
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
353 <repeat name="track_groups" title="Track Group">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
354 <param label="Track Category"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
355 name="category"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
356 type="text"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
357 value="Default"
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
358 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,
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
359 which is very useful for repeatedly updating a JBrowse instance when member databases / underlying tool versions are updated." optional="False"/>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
360 <repeat name="data_tracks" title="Annotation Track">
7
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents: 5
diff changeset
361 <conditional name="data_format" label="Track Data Selection Options">
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
362 <param type="select" label="Track Type" name="data_format_select">
59
f807e219cec3 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit faada92caf5aaabe58e52b161687a30d542a07b9
fubar
parents: 58
diff changeset
363 <option value="bam">BAM track. Recommend convert to faster BED unless mapping annotation needed</option>
48
460d5b6c5d98 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a-dirty
fubar
parents: 46
diff changeset
364 <option value="bed">BED track</option>
35
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 34
diff changeset
365 <option value="bigwig">BigWig track</option>
59
f807e219cec3 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit faada92caf5aaabe58e52b161687a30d542a07b9
fubar
parents: 58
diff changeset
366 <option value="blastxml">Blast XML track (as GFF3)</option>
f807e219cec3 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit faada92caf5aaabe58e52b161687a30d542a07b9
fubar
parents: 58
diff changeset
367 <option value="cram">CRAM track. Currently not advantageous over BAM in Galaxy. Convert to BED like BAM.</option>
f807e219cec3 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit faada92caf5aaabe58e52b161687a30d542a07b9
fubar
parents: 58
diff changeset
368 <option value="gff">GFF/GFF3 track</option>
54
d6b0feb22584 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 53aab6394c715dc2d7fdd9188d6c9834e0516b5c
fubar
parents: 53
diff changeset
369 <option value="cool">HiC as cool/mcool/scool format files</option>
30
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents: 27
diff changeset
370 <option value="hic">HiC as juicebox_hic format file. Tabular hic_matrix will NOT work.</option>
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents: 27
diff changeset
371 <option value="maf">Multiple alignment format. Reference name must match the MAF name exactly to work correctly</option>
21
8e34214ccee4 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aa26b35c213b2ea7c6bb1ab800afc7e03a82508d
fubar
parents: 19
diff changeset
372 <option value="paf">PAF - approximate mapping positions between two set of sequences</option>
59
f807e219cec3 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit faada92caf5aaabe58e52b161687a30d542a07b9
fubar
parents: 58
diff changeset
373 <option value="vcf">VCF SNP track</option>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
374 </param>
35
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 34
diff changeset
375 <when value="blastxml">
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
376 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
377 <param label="Features used in Blast Search"
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
378 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
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
379 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,
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
380 blastp results on a protein sequence don't need this."
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
381 format="gff3"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
382 name="blast_parent"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
383 optional="true"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
384 type="data"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
385 <param label="Minimum Gap Size"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
386 help="before a new match_part feature is created"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
387 name="min_gap"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
388 type="integer"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
389 value="10"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
390 min="2" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
391 <param label="Is this a protein blast search?"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
392 type="boolean"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
393 name="is_protein"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
394 truevalue="true"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
395 falsevalue="false" />
85
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty
fubar
parents: 82
diff changeset
396 <expand macro="track_styling_vgp" />
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
397 <expand macro="track_visibility" />
19
bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
fubar
parents: 18
diff changeset
398 </when>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
399 <when value="vcf">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
400 <expand macro="input_conditional" label="SNP Track Data" format="vcf,vcf_bgzip" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
401 <expand macro="track_styling_vcf"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
402 <expand macro="track_visibility" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
403 </when>
48
460d5b6c5d98 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a-dirty
fubar
parents: 46
diff changeset
404 <when value="gff">
460d5b6c5d98 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a-dirty
fubar
parents: 46
diff changeset
405 <expand macro="input_conditional" label="GFF/GFF3 Track Data" format="gff,gff3" />
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
406 <conditional name="match_part" label="match/match_part data">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
407 <param help="Match part data selection " label="This is match/match_part data" name="match_part_select" type="select">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
408 <option selected="True" value="false">Not match/match part data</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
409 <option value="true">Match/match part data</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
410 </param>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
411 <when value="true">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
412 <param label="Match Part Feature Type"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
413 name="name"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
414 type="text"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
415 value="match"
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
416 help="Match_parts have options for the parent feature type, such as cDNA_match, match, translated_nucleotide_match, etc.
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
417 Please select the appropriate one here. You can leave empty to try autodetection (only works with CanvasFeatures track type)."
