Mercurial > repos > iuc > jbrowse2

annotate jbrowse2.xml @ 0:61add3f58f26 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
author iuc
date Thu, 02 Oct 2025 10:19:44 +0000
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61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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1 <tool id="jbrowse2" name="JBrowse2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="25.0">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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2 <description>genome browser</description>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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3 <macros>
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4 <import>macros.xml</import>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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5 </macros>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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6 <edam_topics>
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7 <edam_topic>topic_3307</edam_topic>
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8 <edam_topic>topic_0092</edam_topic>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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9 </edam_topics>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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10 <edam_operations>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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11 <edam_operation>operation_0573</edam_operation>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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12 <edam_operation>operation_0564</edam_operation>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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13 </edam_operations>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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14 <xrefs>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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15 <xref type="bio.tools">jbrowse_2</xref>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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16 </xrefs>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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17 <expand macro="requirements"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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18 <command><![CDATA[
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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19 mkdir -p '$output.files_path/data';
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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20
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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21 #if $action.action_select == "update":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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22 cp -R '$action.update_jbrowse.extra_files_path/data' '$output.files_path/';
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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23 #end if
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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24
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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25 ## Copy the XML file into the directory, mostly for debugging
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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26 ## but nice if users want to reproduce locally
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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27 cp '$trackxml' '$output.files_path/galaxy.xml';
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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28
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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29 export JBROWSE2_SOURCE_DIR=\$(dirname \$(which jbrowse))/../opt/jbrowse2;
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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30
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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31 ## Once that's done, we run the python script to handle the real work
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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32 python '$__tool_directory__/jbrowse2.py'
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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33 --jbrowse \${JBROWSE2_SOURCE_DIR}
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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34
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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35 #if $action.action_select == "update":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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36 --update
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37 #end if
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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38
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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39 --outdir '$output.files_path'
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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40 '$trackxml';
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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41
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42 cp '$output.files_path/index.html' '$output';
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43 ]]></command>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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44 <configfiles>
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45 <configfile name="trackxml"><![CDATA[<?xml version="1.0"?>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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46 #import json
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47 <root>
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48 <metadata>
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49 <general>
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50 <analytics>${jbgen.enableAnalytics}</analytics>
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51 <primary_color>${jbgen.primary_color}</primary_color>
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52 <secondary_color>${jbgen.secondary_color}</secondary_color>
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53 <tertiary_color>${jbgen.tertiary_color}</tertiary_color>
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54 <quaternary_color>${jbgen.quaternary_color}</quaternary_color>
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55 <font_size>${jbgen.font_size}</font_size>
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56 </general>
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57 <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl>
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58 </metadata>
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59 #for $assembly in $assemblies:
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60 <assembly>
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61 #if str($assembly.reference_genome.genome_type_select) == "indexed":
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62 <genome path="${assembly.reference_genome.genomes.fields.path}" label="${assembly.reference_genome.genomes.fields.name}">
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63 <metadata />
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64 </genome>
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65 #else if str($assembly.reference_genome.genome_type_select) == "remote":
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66 <genome path="${assembly.reference_genome.uri}" label="${assembly.reference_genome.label}" remote="true">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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67 <metadata />
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68 </genome>
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69 #else
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70 <genome path="$assembly.reference_genome.genome" label="${assembly.reference_genome.genome.element_identifier}">
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71 <metadata>
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72 <dataset id="${__app__.security.encode_id($assembly.reference_genome.genome.id)}" hid="${assembly.reference_genome.genome.hid}"
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73 size="${assembly.reference_genome.genome.get_size(nice_size=True)}"
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74 edam_format="${assembly.reference_genome.genome.datatype.edam_format}"
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75 file_ext="${assembly.reference_genome.genome.ext}"
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76 dname = "${assembly.reference_genome.genome.element_identifier}" />
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77 <history id="${__app__.security.encode_id($assembly.reference_genome.genome.history_id)}"
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78 #if $assembly.reference_genome.genome.history.user:
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79 user_email="${assembly.reference_genome.genome.history.user.email}"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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80 user_id="${assembly.reference_genome.genome.history.user_id}"
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81 display_name="${assembly.reference_genome.genome.history.get_display_name()}"/>
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82 #else
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83 user_email="anonymous"
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84 user_id="-1"
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85 display_name="Unnamed History"/>
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86 #end if
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87 <metadata
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88 #for (key, value) in $assembly.reference_genome.genome.get_metadata().items():
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89 #if "_types" not in $key:
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90 #if isinstance($value, list):
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91 #set value_str = "[%s]" % ','.join([str(val) for val in value])
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92 ${key}="$value_str"
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93 #else
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94 ${key}="${value}"
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95 #end if
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96 #end if
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97 #end for
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98 />
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99 <tool
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100 tool_id="${assembly.reference_genome.genome.creating_job.tool_id}"
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101 tool_version="${assembly.reference_genome.genome.creating_job.tool_version}"
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102 />
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103 </metadata>
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104 #if $assembly.ref_name_aliases:
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105 <ref_name_aliases path="${assembly.ref_name_aliases}" />
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106 #end if
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107 #if $assembly.cytobands:
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108 <cytobands path="${assembly.cytobands}" />
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109 #end if
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110 </genome>
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111 #end if
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112 <defaultLocation>${assembly.defaultLocation}</defaultLocation>
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113 <tracks>
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114 #for $tg in $assembly.track_groups:
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115 #for $track in $tg.data_tracks:
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116 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
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117 #if $track.data_format.data_format_select not in ("sparql", "gc"):
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118
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119 #if $track.data_format.annotation_cond.annotation_source == "history":
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120
