Mercurial > repos > fubar > jbrowse2

annotate jbrowse2.xml @ 35:15da358c3108 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
author fubar
date Wed, 28 Feb 2024 10:08:57 +0000
parents 2893ef33fba9
children 5f39f745682f
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1 <tool id="jbrowse2" name="jbrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_5" profile="22.05">
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2 <description>genome browser</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="edamInc"/>
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7 <xrefs>
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8 <xref type="bio.tools">jbrowse2</xref>
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9 </xrefs>
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10 <expand macro="requirements"/>
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11 <version_command>python '${__tool_directory__}/jbrowse2.py' --version</version_command>
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12 <command detect_errors="aggressive"><![CDATA[
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13 mkdir -p '$output.files_path' &&
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14 ## Copy the XML file into the directory, mostly for debugging
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15 ## but nice if users want to reproduce locally
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16 cp '$trackxml' '$output.files_path/galaxy.xml' &&
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17 python '$__tool_directory__/jbrowse2.py'
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18 --outdir '$output.files_path'
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19 --xml '$trackxml' &&
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20 #if $jbgen.zipOut == "true":
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21 (cd '$output.files_path' && zip -r - . ) > '$output'
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22 #else
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23 cp '$output.files_path/index.html' '$output'
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24 #end if
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25 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph.
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26 #if str($uglyTestingHack) == "enabled":
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27 && cp '$trackxml' '$output'
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28 #end if
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29 ]]></command>
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30 <configfiles>
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31 <configfile name="trackxml"><![CDATA[<?xml version="1.0"?>
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32 <root>
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33 <metadata>
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34 <genomes>
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35 #if str($reference_genome.genome_type_select) == "indexed":
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36 <genome path="${reference_genome.genome.fields.path}" label="${reference_genome.genome.fields.name}">
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37 <metadata>
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38 <dataset
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39 dname = "${reference_genome.genome.name}" />
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40 </metadata>
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41 </genome>
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42 #else
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43 <genome path="$reference_genome.genome" label="${reference_genome.genome.name}">
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44 <metadata>
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45 <dataset id="${__app__.security.encode_id($reference_genome.genome.id)}" hid="${reference_genome.genome.hid}"
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46 size="${reference_genome.genome.get_size(nice_size=True)}"
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47 edam_format="${reference_genome.genome.datatype.edam_format}"
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48 file_ext="${reference_genome.genome.ext}"
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49 dname = "${reference_genome.genome.name}" />
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50 <history id="${__app__.security.encode_id($reference_genome.genome.history_id)}"
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51 #if $reference_genome.genome.history.user:
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52 user_email="${reference_genome.genome.history.user.email}"
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53 user_id="${reference_genome.genome.history.user_id}"
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54 display_name="${reference_genome.genome.history.get_display_name()}"/>
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55 #else
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56 user_email="anonymous"
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57 user_id="-1"
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58 display_name="Unnamed History"/>
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59 #end if
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60 <metadata
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61 #for (key, value) in $reference_genome.genome.get_metadata().items():
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62 #if "_types" not in $key:
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63 #if isinstance($value, list):
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64 #set value_str = "[%s]" % ','.join([str(val) for val in value])
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65 ${key}="$value_str"
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66 #else
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67 ${key}="${value}"
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68 #end if
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69 #end if
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70 #end for
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71 />
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72 <tool
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73 tool_id="${reference_genome.genome.creating_job.tool_id}"
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74 tool_version="${reference_genome.genome.creating_job.tool_version}"
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75 />
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76 </metadata>
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77 </genome>
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78 #end if
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79 </genomes>
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80 <general>
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81 <defaultLocation>${jbgen.defaultLocation}</defaultLocation>
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82 <zipOut>${jbgen.zipOut}</zipOut>
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83 <analytics>${jbgen.enableAnalytics}</analytics>
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84 <primary_color>${jbgen.primary_color}</primary_color>
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85 <secondary_color>${jbgen.secondary_color}</secondary_color>
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86 <tertiary_color>${jbgen.tertiary_color}</tertiary_color>
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87 <quaternary_color>${jbgen.quaternary_color}</quaternary_color>
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88 <font_size>${jbgen.font_size}</font_size>
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89 <session_name>${jbgen.session_name}</session_name>
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90 </general>
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91 <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl>
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92 </metadata>
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93 <tracks>
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94 #for $tg in $track_groups:
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95 #for $track in $tg.data_tracks:
35
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96 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
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97 #if $track.data_format.data_format_select != "sparql":
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98 #for $dataset in $track.data_format.annotation:
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99 <files>
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100 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.name}">
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101 <metadata>
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102 <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}"
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103 size="${dataset.get_size(nice_size=True)}"
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104 edam_format="${dataset.datatype.edam_format}"
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105 file_ext="${dataset.ext}" />
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106 <history id="${__app__.security.encode_id($dataset.history_id)}"
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107 #if $dataset.history.user:
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108 user_email="${dataset.history.user.email}"
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109 user_id="${dataset.history.user_id}"
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110 display_name="${dataset.history.get_display_name()}"/>
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111 #else
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112 user_email="anonymous"
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113 user_id="-1"
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114 display_name="Unnamed History"/>
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115 #end if
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116 <metadata
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117 #for (key, value) in $dataset.get_metadata().items():