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
418 optional="True"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
419 </when>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
420 <when value="false" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
421 </conditional>
85
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty
fubar
parents: 82
diff changeset
422 <expand macro="track_styling_vgp" />
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
423 <expand macro="track_visibility" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
424 </when>
35
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 34
diff changeset
425 <when value="bam">
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
426 <expand macro="input_conditional" label="BAM Track Data" format="bam" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
427 <expand macro="track_visibility" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
428 </when>
48
460d5b6c5d98 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a-dirty
fubar
parents: 46
diff changeset
429 <when value="bed">
460d5b6c5d98 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a-dirty
fubar
parents: 46
diff changeset
430 <expand macro="input_conditional" label="BED Track Data" format="bed" />
85
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty
fubar
parents: 82
diff changeset
431 <expand macro="track_styling_vgp" />
48
460d5b6c5d98 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a-dirty
fubar
parents: 46
diff changeset
432 <expand macro="track_visibility" />
460d5b6c5d98 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a-dirty
fubar
parents: 46
diff changeset
433 </when>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
434 <when value="cram">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
435 <expand macro="input_conditional" label="CRAM Track Data" format="cram" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
436 <expand macro="track_visibility" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
437 </when>
19
bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
fubar
parents: 18
diff changeset
438 <when value="maf">
bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
fubar
parents: 18
diff changeset
439 <expand macro="input_conditional" label="MAF Track Data" format="maf" />
85
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty
fubar
parents: 82
diff changeset
440 <expand macro="track_styling_vgp" />
19
bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
fubar
parents: 18
diff changeset
441 <expand macro="track_visibility" />
bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
fubar
parents: 18
diff changeset
442 </when>
35
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 34
diff changeset
443 <when value="bigwig">
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
444 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" />
7
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents: 5
diff changeset
445 <expand macro="track_visibility" />
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
446 </when>
21
8e34214ccee4 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aa26b35c213b2ea7c6bb1ab800afc7e03a82508d
fubar
parents: 19
diff changeset
447 <when value="paf">
59
f807e219cec3 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit faada92caf5aaabe58e52b161687a30d542a07b9
fubar
parents: 58
diff changeset
448 <expand macro="input_conditional" label="PAF format synteny mapping data" format="paf"
f807e219cec3 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit faada92caf5aaabe58e52b161687a30d542a07b9
fubar
parents: 58
diff changeset
449 help="PAF made with mashmap or minimap2 mapping the real reference as a query on the comparison genomes as references"/>
f807e219cec3 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit faada92caf5aaabe58e52b161687a30d542a07b9
fubar
parents: 58
diff changeset
450 <expand macro="pafref_conditional" label="Comparison genome sequence(s)"
f807e219cec3 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit faada92caf5aaabe58e52b161687a30d542a07b9
fubar
parents: 58
diff changeset
451 format="fasta" help="Paf from these as the reference(s), using the common reference as the reads to map"/>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
452 <expand macro="track_visibility" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
453 </when>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
454 <when value="hic">
27
4ff1ed2065cc planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit d733fb18a02929c9e9959ad30bd0f1368118e924-dirty
fubar
parents: 23
diff changeset
455 <expand macro="input_conditional" label="Binary Juicebox HiC data" format="hic,juicebox_hic" />
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
456 <expand macro="track_visibility" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
457 </when>
23
39b717d934a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty
fubar
parents: 22
diff changeset
458 <when value="cool">
39b717d934a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty
fubar
parents: 22
diff changeset
459 <expand macro="input_conditional" label="HiC data in cool/mcool/scool format" format="cool,mcool,scool" />
39b717d934a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty
fubar
parents: 22
diff changeset
460 <expand macro="track_visibility" />
39b717d934a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty
fubar
parents: 22
diff changeset
461 </when>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
462 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
463 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
464 </repeat>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
465 </repeat>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
466 <expand macro="general_options" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
467 <param type="hidden" name="uglyTestingHack" value="" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
468 </inputs>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
469 <outputs>
89
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11
fubar
parents: 88
diff changeset
470 <data format="html" name="output" label="JBrowse2: ${jbgen.session_name}">
31
cb4b32ca9968 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
fubar
parents: 30
diff changeset
471 <change_format>
cb4b32ca9968 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
fubar
parents: 30
diff changeset
472 <when input="zipOut" value="true" format="zip" />
cb4b32ca9968 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
fubar
parents: 30
diff changeset
473 </change_format>
cb4b32ca9968 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
fubar
parents: 30
diff changeset
474 </data>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
475 </outputs>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
476 <tests>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
477 <test>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
478 <repeat name="assemblies">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
479 <conditional name="reference_genome">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
480 <param name="genome_type_select" value="history"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
481 <param name="genome" location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/Merlin" />
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
482 <param name="genome.ext" value="fasta"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
483 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
484 <repeat name="track_groups">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
485 <param name="category" value="Assembly properties"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
486 <repeat name="data_tracks">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
487 <conditional name="data_format">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
488 <param name="data_format_select" value="gff"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
489 <conditional name="useuri">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
490 <param name="insource" value="history"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
491 <param name="annotation" location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/merlin.gff3"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
492 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
493 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
494 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
495 <repeat name="data_tracks">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
496 <conditional name="data_format">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
497 <param name="data_format_select" value="bigwig"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
498 <conditional name="useuri">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
499 <param name="insource" value="history"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
500 <param name="annotation" location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/merlin.bw"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
501 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
502 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
503 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
504 <repeat name="data_tracks">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
505 <conditional name="data_format">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
506 <param name="data_format_select" value="bed"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
507 <conditional name="useuri">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
508 <param name="insource" value="history"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
509 <param name="annotation" location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/test-6.bed"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
510 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
511 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