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121 #if not isinstance($track.data_format.annotation_cond.annotation, list):
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122 ## Synteny tracks allow only one file
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123 #set $annotations = [$track.data_format.annotation_cond.annotation]
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124 #else
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125 #set $annotations = $track.data_format.annotation_cond.annotation
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126 #end if
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127 <files>
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128 #for $dataset in $annotations:
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129 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}">
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130 <metadata>
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131 #if $track.data_format.metadata.galaxy_metadata:
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132 <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}"
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133 size="${dataset.get_size(nice_size=True)}"
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134 edam_format="${dataset.datatype.edam_format}"
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135 file_ext="${dataset.ext}" />
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136 <history id="${__app__.security.encode_id($dataset.history_id)}"
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137 #if $dataset.history.user:
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138 user_email="${dataset.history.user.email}"
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139 user_id="${dataset.history.user_id}"
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140 display_name="${dataset.history.get_display_name()}"/>
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141 #else
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142 user_email="anonymous"
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143 user_id="-1"
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144 display_name="Unnamed History"/>
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145 #end if
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146 <metadata
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147 #for (key, value) in $dataset.get_metadata().items():
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148 #if "_types" not in $key and $value is not None and len(str($value)) < 5000:
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149 #if isinstance($value, list) or isinstance($value, dict):
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150 #set value_str = json.dumps(value).replace('"', "&quot;")
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151 ${key}="${value_str}"
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152 #else
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153 ${key}="${value}"
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154 #end if
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155 #end if
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156 #end for
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157 />
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158 <tool
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159 tool_id="${dataset.creating_job.tool_id}"
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160 tool_version="${dataset.creating_job.tool_version}"
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161 />
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162 #end if
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163 #if $track.data_format.metadata.metadata_bonus:
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164 <bonus src="${track.data_format.metadata.metadata_bonus}" />
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165 #end if
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166 </metadata>
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167 </trackFile>
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168 #end for
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169 </files>
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170 #else
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171
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172 #set $annotations = $track.data_format.annotation_cond.uri
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173 <files>
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174 <trackFile path="${track.data_format.annotation_cond.uri}" ext="${track.data_format.annotation_cond.format}" label="${track.data_format.annotation_cond.label}" remote="true">
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175 <metadata>
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176 #if $track.data_format.metadata.metadata_bonus:
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177 <bonus src="${track.data_format.metadata.metadata_bonus}" />
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178 #end if
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179 </metadata>
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180 </trackFile>
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181 </files>
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182 #end if
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183 #end if
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184
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185 <options>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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186 <style>
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187 #if str($track.data_format.data_format_select) in ("gene_calls", "pileup", "cram", "wiggle", "vcf", "synteny"):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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188 <display>${track.data_format.jbstyle.track_style.display}</display>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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189 #else if str($track.data_format.data_format_select) in ("hic", "gc", "maf"):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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190 <display>${track.data_format.track_display}</display>
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191 #end if
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192
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193 #if str($track.data_format.data_format_select) in ("gene_calls"):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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194 #if str($track.data_format.jbstyle.track_style.display) == "LinearBasicDisplay":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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195 <show_labels type="boolean">${track.data_format.jbstyle.track_style.show_labels}</show_labels>
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196 <show_descriptions type="boolean">${track.data_format.jbstyle.track_style.show_descriptions}</show_descriptions>
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197 <labels_name>${track.data_format.jbstyle.track_style.labels_name}</labels_name>
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198 <descriptions_name>${track.data_format.jbstyle.track_style.descriptions_name}</descriptions_name>
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199 <display_mode>${track.data_format.jbstyle.track_style.display_mode}</display_mode>
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200 <max_height type="integer">${track.data_format.jbstyle.track_style.max_height}</max_height>
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201 #else if str($track.data_format.jbstyle.track_style.display) == "LinearArcDisplay":
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202 <labels_name>${track.data_format.jbstyle.track_style.labels_name}</labels_name>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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203 <display_mode>${track.data_format.jbstyle.track_style.display_mode}</display_mode>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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204 #end if
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205 #end if
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206
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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207 #if str($track.data_format.data_format_select) in ("pileup", "cram"):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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208 #if str($track.data_format.jbstyle.track_style.display) == "LinearSNPCoverageDisplay":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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209 <scale_type>${track.data_format.jbstyle.track_style.scale_type}</scale_type>
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210 #if str($track.data_format.jbstyle.track_style.min_score) != "":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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211 <min_score type="integer">${track.data_format.jbstyle.track_style.min_score}</min_score>
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212 #end if
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213 #if str($track.data_format.jbstyle.track_style.max_score) != "":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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214 <max_score type="integer">${track.data_format.jbstyle.track_style.max_score}</max_score>
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215 #end if
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216 #end if
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217 #end if
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218
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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219 #if str($track.data_format.data_format_select) in ("wiggle"):
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220 <renderer>${track.data_format.jbstyle.track_style.wig_renderer}</renderer>
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221 #end if
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222 </style>
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223
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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224 #if str($track.data_format.data_format_select) in ("gene_calls"):
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225 <formatdetails>
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226 #if str($track.data_format.formatdetails.formatdetails_feature) != "":
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227 <feature>${track.data_format.formatdetails.formatdetails_feature}</feature>
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228 #end if
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229 #if str($track.data_format.formatdetails.formatdetails_subfeature) != "":
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230 <subfeature>${track.data_format.formatdetails.formatdetails_subfeature}</subfeature>
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231 #end if
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232 #if str($track.data_format.formatdetails.formatdetails_depth) != "":
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233 <depth>${track.data_format.formatdetails.formatdetails_depth}</depth>
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234 #end if
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235 </formatdetails>
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236 #end if
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237
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238 #if str($track.data_format.data_format_select) in ("wiggle"):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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239 #if str($track.data_format.jbstyle.track_style.display) == "MultiLinearWiggleDisplay":
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240 <multitrack type="boolean">True</multitrack>
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241 #end if
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242 #end if
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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243
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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244 #if str($track.data_format.data_format_select) == "pileup":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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245 <pileup>
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246 #if $track.data_format.annotation_cond.annotation_source == "history":
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247 <bam_indices>
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248 #for $dataset in $track.data_format.annotation_cond.annotation:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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249 <bam_index>${dataset.metadata.bam_index}</bam_index>
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250 #end for
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251 </bam_indices>
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252 #end if
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253 </pileup>
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254 #else if str($track.data_format.data_format_select) == "cram":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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255 <cram>
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256 #if $track.data_format.annotation_cond.annotation_source == "history":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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257 <cram_indices>
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258 #for $dataset in $track.data_format.annotation_cond.annotation:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
259 <cram_index>${dataset.metadata.cram_index}</cram_index>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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parents:
diff changeset
260 #end for
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
261 </cram_indices>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
262 #end if
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
263 </cram>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
264 #else if str($track.data_format.data_format_select) == "gene_calls":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
265 <gff>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
266 <index>${track.data_format.index}</index>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
267 </gff>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
268 #else if str($track.data_format.data_format_select) == "synteny":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
269 <synteny>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
270 </synteny>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
271 #else if str($track.data_format.data_format_select) == "hic":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
272 <hic>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
273 </hic>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
274 #else if str($track.data_format.data_format_select) == "maf":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
275 <maf>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
276 <assembly_name>${track.data_format.assembly_name}</assembly_name>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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diff changeset
277 </maf>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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278 #else if str($track.data_format.data_format_select) == "sparql":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
279 <label>${track.data_format.label}</label>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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diff changeset
280 <sparql>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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diff changeset
281 <url>${track.data_format.url}</url>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
282 <query>${track.data_format.query}</query>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
283 <query_refnames>${track.data_format.query_refnames}</query_refnames>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
284 </sparql>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
285 #else if str($track.data_format.data_format_select) == "wiggle":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
286 <wiggle>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
287 </wiggle>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
288 #else if str($track.data_format.data_format_select) == "gc":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
289 <label>GC Content</label>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
290 #end if
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
291 </options>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
292 </track>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
293 #end for
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
294 #end for
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
295 </tracks>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
296 </assembly>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
297 #end for
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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diff changeset
298 </root>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
299 ]]></configfile>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
300 </configfiles>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
301 <inputs>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
302 <conditional name="action">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
303 <param type="select" label="Action" name="action_select">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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304 <option value="create">New JBrowse Instance</option>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
305 <option value="update">Update exising JBrowse Instance</option>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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diff changeset
306 </param>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
307 <when value="create" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
308 <when value="update">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
309 <param name="update_jbrowse" type="data" format="html" label="Previous JBrowse Instance" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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diff changeset
310 </when>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
311 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
312
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
313 <repeat name="assemblies" min="1" title="Genome Assemblies">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
314 <conditional name="reference_genome">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
315 <param label="Reference genome to display" name="genome_type_select" type="select">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
316 <option selected="True" value="indexed">Use a built-in genome</option>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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diff changeset
317 <option value="history">Use a genome from history</option>
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iuc
parents:
diff changeset
318 <option value="remote">Use a genome from a remote source (not recommended)</option>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
319 </param>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
320 <when value="indexed">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
321 <param
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
322 help="If your genome of interest is not listed, contact the Galaxy team"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
323 label="Select a reference genome"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
324 name="genomes"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
325 type="select"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
326 >
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
327 <options from_data_table="all_fasta">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
328 <filter column="2" type="sort_by" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
329 <validator message="No genomes are available for the selected input dataset" type="no_options" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
330 </options>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
331 </param>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
332 </when>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
333 <when value="history">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
334 <param
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
335 format="fasta"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
336 label="Select the reference genome"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
337 name="genome"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
338 type="data" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
339 </when>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
340 <when value="remote">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
341 <param name="label" type="text" label="Display name of the genome"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
342 <param name="uri" type="text" label="URI pointing to a bgzip compressed fasta (.fai and .gzi files expected to be present)"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
343 help="⚠️ WARNING: If this URI is not available for any reason, your JBrowse dataset will be unusable." />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
344 </when>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
345 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
346
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
347 <!-- TODO genetic code not yet supported in jbrowse2
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
348 https://github.com/GMOD/jbrowse-components/issues/1765
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
349 -->
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
350
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
351 <param label="Default region to display" type="text" name="defaultLocation" value="" help="e.g. 'ctgA:1234..5678'"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
352
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
353 <param name="ref_name_aliases" type="data" format="tsv,tabular" label="Reference sequence name aliases" help="Use when chromosomes have alternate names (TSV file: first column is the names from your genome sequence, the rest of the columns are aliases." optional="true" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
354
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
355 <param name="cytobands" type="data" format="bed" label="cytobands data" help="BED file containing cytobands locations" optional="true" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
356
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
357 <repeat name="track_groups" title="Track Group">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
358 <param label="Track Category"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
359 name="category"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
360 type="text"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
361 value="Default"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
362 help="Organise your tracks into Categories for a nicer end-user experience. You can use #date# and it will be replaced with the current date in 'yyyy-mm-dd' format, which is very useful for repeatedly updating a JBrowse instance when member databases / underlying tool versions are updated." optional="False"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
363 <repeat name="data_tracks" title="Annotation Track">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
364 <conditional name="data_format" label="Track Options">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
365 <param type="select" label="Track Type" name="data_format_select">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
366 <option value="gene_calls">GFF/GFF3/BED Features</option>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
367 <option value="pileup">BAM Pileups</option>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
368 <option value="cram">CRAM</option>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
369 <option value="wiggle">BigWig</option>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
370 <option value="vcf">VCF SNPs</option>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
371 <option value="hic">HiC</option>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
372 <option value="maf">MAF</option>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
373 <option value="synteny">Synteny</option>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
374 <option value="sparql">SPARQL</option>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
375 <option value="gc">GC content</option>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
376 </param>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
377 <when value="gene_calls">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
378 <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
379
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
380 <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
381
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
382 <expand macro="track_styling_feature"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
383 <expand macro="details_panel" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