512 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
513 <repeat name="data_tracks">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
514 <conditional name="data_format">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
515 <param name="data_format_select" value="vcf"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
516 <conditional name="useuri">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
517 <param name="insource" value="history"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
518 <param name="annotation" location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/merlin.vcf"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
519 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
520 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
521 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
522 <repeat name="data_tracks">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
523 <conditional name="data_format">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
524 <param name="data_format_select" value="cram"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
525 <conditional name="useuri">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
526 <param name="insource" value="history"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
527 <param name="annotation" location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/merlin.cram"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
528 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
529 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
530 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
531 <repeat name="data_tracks">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
532 <conditional name="data_format">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
533 <param name="data_format_select" value="bam"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
534 <conditional name="useuri">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
535 <param name="insource" value="history"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
536 <param name="annotation" location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/merlin-sample.bam"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
537 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
538 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
539 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
540 <repeat name="data_tracks">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
541 <conditional name="data_format">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
542 <param name="data_format_select" value="maf"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
543 <conditional name="useuri">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
544 <param name="insource" value="history"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
545 <param name="annotation" location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/merlinlastz.maf"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
546 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
547 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
548 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
549 <repeat name="data_tracks">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
550 <conditional name="data_format">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
551 <param name="data_format_select" value="blastxml"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
552 <conditional name="useuri">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
553 <param name="insource" value="history"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
554 <param name="annotation" location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/merlin.blastxml"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
555 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
556 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
557 </repeat>
88
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
558 <repeat name="data_tracks">
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
559 <conditional name="data_format">
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
560 <param name="data_format_select" value="bam"/>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
561 <conditional name="useuri">
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
562 <param name="insource" value="history"/>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
563 <param name="annotation" value=""/>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
564 </conditional>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
565 </conditional>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
566 </repeat>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
567 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
568 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
569 <repeat name="assemblies">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
570 <conditional name="reference_genome">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
571 <param name="genome_type_select" value="history"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
572 <param name="genome" location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/dm3.fa" />
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
573 <param name="genome.ext" value="fasta"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
574 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
575 <repeat name="track_groups">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
576 <param name="category" value="Assembly properties"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
577 <repeat name="data_tracks">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
578 <conditional name="data_format">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
579 <param name="data_format_select" value="cool"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
580 <conditional name="useuri">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
581 <param name="insource" value="history"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
582 <param name="annotation" location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/dm3test.cool"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
583 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
584 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
585 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
586 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
587 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
588 <repeat name="assemblies">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
589 <conditional name="reference_genome">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
590 <param name="genome_type_select" value="history"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
591 <param name="genome" location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/Ppersica1.fa" />
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
592 <param name="genome.ext" value="fasta"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
593 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
594 <repeat name="track_groups">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
595 <param name="category" value="Assembly properties"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
596 <repeat name="data_tracks">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
597 <conditional name="data_format">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
598 <param name="data_format_select" value="paf"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
599 <conditional name="useuri">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
600 <param name="insource" value="history"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
601 <param name="annotation" location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/peach-grape-map.paf"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
602 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
603 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
604
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
605 <conditional name="pafsuseuri">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
606 <conditional name="useuri">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
607 <param name="insource" value="history"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
608 <param name="annotation" location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/Vvinifera1.fa"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
609 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
610 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
611 </repeat>
91
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents: 90
diff changeset
612 <repeat name="data_tracks">
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents: 90
diff changeset
613 <conditional name="data_format">
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents: 90
diff changeset
614 <param name="data_format_select" value="paf"/>
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents: 90
diff changeset
615 <conditional name="useuri">
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents: 90
diff changeset
616 <param name="insource" value="history"/>
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents: 90
diff changeset
617 <param name="annotation" location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/arabgrapepeach.paf"/>
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents: 90
diff changeset
618 </conditional>
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents: 90
diff changeset
619 </conditional>
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents: 90
diff changeset
620
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents: 90
diff changeset
621 <conditional name="pafsuseuri">
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents: 90
diff changeset
622 <conditional name="useuri">
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents: 90