384 <expand macro="track_metadata" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
385 <expand macro="track_visibility" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
386 </when>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
387 <when value="pileup">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
388 <expand macro="input_conditional" label="BAM Track Data" format="bam" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
389 <expand macro="track_styling_xam"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
390 <expand macro="track_metadata" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
391 <expand macro="track_visibility" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
392 </when>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
393 <when value="cram">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
394 <expand macro="input_conditional" label="CRAM Track Data" format="cram" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
395 <expand macro="track_styling_xam"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
396 <expand macro="track_metadata" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
397 <expand macro="track_visibility" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
398 </when>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
399 <when value="wiggle">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
400 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
401 <expand macro="track_styling_bigwig"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
402 <expand macro="track_metadata" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
403 <expand macro="track_visibility" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
404 </when>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
405 <when value="vcf">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
406 <expand macro="input_conditional" label="SNP Track Data" format="vcf,vcf_bgzip" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
407 <expand macro="track_styling_vcf"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
408 <expand macro="details_panel" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
409 <expand macro="track_metadata" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
410 <expand macro="track_visibility" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
411 </when>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
412 <when value="hic">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
413 <expand macro="input_conditional" label="HiC data" format="hic" help="Cool files can be converted to hic format with hictk tool" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
414 <expand macro="track_styling_hic"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
415 <expand macro="track_metadata" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
416 <expand macro="track_visibility" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
417 </when>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
418 <when value="maf">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
419 <expand macro="input_conditional_no_remote" label="MAF Track Data" format="maf" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
420 <param name="assembly_name" type="text" label="Assembly name" optional="True" help="As used when creating the MAF file (default: guessed from selected genome assembly)" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
421 <expand macro="track_styling_maf"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
422 <expand macro="track_metadata" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
423 <expand macro="track_visibility" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
424 </when>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
425 <when value="synteny">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
426 <expand macro="input_conditional" label="PAF Alignment Data" format="paf" multiple="False" help="Query is current assembly, and target is the next assembly. You should not fill this field on the last assembly." />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
427 <expand macro="track_styling_synteny"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
428 <expand macro="track_metadata" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
429 <expand macro="track_visibility" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
430 </when>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
431 <when value="sparql">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
432 <!-- Not totally sure it works in real life, probably very rare use case -->
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
433 <param type="text" label="SPARQL Server URL" name="url" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
434 <param type="text" label="Track Label" name="label" value="SPARQL Genes" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
435 <param type="text" label="SPARQL Query" name="query" area="true">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
436 <sanitizer>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
437 <mapping initial="galaxy.util.mapped_chars">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
438 <add source="&#10;" target=" " />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
439 <add source="&gt;" target="__gt__" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
440 <add source="&lt;" target="__lt__" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
441 </mapping>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
442 <valid initial="default">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
443 <add value="|" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
444 <add value="#" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
445 <add value="{"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
446 <add value="}"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
447 <add value="!"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
448 <add value="?"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
449 <add value="&amp;"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
450 <add value="+"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
451 <add value="="/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
452 <add value="'"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
453 <add value='"'/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
454 </valid>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
455 </sanitizer>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
456 </param>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
457 <param type="text" label="SPARQL reference names query" help="This query should return a line for each reference name in a `refName` column" name="query_refnames" area="true">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
458 <sanitizer>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
459 <mapping initial="galaxy.util.mapped_chars">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
460 <add source="&#10;" target=" " />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
461 <add source="&gt;" target="__gt__" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
462 <add source="&lt;" target="__lt__" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
463 </mapping>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
464 <valid initial="default">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
465 <add value="|" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
466 <add value="#" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
467 <add value="{"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
468 <add value="}"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
469 <add value="!"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
470 <add value="?"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
471 <add value="&amp;"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
472 <add value="+"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
473 <add value="="/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
474 <add value="'"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
475 <add value='"'/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
476 </valid>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
477 </sanitizer>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
478 </param>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
479 <expand macro="track_visibility" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
480 </when>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
481
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
482 <when value="gc">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
483 <expand macro="track_styling_gc"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
484 <expand macro="track_metadata" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
485 <expand macro="track_visibility" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
486 </when>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
487 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
488 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
489 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
490 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
491 <expand macro="general_options" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
492 </inputs>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
493 <outputs>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
494 <data format="html" name="output" label="JBrowse2 on $on_string"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
495 </outputs>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
496 <tests>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
497 <test>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
498 <repeat name="assemblies">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
499 <conditional name="reference_genome">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
500 <param name="genome_type_select" value="history"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
501 <param name="genome" value="merlin.fa"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
502 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
503 <repeat name="track_groups">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
504 <repeat name="data_tracks">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
505 <conditional name="data_format">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
506 <param name="data_format_select" value="gene_calls" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
507 <conditional name="annotation_cond">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
508 <param name="annotation_source" value="history" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
509 <param name="annotation" value="gff3/merlin.gff" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
510 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
511 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
512 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
513 <repeat name="data_tracks">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
514 <conditional name="data_format">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
515 <param name="data_format_select" value="gene_calls"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
516 <conditional name="annotation_cond">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
517 <param name="annotation_source" value="history" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
518 <param name="annotation" value="bed/test-3.bed,bed/test-6.bed"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
519 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
520 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
521 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
522 <repeat name="data_tracks">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
523 <conditional name="data_format">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
524 <param name="data_format_select" value="pileup" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
525 <conditional name="annotation_cond">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
526 <param name="annotation_source" value="history" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
527 <param name="annotation" value="bam/merlin-sample.bam" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
528 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
529 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
530 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
531 <repeat name="data_tracks">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
532 <conditional name="data_format">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
533 <param name="data_format_select" value="wiggle"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
534 <conditional name="annotation_cond">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
535 <param name="annotation_source" value="history" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
536 <param name="annotation" value="bw/data.bw"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