diff changeset
623 <param name="insource" value="history"/>
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents: 90
diff changeset
624 <param name="annotation" location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/arabidopsis.fa"/>
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents: 90
diff changeset
625 </conditional>
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents: 90
diff changeset
626 </conditional>
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents: 90
diff changeset
627 <conditional name="pafsuseuri">
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents: 90
diff changeset
628 <conditional name="useuri">
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents: 90
diff changeset
629 <param name="insource" value="history"/>
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents: 90
diff changeset
630 <param name="annotation" location="https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/merlin/Vvinifera1.fa"/>
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents: 90
diff changeset
631 </conditional>
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents: 90
diff changeset
632 </conditional>
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents: 90
diff changeset
633 </repeat>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
634 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
635 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
636 <repeat name="assemblies">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
637 <conditional name="reference_genome">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
638 <param name="genome_type_select" value="uri"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
639 <param name="uri" value="https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz" />
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
640 <param name="refname" value="hg38"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
641 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
642 <repeat name="track_groups">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
643 <param name="category" value="Assembly properties"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
644 <repeat name="data_tracks">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
645 <conditional name="data_format">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
646 <param name="data_format_select" value="hic"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
647 <conditional name="useuri">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
648 <param name="insource" value="uri"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
649 <param name="annouri" value="https://s3.amazonaws.com/igv.broadinstitute.org/data/hic/intra_nofrag_30.hic"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
650 <param name="annoname" value="humanhic"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
651 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
652 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
653 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
654 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
655 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
656 <section name="jbgen">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
657 <param name="zipOut" value="true" />
89
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11
fubar
parents: 88
diff changeset
658 <param name="session_name" value="New test session"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
659 </section>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
660 <output name="output" file="jbrowse2_result02.zip" ftype="zip" compare="sim_size">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
661 <assert_contents>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
662 <has_archive_member path=".*" n="616" delta="10"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
663 <has_archive_member path="index.html"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
664 <has_archive_member path="static/media/roboto-latin-400-normal.3f2b9a42f643e62a49b7.woff"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
665 <has_archive_member path="manifest.json">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
666 <has_text text="favicon.ico"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
667 <has_text text="background_color"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
668 </has_archive_member>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
669 <has_archive_member path="galaxy.xml">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
670 <is_valid_xml />
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
671 <xml_element path="./metadata/general/session_name" n="1">
89
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11
fubar
parents: 88
diff changeset
672 <has_text_matching expression="New test session"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
673 <not_has_text text="Newton"/>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
674 </xml_element>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
675 </has_archive_member>
89
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11
fubar
parents: 88
diff changeset
676 <has_archive_member path="merlin.gff3_0.gz"/>
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11
fubar
parents: 88
diff changeset
677 <has_archive_member path="merlin.bw_1"/>
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11
fubar
parents: 88
diff changeset
678 <has_archive_member path="test-6.bed_2.gz"/>
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11
fubar
parents: 88
diff changeset
679 <has_archive_member path="merlin.vcf_3.tbi"/>
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11
fubar
parents: 88
diff changeset
680 <has_archive_member path="merlin.cram_4"/>
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11
fubar
parents: 88
diff changeset
681 <has_archive_member path="merlin-sample.bam_5"/>
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11
fubar
parents: 88
diff changeset
682 <has_archive_member path="merlinlastz.maf_6.sorted.bed.gz.tbi"/>
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11
fubar
parents: 88
diff changeset
683 <has_archive_member path="merlin.blastxml_7.gz"/>
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11
fubar
parents: 88
diff changeset
684 <has_archive_member path="dm3test.cool_9.hic"/>
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11
fubar
parents: 88
diff changeset
685 <has_archive_member path="peach-grape-map.paf_10"/>
91
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents: 90
diff changeset
686 <has_archive_member path="arabgrapepeach.paf_11"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
687 <has_archive_member path="Merlin.fa.gz.fai"/>
91
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents: 90
diff changeset
688 <has_archive_member path="dm3.fa.fa.gz.fai"/>
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents: 90
diff changeset
689 <has_archive_member path="Ppersica1.fa.fa.gz.fai"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
690 <has_archive_member path="config.json">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
691 <has_json_property_with_text property="name" text="Merlin" />
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
692 </has_archive_member>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
693 </assert_contents>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
694 </output>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
695 </test>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
696 <test>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
697 <repeat name="assemblies">
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
698 <conditional name="reference_genome">
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
699 <param name="genome_type_select" value="history"/>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
700 <param name="genome" value="merlin.fa"/>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
701 <param name="genome.ext" value="fasta"/>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
702 <param name="genome.name" value="Merlin"/>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
703 </conditional>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
704 <repeat name="track_groups">
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
705 <param name="category" value="Default" />
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
706 <repeat name="data_tracks">
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
707 <conditional name="data_format">
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
708 <param name="data_format_select" value="bigwig"/>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
709 <conditional name="useuri">
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
710 <param name="annotation" value="bw/merlin.bw"/>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
711 <param name="insource" value="history"/>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
712 </conditional>
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
713 </conditional>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
714 </repeat>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
715 </repeat>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
716 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
717 <param name="uglyTestingHack" value="enabled" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
718 <output name="output">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
719 <assert_contents>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
720 <has_text text="genome path="></has_text>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
721 <has_text text="label="></has_text>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
722 <has_text text="format="></has_text>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
723 <has_text text="metadata"></has_text>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