537 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
538 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
539 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
540 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
541 <repeat name="track_groups">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
542 <param name="category" value="Second category" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
543 <repeat name="data_tracks">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
544 <conditional name="data_format">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
545 <param name="data_format_select" value="cram" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
546 <conditional name="annotation_cond">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
547 <param name="annotation_source" value="history" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
548 <param name="annotation" value="cram/merlin-sample.cram" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
549 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
550 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
551 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
552 <repeat name="data_tracks">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
553 <conditional name="data_format">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
554 <param name="data_format_select" value="wiggle"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
555 <conditional name="annotation_cond">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
556 <param name="annotation_source" value="history" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
557 <param name="annotation" value="bw/data.bw,bw/smaller2.bw"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
558 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
559 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
560 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
561 <repeat name="data_tracks">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
562 <conditional name="data_format">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
563 <param name="data_format_select" value="vcf" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
564 <conditional name="annotation_cond">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
565 <param name="annotation_source" value="history" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
566 <param name="annotation" value="vcf/test.vcf" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
567 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
568 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
569 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
570 <repeat name="data_tracks">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
571 <conditional name="data_format">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
572 <param name="data_format_select" value="hic" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
573 <conditional name="annotation_cond">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
574 <param name="annotation_source" value="history" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
575 <param name="annotation" value="hic/merlin.hic" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
576 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
577 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
578 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
579 <repeat name="data_tracks">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
580 <conditional name="data_format">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
581 <param name="data_format_select" value="maf" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
582 <conditional name="annotation_cond">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
583 <param name="annotation_source" value="history" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
584 <param name="annotation" value="maf/merlinlastz.maf" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
585 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
586 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
587 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
588 <repeat name="data_tracks">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
589 <conditional name="data_format">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
590 <param name="data_format_select" value="gc" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
591 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
592 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
593 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
594 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
595 <output name="output">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
596 <extra_files name="galaxy.xml" type="file" value="out/01_all_tracks/galaxy.xml" compare="sim_size" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
597 <extra_files name="config.json" type="file" value="out/01_all_tracks/config.json" compare="sim_size" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
598 </output>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
599 </test>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
600 <test> <!-- Remote data -->
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
601 <repeat name="assemblies">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
602 <conditional name="reference_genome">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
603 <param name="genome_type_select" value="remote"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
604 <param name="uri" value="https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
605 <param name="label" value="hg19"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
606 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
607 <repeat name="track_groups">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
608 <repeat name="data_tracks">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
609 <conditional name="data_format">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
610 <param name="data_format_select" value="wiggle" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
611 <conditional name="annotation_cond">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
612 <param name="annotation_source" value="remote" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
613 <param name="uri" value="https://s3.amazonaws.com/jbrowse.org/genomes/hg19/reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.bam.regions.bw" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
614 <param name="label" value="SKBR3 pacbio coverage (NGMLR)" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
615 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
616 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
617 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
618 <repeat name="data_tracks">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
619 <conditional name="data_format">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
620 <param name="data_format_select" value="wiggle" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
621 <conditional name="annotation_cond">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
622 <param name="annotation_source" value="remote" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
623 <param name="uri" value="https://s3.amazonaws.com/jbrowse.org/genomes/hg19/reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.bam.regions.bw" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
624 <param name="label" value="SKBR3 pacbio coverage (NGMLR)" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
625 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
626 <section name="jbstyle">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
627 <conditional name="track_style">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
628 <param name="display" value="MultiLinearWiggleDisplay" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
629 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
630 </section>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
631 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
632 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
633 <repeat name="data_tracks">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
634 <conditional name="data_format">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
635 <param name="data_format_select" value="pileup" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
636 <conditional name="annotation_cond">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
637 <param name="annotation_source" value="remote" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
638 <param name="uri" value="https://s3.amazonaws.com/1000genomes/phase3/data/NA12878/exome_alignment/NA12878.mapped.ILLUMINA.bwa.CEU.exome.20121211.bam" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
639 <param name="label" value="NA12878 Exome" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
640 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
641 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
642 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
643 <repeat name="data_tracks">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
644 <conditional name="data_format">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
645 <param name="data_format_select" value="cram" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
646 <conditional name="annotation_cond">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
647 <param name="annotation_source" value="remote" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
648 <param name="uri" value="https://s3.amazonaws.com/jbrowse.org/genomes/hg19/alzheimers_isoseq/hq_isoforms.fasta.cram" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
649 <param name="label" value="hg_isoforms.fasta_cram" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
650 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
651 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
652 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
653 <repeat name="data_tracks">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
654 <conditional name="data_format">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
655 <param name="data_format_select" value="hic" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
656 <conditional name="annotation_cond">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
657 <param name="annotation_source" value="remote" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
658 <param name="uri" value="https://jbrowse.org/genomes/hg19/intra_nofrag_30.hic" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
659 <param name="label" value="hg_isoforms.fasta_cram" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
660 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
661 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
662 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
663 <repeat name="data_tracks">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
664 <conditional name="data_format">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
665 <param name="data_format_select" value="vcf" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
666 <conditional name="annotation_cond">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
667 <param name="annotation_source" value="remote" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
668 <param name="uri" value="https://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_study/vcf/nstd175.GRCh37.variant_call.vcf.gz" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
669 <param name="label" value="HG002 dbVar variant calls" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
670 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
671 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
672 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
673 <repeat name="data_tracks">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
674 <conditional name="data_format">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
675 <param name="data_format_select" value="vcf" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
676 <conditional name="annotation_cond">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
677 <param name="annotation_source" value="remote" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
678 <param name="uri" value="https://s3.amazonaws.com/jbrowse.org/genomes/hg19/COLO829/truthset_somaticSVs_COLO829.vcf" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
679 <param name="label" value="truthset_somaticSVs_COLO829" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
680 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
681 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
682 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
683 <repeat name="data_tracks">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
684 <conditional name="data_format">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
685 <param name="data_format_select" value="gene_calls" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