724 <has_text text="useuri="></has_text>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
725 <has_text text="trackFile path="></has_text>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
726 <has_text text="ext=&quot;bigwig&quot;"></has_text>
38
07849bf248e3 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a74e469a81b38c7142f63de510ae31d3754d1767
fubar
parents: 36
diff changeset
727 <has_text text="format=&quot;bigwig&quot;"></has_text>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
728 </assert_contents>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
729 </output>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
730 </test>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
731 <test>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
732 <repeat name="assemblies">
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
733 <conditional name="reference_genome">
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
734 <param name="genome_type_select" value="history"/>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
735 <param name="genome" value="merlin.fa"/>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
736 <param name="genome.ext" value="fasta"/>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
737 <param name="genome.name" value="Merlin"/>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
738 </conditional>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
739 <repeat name="track_groups">
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
740 <param name="category" value="Default" />
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
741 <repeat name="data_tracks">
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
742 <conditional name="data_format">
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
743 <param name="data_format_select" value="vcf"/>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
744 <conditional name="useuri">
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
745 <param name="insource" value="history"/>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
746 <param name="annotation" value="vcf/merlin.vcf"/>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
747 </conditional>
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
748 </conditional>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
749 </repeat>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
750 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
751 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
752 <param name="uglyTestingHack" value="enabled" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
753 <output name="output">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
754 <assert_contents>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
755 <has_text text="genome path="></has_text>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
756 <has_text text="label="></has_text>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
757 <has_text text="format="></has_text>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
758 <has_text text="metadata"></has_text>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
759 <has_text text="useuri="></has_text>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
760 <has_text text="trackFile path="></has_text>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
761 <has_text text="ext=&quot;vcf&quot; label=&quot;merlin.vcf&quot;"></has_text>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
762 </assert_contents>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
763 </output>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
764 </test>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
765 <test>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
766 <repeat name="assemblies">
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
767 <conditional name="reference_genome">
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
768 <param name="genome_type_select" value="history"/>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
769 <param name="genome" value="merlin.fa"/>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
770 <param name="genome.ext" value="fasta"/>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
771 <param name="genome.name" value="Merlin"/>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
772 </conditional>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
773 </repeat>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
774 <param name="uglyTestingHack" value="enabled" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
775 <output name="output">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
776 <assert_contents>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
777 <has_text text="genome path="></has_text>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
778 <has_text text="label="></has_text>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
779 <has_text text="useuri="></has_text>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
780 <has_text text="metadata"></has_text>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
781 </assert_contents>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
782 </output>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
783 </test>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
784 <test>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
785 <repeat name="assemblies">
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
786 <conditional name="reference_genome">
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
787 <param name="genome_type_select" value="history"/>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
788 <param name="genome" value="merlin.fa"/>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
789 <param name="genome.ext" value="fasta"/>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
790 <param name="genome.name" value="Merlin"/>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
791 </conditional>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
792 <repeat name="track_groups">
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
793 <param name="category" value="Default" />
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
794 <repeat name="data_tracks">
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
795 <conditional name="data_format">
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
796 <param name="data_format_select" value="vcf"/>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
797 <conditional name="useuri">
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
798 <param name="insource" value="history"/>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
799 <param name="annotation" value="vcf/merlin.vcf"/>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
800 </conditional>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
801 </conditional>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
802 </repeat>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
803 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
804 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
805 <param name="uglyTestingHack" value="enabled" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
806 <output name="output">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
807 <assert_contents>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
808 <has_text text="genome path="></has_text>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
809 <has_text text="label="></has_text>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
810 <has_text text="format="></has_text>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
811 <has_text text="metadata"></has_text>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
812 <has_text text="useuri="></has_text>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
813 <has_text text="trackFile path="></has_text>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
814 <has_text text="ext=&quot;vcf&quot; label=&quot;merlin.vcf&quot;"></has_text>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
815 </assert_contents>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
816 </output>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
817 </test>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
818 <test>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
819 <repeat name="assemblies">
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
820 <conditional name="reference_genome">
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
821 <param name="genome_type_select" value="history"/>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
822 <param name="genome" value="merlin.fa"/>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
823 <param name="genome.ext" value="fasta"/>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
824 <param name="genome.name" value="Merlin"/>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
825 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
826 <repeat name="track_groups">
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
827 <param name="category" value="Default" />
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
828 <repeat name="data_tracks">
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
829 <conditional name="data_format">
48
460d5b6c5d98 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a-dirty
fubar
parents: 46
diff changeset
830 <param name="data_format_select" value="gff"/>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
831 <conditional name="useuri">
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
832 <param name="insource" value="history"/>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
833 <param name="annotation" value="gff3/A.gff"/>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
834 </conditional>
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
835 </conditional>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
836 <conditional name="match_part">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