686 <conditional name="annotation_cond">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
687 <param name="annotation_source" value="remote" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
688 <param name="uri" value="https://s3.amazonaws.com/jbrowse.org/genomes/hg19/gencode/gencode.v36lift37.annotation.sort.gff3.gz" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
689 <param name="label" value="Gencode v36 (GRCh37 liftover)" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
690 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
691 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
692 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
693 <repeat name="data_tracks">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
694 <conditional name="data_format">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
695 <param name="data_format_select" value="gene_calls" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
696 <conditional name="annotation_cond">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
697 <param name="annotation_source" value="remote" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
698 <param name="uri" value="https://s3.amazonaws.com/jbrowse.org/genomes/hg19/mappability/wgEncodeDukeMapabilityRegionsExcludable.bed.gz" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
699 <param name="label" value="wgEncodeDukeMapabilityRegionsExcludable" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
700 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
701 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
702 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
703 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
704 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
705 <output name="output">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
706 <extra_files name="galaxy.xml" type="file" value="out/02_remote/galaxy.xml" compare="sim_size" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
707 <extra_files name="config.json" type="file" value="out/02_remote/config.json" compare="sim_size" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
708 </output>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
709 </test>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
710 <test> <!-- Synteny merlin -->
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
711 <repeat name="assemblies">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
712 <conditional name="reference_genome">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
713 <param name="genome_type_select" value="history"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
714 <param name="genome" value="merlun.fa"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
715 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
716 <repeat name="track_groups">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
717 <repeat name="data_tracks">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
718 <conditional name="data_format">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
719 <param name="data_format_select" value="synteny"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
720 <conditional name="annotation_cond">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
721 <param name="annotation_source" value="history" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
722 <param name="annotation" value="paf/merlun_on_merlon.paf"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
723 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
724 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
725 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
726 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
727 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
728 <repeat name="assemblies">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
729 <conditional name="reference_genome">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
730 <param name="genome_type_select" value="history"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
731 <param name="genome" value="merlon.fa"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
732 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
733 <repeat name="track_groups">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
734 <repeat name="data_tracks">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
735 <conditional name="data_format">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
736 <param name="data_format_select" value="synteny"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
737 <conditional name="annotation_cond">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
738 <param name="annotation_source" value="history" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
739 <param name="annotation" value="paf/merlon_on_merlin.paf"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
740 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
741 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
742 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
743 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
744 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
745 <repeat name="assemblies">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
746 <conditional name="reference_genome">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
747 <param name="genome_type_select" value="history"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
748 <param name="genome" value="merlin.fa"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
749 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
750 <repeat name="track_groups">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
751 <repeat name="data_tracks">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
752 <conditional name="data_format">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
753 <param name="data_format_select" value="wiggle"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
754 <conditional name="annotation_cond">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
755 <param name="annotation_source" value="history" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
756 <param name="annotation" value="bw/data.bw"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
757 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
758 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
759 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
760 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
761 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
762 <output name="output">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
763 <extra_files name="galaxy.xml" type="file" value="out/03_synteny/galaxy.xml" compare="sim_size" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
764 <extra_files name="config.json" type="file" value="out/03_synteny/config.json" compare="sim_size" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
765 </output>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
766 </test>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
767 <test> <!-- Synteny with remote genomes -->
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
768 <repeat name="assemblies">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
769 <conditional name="reference_genome">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
770 <param name="genome_type_select" value="remote"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
771 <param name="uri" value="https://s3.amazonaws.com/jbrowse.org/genomes/peach/Ppersica_298_v2.0.fa.gz"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
772 <param name="label" value="Peach"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
773 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
774 <repeat name="track_groups">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
775 <repeat name="data_tracks">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
776 <conditional name="data_format">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
777 <param name="data_format_select" value="synteny"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
778 <conditional name="annotation_cond">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
779 <param name="annotation_source" value="history" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
780 <param name="annotation" value="paf/peach-grape-map.paf"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
781 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
782 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
783 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
784 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
785 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
786 <repeat name="assemblies">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
787 <conditional name="reference_genome">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
788 <param name="genome_type_select" value="remote"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
789 <param name="uri" value="https://s3.amazonaws.com/jbrowse.org/genomes/grape/Vvinifera_145_Genoscope.12X.fa.gz"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
790 <param name="label" value="Grape"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
791 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
792 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
793 <output name="output">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
794 <extra_files name="galaxy.xml" type="file" value="out/04_synteny_remote/galaxy.xml" compare="sim_size" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
795 <extra_files name="config.json" type="file" value="out/04_synteny_remote/config.json" compare="sim_size" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
796 </output>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
797 </test>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
798 <test> <!-- Synteny with remote genomes *and* paf -->
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
799 <repeat name="assemblies">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
800 <conditional name="reference_genome">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
801 <param name="genome_type_select" value="remote"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
802 <param name="uri" value="https://s3.amazonaws.com/jbrowse.org/genomes/peach/Ppersica_298_v2.0.fa.gz"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
803 <param name="label" value="Peach"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
804 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
805 <repeat name="track_groups">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
806 <repeat name="data_tracks">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
807 <conditional name="data_format">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
808 <param name="data_format_select" value="synteny"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
809 <conditional name="annotation_cond">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
810 <param name="annotation_source" value="remote" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
811 <param name="uri" value="https://s3.amazonaws.com/jbrowse.org/genomes/synteny/peach_grape.paf.gz" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
812 <param name="label" value="Peach vs grape" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
813 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
814 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
815 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
816 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
817 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
818 <repeat name="assemblies">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
819 <conditional name="reference_genome">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
820 <param name="genome_type_select" value="remote"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
821 <param name="uri" value="https://s3.amazonaws.com/jbrowse.org/genomes/grape/Vvinifera_145_Genoscope.12X.fa.gz"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
822 <param name="label" value="Grape"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
823 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
824 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
825 <output name="output">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
826 <extra_files name="galaxy.xml" type="file" value="out/05_synteny_full_remote/galaxy.xml" compare="sim_size" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
827 <extra_files name="config.json" type="file" value="out/05_synteny_full_remote/config.json" compare="sim_size" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
828 </output>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
829 </test>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
830 <test> <!-- various options, cytobands, ref name aliases -->
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
831 <repeat name="assemblies">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
832 <conditional name="reference_genome">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
833 <param name="genome_type_select" value="history"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
834 <param name="genome" value="merlin.fa"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
835 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
836 <param name="ref_name_aliases" value="aliases.tsv"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
837 <param name="cytobands" value="cytobands.bed"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
838 <param name="defaultLocation" value="Merlin:1000..2000"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
839 <repeat name="track_groups">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
840 <repeat name="data_tracks">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
841 <conditional name="data_format">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
842 <param name="data_format_select" value="gene_calls" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
843 <conditional name="annotation_cond">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
844 <param name="annotation_source" value="history" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
845 <param name="annotation" value="gff3/merlin.gff" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
846 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
847 <param name="index" value="true" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
848 <section name="jbstyle">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
849 <conditional name="track_style">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
850 <param name="display" value="LinearBasicDisplay" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
851 <param name="display_mode" value="reducedRepresentation" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
852 <param name="labels_name" value="jexl:get(feature,'id')" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
853 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
854 </section>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
855 <section name="metadata">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
856 <param name="galaxy_metadata" value="false" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
857 <param name="metadata_bonus" value="metadata.tsv" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
858 </section>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
859 <section name="formatdetails">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
860 <param name="formatdetails_feature" value="jexl:{newfield:'Top custom contents here: '+feature.name}"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
861 <param name="formatdetails_subfeature" value="jexl:{newfield:'Sub custom contents here: '+feature.name}"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
862 <param name="formatdetails_depth" value="2"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
863 </section>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
864 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
865 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
866 <repeat name="data_tracks">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
867 <conditional name="data_format">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
868 <param name="data_format_select" value="gene_calls" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
869 <conditional name="annotation_cond">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
870 <param name="annotation_source" value="history" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
871 <param name="annotation" value="gff3/1.gff" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
872 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
873 <param name="index" value="true" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
874 <section name="jbstyle">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
875 <conditional name="track_style">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
876 <param name="display" value="LinearArcDisplay" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
877 <param name="display_mode" value="semicircles" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
878 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
879 </section>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
880 <param name="track_visibility" value="default_off" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
881 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
882 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
883 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
884 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
885 <section name="jbgen">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
886 <param name="enableAnalytics" value="true" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
887 <param name="primary_color" value="#9d233f"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
888 <param name="secondary_color" value="#421e63"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
889 <param name="tertiary_color" value="#935560"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
890 <param name="quaternary_color" value="#9fb11d"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
891 <param name="font_size" value="15" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
892 </section>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
893 <output name="output">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
894 <extra_files name="galaxy.xml" type="file" value="out/06_various_options/galaxy.xml" compare="sim_size" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
895 <extra_files name="config.json" type="file" value="out/06_various_options/config.json" compare="sim_size" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
896 </output>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
897 </test>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
898 <test> <!-- Synteny, mixed basic / viewer -->
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
899 <repeat name="assemblies">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
900 <conditional name="reference_genome">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
901 <param name="genome_type_select" value="history"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
902 <param name="genome" value="merlun.fa"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
903 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
904 <repeat name="track_groups">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
905 <repeat name="data_tracks">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
906 <conditional name="data_format">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
907 <param name="data_format_select" value="synteny"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
908 <conditional name="annotation_cond">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
909 <param name="annotation_source" value="history" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
910 <param name="annotation" value="paf/merlun_on_merlon.paf"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
911 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
912 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
913 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
914 <repeat name="data_tracks">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
915 <conditional name="data_format">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
916 <param name="data_format_select" value="synteny"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
917 <conditional name="annotation_cond">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
918 <param name="annotation_source" value="history" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
919 <param name="annotation" value="paf/merlun_on_merlon.paf"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
920 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
921 <section name="jbstyle">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
922 <conditional name="track_style">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
923 <param name="display" value="LinearBasicDisplay" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
924 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
925 </section>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
926 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
927 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
928 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
929 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
930 <repeat name="assemblies">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
931 <conditional name="reference_genome">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
932 <param name="genome_type_select" value="history"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
933 <param name="genome" value="merlon.fa"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
934 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
935 <repeat name="track_groups">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
936 <repeat name="data_tracks">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
937 <conditional name="data_format">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
938 <param name="data_format_select" value="synteny"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
939 <conditional name="annotation_cond">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
940 <param name="annotation_source" value="history" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
941 <param name="annotation" value="paf/merlon_on_merlin.paf"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
942 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
943 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
944 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
945 <repeat name="data_tracks">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
946 <conditional name="data_format">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
947 <param name="data_format_select" value="synteny"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
948 <conditional name="annotation_cond">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
949 <param name="annotation_source" value="history" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
950 <param name="annotation" value="paf/merlon_on_merlin.paf"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
951 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
952 <section name="jbstyle">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
953 <conditional name="track_style">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
954 <param name="display" value="LinearBasicDisplay" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
955 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
956 </section>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
957 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
958 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
959 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
960 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
961 <repeat name="assemblies">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
962 <conditional name="reference_genome">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
963 <param name="genome_type_select" value="history"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
964 <param name="genome" value="merlin.fa"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
965 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
966 <repeat name="track_groups">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
967 <repeat name="data_tracks">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
968 <conditional name="data_format">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
969 <param name="data_format_select" value="wiggle"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
970 <conditional name="annotation_cond">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
971 <param name="annotation_source" value="history" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
972 <param name="annotation" value="bw/data.bw"/>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
973 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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diff changeset
974 </conditional>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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diff changeset
975 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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diff changeset
976 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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diff changeset
977 </repeat>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
978 <output name="output">
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
979 <extra_files name="galaxy.xml" type="file" value="out/07_synteny_mixed/galaxy.xml" compare="sim_size" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
980 <extra_files name="config.json" type="file" value="out/07_synteny_mixed/config.json" compare="sim_size" />