837 <param name="match_part_select" value="false"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
838 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
839 <section name="jbcolor_scale">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
840 <conditional name="color_score">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
841 <param name="color_score_select" value="none"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
842 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
843 <conditional name="color">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
844 <param name="color_select" value="automatic"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
845 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
846 </section>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
847 </repeat>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
848 </repeat>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
849 <repeat name="track_groups">
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
850 <param name="category" value="Ignore Scale" />
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
851 <repeat name="data_tracks">
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
852 <conditional name="data_format">
48
460d5b6c5d98 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a-dirty
fubar
parents: 46
diff changeset
853 <param name="data_format_select" value="gff"/>
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
854 <conditional name="useuri">
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
855 <param name="insource" value="history"/>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
856 <param name="annotation" value="gff3/1.gff"/>
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
857 </conditional>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
858 <conditional name="match_part">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
859 <param name="match_part_select" value="false"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
860 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
861 <section name="jbcolor_scale">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
862 <conditional name="color_score">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
863 <param name="color_score_select" value="none"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
864 <conditional name="color">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
865 <param name="color_select" value="manual"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
866 <param name="style_color" value="#ff00ff"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
867 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
868 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
869 </section>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
870 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
871 </repeat>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
872 </repeat>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
873 <repeat name="track_groups">
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
874 <param name="category" value="Scaled Colour" />
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
875 <repeat name="data_tracks">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
876 <conditional name="data_format">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
877 <param name="data_format_select" value="gff"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
878 <conditional name="useuri">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
879 <param name="insource" value= "history"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
880 <param name="annotation" value="gff3/C.gff"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
881 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
882 <conditional name="match_part">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
883 <param name="match_part_select" value="false"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
884 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
885 <section name="jbcolor_scale">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
886 <conditional name="color_score">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
887 <param name="color_score_select" value="score"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
888 <param name="score_scaling" value="linear"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
889 <conditional name="score_scales">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
890 <param name="scale_select" value="automatic"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
891 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
892 <conditional name="color_scheme">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
893 <param name="score_scheme" value="opacity"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
894 <conditional name="color">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
895 <param name="color_select" value="automatic"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
896 </conditional>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
897 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
898 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
899 </section>
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
900 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
901 </repeat>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
902 <repeat name="data_tracks">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
903 <conditional name="data_format">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
904 <param name="data_format_select" value="gff"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
905 <conditional name="useuri">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
906 <param name="annotation" value="gff3/B.gff"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
907 <param name="insource" value= "history"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
908 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
909 <conditional name="match_part">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
910 <param name="match_part_select" value="false"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
911 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
912 <section name="jbcolor_scale">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
913 <conditional name="color_score">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
914 <param name="color_score_select" value="score"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
915 <param name="score_scaling" value="linear"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
916 <conditional name="score_scales">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
917 <param name="scale_select" value="automatic"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
918 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
919 <conditional name="color_scheme">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
920 <param name="score_scheme" value="opacity"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
921 <conditional name="color">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
922 <param name="color_select" value="manual"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
923 <param name="style_color" value="#0000ff"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
924 </conditional>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
925 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
926 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
927 </section>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
928 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
929 </repeat>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
930 <repeat name="data_tracks">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
931 <conditional name="data_format">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
932 <param name="data_format_select" value="gff"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
933 <conditional name="useuri">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
934 <param name="annotation" value="gff3/A.gff"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
935 <param name="insource" value= "history"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
936 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
937 <conditional name="match_part">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
938 <param name="match_part_select" value="false"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
939 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
940 <section name="jbcolor_scale">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
941 <conditional name="color_score">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
942 <param name="color_score_select" value="score"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
943 <param name="score_scaling" value="linear"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
944 <conditional name="score_scales">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
945 <param name="scale_select" value="manual"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
946 <param name="minimum" value="0"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
947 <param name="maximum" value="1000"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
948 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
949 <conditional name="color_scheme">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
950 <param name="score_scheme" value="opacity"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
951 <conditional name="color">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
952 <param name="color_select" value="automatic"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
953 </conditional>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
954 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
955 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
956 </section>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
957 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
958 </repeat>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
959 <repeat name="data_tracks">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
960 <conditional name="data_format">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
961 <param name="data_format_select" value="gff"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
962 <conditional name="useuri">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
963 <param name="annotation" value="gff3/1.gff"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
964 <param name="insource" value= "history"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
965 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
966 <conditional name="match_part">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
967 <param name="match_part_select" value="false"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
968 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
969 <section name="jbcolor_scale">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
970 <conditional name="color_score">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
971 <param name="color_score_select" value="score"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
972 <param name="score_scaling" value="linear"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
973 <conditional name="score_scales">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
974 <param name="scale_select" value="manual"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
975 <param name="minimum" value="0"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
976 <param name="maximum" value="1000"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
977 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
978 <conditional name="color_scheme">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
979 <param name="score_scheme" value="opacity"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
980 <conditional name="color">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
981 <param name="color_select" value="manual"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
982 <param name="style_color" value="#ff0000"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
983 </conditional>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
984 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
985 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
986 </section>
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
987 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
988 </repeat>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
989 </repeat>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
990 <repeat name="track_groups">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
991 <param name="category" value="Realistic" />
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
992 <repeat name="data_tracks">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
993 <conditional name="data_format">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
994 <param name="data_format_select" value="gff"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
995 <conditional name="useuri">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
996 <param name="annotation" value="gff3/interpro.gff"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
997 <param name="insource" value= "history"/>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
998 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
999 <conditional name="match_part">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1000 <param name="match_part_select" value="false"/>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1001 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1002 <section name="jbcolor_scale">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1003 <conditional name="color_score">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1004 <param name="color_score_select" value="none"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1005 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1006 <conditional name="color">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1007 <param name="color_select" value="automatic"/>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1008 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1009 </section>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1010 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1011 </repeat>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1012 <repeat name="data_tracks">
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1013 <conditional name="data_format">
48
460d5b6c5d98 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a-dirty
fubar
parents: 46
diff changeset
1014 <param name="data_format_select" value="gff"/>
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
1015 <conditional name="useuri">
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
1016 <param name="annotation" value="gff3/2.gff"/>
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
1017 <param name="insource" value= "history"/>
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
1018 </conditional>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1019 <conditional name="match_part">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1020 <param name="match_part_select" value="true"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1021 <param name="name" value="cDNA_match"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1022 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1023 <section name="jbcolor_scale">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1024 <conditional name="color_score">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1025 <param name="color_score_select" value="none"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1026 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1027 <conditional name="color">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1028 <param name="color_select" value="automatic"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1029 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1030 </section>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1031 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1032 </repeat>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1033 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1034 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1035
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1036 <param name="uglyTestingHack" value="enabled" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1037 <output name="output">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1038 <assert_contents>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1039 <has_text text="Ignore Scale"/>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1040 <has_text text="A.gff"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1041 <has_text text="B.gff"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1042 <has_text text="C.gff"/>
34
2893ef33fba9 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd
fubar
parents: 33
diff changeset
1043 <has_text text="interpro.gff"/>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1044 <has_text text="Scaled Colour"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1045 <has_text text="1.gff"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1046 <has_text text="2.gff"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1047 </assert_contents>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1048 </output>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1049 </test>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1050
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1051 <!-- TODO add a synteny test -->
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1052 <!-- TODO add a bam and a cram test -->
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1053 <!-- TODO add an hic test -->
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1054 <!-- TODO add a vcf_bgzip test -->
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1055 </tests>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1056 <help><![CDATA[
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1057
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1058 JBrowse2-in-Galaxy
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1059 ==================
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1060
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1061 JBrowse2-in-Galaxy offers a highly configurable, workflow-compatible
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1062 alternative to JBrowse1-in-Galaxy and Trackster.
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1063
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1064 Compared to JBrowse1-in-Galaxy, there is no support for alternative codons for unusual genomes,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1065 and detailed track styling is not yet implemented. Send code.
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1066 JBrowse1 development has now ceased in favour of JBrowse2.
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1067
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1068 Use and local viewing
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1069 =====================
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1070
7
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents: 5
diff changeset
1071
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1072 A JBrowse2 history item can be opened by viewing it (the "eye" icon).
7
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents: 5
diff changeset
1073
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents: 5
diff changeset
1074 The same browser data and setup can also be downloaded as a compressed zip archive by clicking the download ("floppy disk") icon in the history.