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
981 </output>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
982 </test>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
983 </tests>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
984 <help format="markdown"><![CDATA[
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
985 # JBrowse2
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
986
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
987 JBrowse2 (or simply JBrowse) is a fast, embeddable genome browser built completely with
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
988 JavaScript and HTML5.
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
989
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
990 The JBrowse2 Galaxy tool was written to help build complex
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
991 JBrowse installations straight from Galaxy, taking advantage of the
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
992 latest Galaxy features such as dataset collections and sections.
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
993 It allows you to build up a JBrowse instance without worrying
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
994 about how to run the command line tools to format your data, and which
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
995 options need to be supplied and where.
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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diff changeset
996
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
997 With this tool, you can easily generate a standalone JBrowse browser,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
998 that you can download, share with collaborators or even publish publicly.
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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diff changeset
999 You can even deposit it as an archive on data repositories for long term
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
1000 archival and reuse.
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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1001
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parents:
diff changeset
1002 ## Options
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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1003
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iuc
parents:
diff changeset
1004 ### Action
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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diff changeset
1005
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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diff changeset
1006 The default action of this tool is to create a new JBrowse dataset from scratch.
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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diff changeset
1007 However, you have the possibility to add new data (genomes and tracks) to a JBrowse2
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
1008 dataset previously generated with the same tool. Note however that mixing synteny and
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
1009 non-synteny dataset can give unwanted results.
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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diff changeset
1010
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
1011 ### Genome assemblies
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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diff changeset
1012
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
1013 In JBrowse2 you can as many genome assemblies as needed, each one having its specific
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
1014 set of tracks.
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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diff changeset
1015
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
1016 To add an assembly, you will need to input its sequence, either from a FASTA file in your history
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
1017 or from a genome pre-installed by your server administrators.
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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parents:
diff changeset
1018
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
1019 ### Track Groups
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
1020
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
1021 Track groups represent a set of tracks in a single category. These
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
1022 can be used to let your users understand relationships between large
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
1023 groups of tracks.
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
1024
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
1025 ### Annotation Tracks
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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diff changeset
1026
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
1027 Within Track Groups, you have one or more **Annotation Tracks**. Each
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
1028 Annotation Track is a dataset, or a group of datasets which have similar styling.
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
1029 This allows you to rapidly build up JBrowse instances without having to
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
1030 configure tracks individually. For example, if you have five different GFF3 files from
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
1031 various gene callers that you wish to display, you can take advantage of
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
1032 this feature to style all of them similarly.
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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parents:
diff changeset
1033
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
1034 For each track, or group of tracks, you will need to select the corresponding data type
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
1035 (GFF, BED, VCF, BAM, CRAM, ...) and the corresponding input files. Depending on the selected
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
1036 track type, you will get access to advanced configuration sections where you will be able to
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
1037 change the styling of the track. Please consult the [JBrowse2 documentation](https://jbrowse.org/jb2/docs/)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
1038 for more details on all the possibilities. These options will only change the default styling
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
1039 of your JBrowse dataset: when visualising it, you will be able to use the JBrowse menus to switch to different
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
1040 styling.
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
1041
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
1042 When clicking on features in JBrowse (like genes from a GFF), JBrowse opens a panel with detailed
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
1043 information about this feature. This panel can also be customized directly from this Galaxy tool, by
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
1044 adding new fields, or modifying/removing existing ones.
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
1045
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
1046 On different type of tracks, you also have the possiblity to customize metadata associated to tracks.
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff changeset
1047 Metadata is used by JBrowse to easily sort track in its Faceted Track Selector.
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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1048
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1049 ## Special data
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1050
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1051 ### Synteny
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1052
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1053 JBrowse2 allows to display synteny relationships between different genomes. To use it with this tool,
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1054 generate alignement data between your different genomes (with minimap2 for example), then add the different genomes
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1055 one by one, and a synteny track to the each genome corresponding to alignements to the
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1056 next one.
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1057
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1058 For example, say you have 3 genomes : A, B and C
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1059 - align genome B on genome A, and genome C on genome B
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1060 - add genome C, B, and A in the Galaxy tool
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1061 - add a synteny track on genome C where you input the alignement against genome B
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1062 - add a synteny track on genome B where you input the alignement against genome A
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1063
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1064 Multiway synteny representation is not yet possible.
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1065
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1066 ### Remote data sources
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1067
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1068 We have made the choice to allow selecting data from remote sources (HTTP) instead of datasets from your history.
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1069 Please be **very careful** when using this feature: by using it, your dataset will no longer be standalone, it will
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1070 depend on the existence of the remote data. If for any reason the remote server administrator decides to remove or change
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1071 the access rights to the corresponding file, your JBrowse dataset will become unusable.
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1072
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1073 Using remote data sources can be useful when using this tool for specific projects with associated reliable data
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1074 repositories, but for most other use cases, selecting datasets from history is much more recommended.
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1075 ]]></help>
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1076 <expand macro="citations"/>
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1077 </tool>