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents: 5
diff changeset
1075 This can be shared and viewed without Galaxy.
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1076
7
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents: 5
diff changeset
1077 A replacement application to serve the browser is required without Galaxy. A local python web server can be started using a script included in each archive,
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents: 5
diff changeset
1078 assuming that Python3 is already working on your desktop - if not you will have to install it first. Unzip the archive (*unzip [filename].zip*) and change
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents: 5
diff changeset
1079 directory to the first level in that zip archive. It contains a file named *jb2_webserver.py*
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1080
7
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents: 5
diff changeset
1081 With python3 installed,
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1082
7
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents: 5
diff changeset
1083 *python3 jb2_webserver.py*
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents: 5
diff changeset
1084
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents: 5
diff changeset
1085 will serve the unarchived JBrowse2 configuration from the same directory as the python script automatically. If a new browser window does not open,
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents: 5
diff changeset
1086 but the script appears to be running, try pointing your web browser to the default of *localhost:8080*
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1087
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1088 Overview
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1089 --------
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1090
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1091 JBrowse is a fast, embeddable genome browser built completely with
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1092 JavaScript and HTML5.
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1093
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1094 The JBrowse-in-Galaxy (JiG) tool was written to help build complex
7
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents: 5
diff changeset
1095 JBrowse installations straight from Galaxy. It allows you to build up a JBrowse instance without worrying
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1096 about how to run the command line tools to format your data, and which
7
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents: 5
diff changeset
1097 options need to be supplied and where.
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1098
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1099 Options
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1100 -------
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1101
17
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents: 16
diff changeset
1102 **Reference or Assembly**
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents: 16
diff changeset
1103
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents: 16
diff changeset
1104 Choose either a built-in or select one from your history.
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1105
17
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents: 16
diff changeset
1106 Track coordinates and contig names *must* match this reference precisely
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents: 16
diff changeset
1107 or they will not display.
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents: 16
diff changeset
1108
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents: 16
diff changeset
1109 **Track Groups** represent a set of tracks in a single category.
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1110
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1111 Annotation Tracks
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1112 -----------------
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1113
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
1114 MAF
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
1115 ~~~
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
1116
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
1117 For history references, the name of the reference genome dataset in your history is very important for MAF tracks,
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
1118 because it becomes the "dbkey" for that reference. So, it must be exactly the same as the genome name (dbkey) used
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
1119 when making the MAF, typically in the Lastz tool.
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
1120
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
1121 If you used "hg38" as the reference in Lastz, that is exactly what the reference fasta should be named for any MAF track.
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
1122 Change it using the "pencil" icon on the reference data in your history. Any other name, such as "hg38.fasta"
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
1123 will cause the MAF track to show no data since there are no matches with that reference dbkey.
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
1124
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
1125
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1126 GFF3/BED
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1127 ~~~~~~~~
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1128
17
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents: 16
diff changeset
1129 Standard feature tracks. They usually highlight genes, mRNAs and other features of interest along a genomic region.
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1130
5
efc64d8f4b72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9
fubar
parents: 3
diff changeset
1131 When these contain tens of millions of features, such as repeat regions from a VGP assembly, displaying one at a time leads
efc64d8f4b72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9
fubar
parents: 3
diff changeset
1132 to extremely slow loading times when a large region is in view, unless the "LinearPileupDisplay" display option is
efc64d8f4b72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9
fubar
parents: 3
diff changeset
1133 selected for that track in the styling options section. The default is LinearBasicDisplay, which shows all details and works
17
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents: 16
diff changeset
1134 well for relatively sparse bed files. A better option is to make a bigwig track using a set of windows based on the
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents: 16
diff changeset
1135 lengths of each assembly or reference contig.
5
efc64d8f4b72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9
fubar
parents: 3
diff changeset
1136
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1137 BAM Pileups
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1138 ~~~~~~~~~~~
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1139
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1140 We support BAM files and can automatically generate SNP tracks based on
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1141 that bam data.
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1142
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1143
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1144 BlastXML
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1145 ~~~~~~~~
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1146
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1147 JiG now supports both blastn and blastp datasets. JiG internally uses a
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1148 blastXML to gapped GFF3 tool to convert your blastxml datasets into a
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1149 format amenable to visualization in JBrowse. This tool is also
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1150 available separately from the IUC on the toolshed.
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1151
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1152 **Minimum Gap Size** reflects how long a gap must be before it becomes a
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1153 real gap in the processed gff3 file. In the picture above, various sizes
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1154 of gaps can be seen. If the minimum gap size was set much higher, say
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1155 100nt, many of the smaller gaps would disappear, and the features on
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1156 both sides would be merged into one, longer feature. This setting is
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1157 inversely proportional to runtime and output file size. *Do not set this
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1158 to a low value for large datasets*. By setting this number lower, you
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1159 will have extremely large outputs and extremely long runtimes. The
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1160 default was configured based off of the author's experience, but the
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1161 author only works on small viruses. It is *strongly* recommended that
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1162 you filter your blast results before display, e.g. picking out the top
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1163 10 hits or so.
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1164
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1165 **Protein blast search** option merely informs underlying tools that
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1166 they should adjust feature locations by 3x.
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1167
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1168
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1169 @ATTRIBUTION@
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1170 ]]></help>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1171 <expand macro="citations"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
1172 </tool>