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118 #if "_types" not in $key and $value is not None and len(str($value)) < 5000:
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119 #if isinstance($value, list):
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120 #set value_str = "[%s]" % ','.join([str(val) for val in value])
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121 ${key}="$value_str"
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122 #else
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123 ${key}="${value}"
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124 #end if
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125 #end if
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126 #end for
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127 />
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128 <tool
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129 tool_id="${dataset.creating_job.tool_id}"
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130 tool_version="${dataset.creating_job.tool_version}"
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131 />
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132 </metadata>
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133 </trackFile>
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134 </files>
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135 #end for
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136 #else
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137 <track cat="${tg.category}" format="sparql" visibility="off">
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138 #end if
0
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139
35
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140 <options>
0
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141
35
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142 #if str($track.data_format.data_format_select) == "bam":
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143 <pileup>
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144 #for $dataset in $track.data_format.annotation:
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145 <bam_index>${dataset.metadata.bam_index}</bam_index>
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146 #end for
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147 </pileup>
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148 #else if str($track.data_format.data_format_select) == "cram":
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149 <cram>
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150 <cram_indices>
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151 #for $dataset in $track.data_format.annotation:
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152 <cram_index>${dataset.metadata.cram_index}</cram_index>
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153 #end for
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154 </cram_indices>
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155 </cram>
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156 #else if str($track.data_format.data_format_select) == "blastxml":
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157 <blast>
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158 #if str($track.data_format.blast_parent) != "":
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159 <parent>${track.data_format.blast_parent}</parent>
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160 #end if
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161 <protein>${track.data_format.is_protein}</protein>
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162 <min_gap>${track.data_format.min_gap}</min_gap>
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163 </blast>
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164 #else if str($track.data_format.data_format_select) == "gene_calls":
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165 <gff>
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166 #if $track.data_format.match_part.match_part_select == "true":
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167 <match>${track.data_format.match_part.name}</match>
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168 #end if
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169 </gff>
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170 #else if str($track.data_format.data_format_select) == "paf":
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171 <paf>
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172 <genome>
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173 #for gnome in $track.data_format.synteny_genome:
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174 $gnome,
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175 #end for
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176 </genome>
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177 <genome_label>
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178 #for gnome in $track.data_format.synteny_genome:
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179 $gnome.name,
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180 #end for
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181 </genome_label>
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182 </paf>
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183 #else if str($track.data_format.data_format_select) == "hic":
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184 <hic>
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185 </hic>
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186 #else if str($track.data_format.data_format_select) == "cool":
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187 <cool>
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188 </cool>
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189 #else if str($track.data_format.data_format_select) == "sparql":
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190 <label>${track.data_format.label}</label>
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191 <sparql>
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192 <url>${track.data_format.url}</url>
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193 <query>${track.data_format.query}</query>
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194 <query_refnames>${track.data_format.query_refnames}</query_refnames>
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195 </sparql>
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196 #end if
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197 </options>
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198 </track>
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199 #end for
31
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200 #end for
0
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201 </tracks>
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202 </root>
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203 ]]></configfile>
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204 </configfiles>
18
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205
0
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206 <inputs>
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207 <conditional name="reference_genome">
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208 <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select">
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209 <option selected="True" value="indexed">Use a built-in genome</option>
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210 <option value="history">Use a genome from history</option>
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211 </param>
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212 <when value="indexed">
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213 <param
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214 help="If your genome of interest is not listed, contact the Galaxy team"
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215 label="Select a reference genome"
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216 name="genome"
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217 type="select">
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218 <options from_data_table="all_fasta">
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219 <filter column="2" type="sort_by"/>
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220 <validator message="No genomes are available for the selected input dataset" type="no_options">
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221 </validator>
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222 </options>
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223 </param>
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224 </when>
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225 <when value="history">
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226 <param
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227 format="fasta"
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228 label="Select the reference genome"
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229 name="genome"
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230 type="data">
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231 </param>
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232 </when>
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233 </conditional>
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234
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235 <repeat name="track_groups" title="Track Group">
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236 <param label="Track Category"
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237 name="category"
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238 type="text"
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239 value="Default"
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240 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"/>
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241 <repeat name="data_tracks" title="Annotation Track">
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242 <conditional name="data_format" label="Track Data Selection Options">
0
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243 <param type="select" label="Track Type" name="data_format_select">
35
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244 <option value="bam">BAM Pileup track</option>
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245 <option value="bigwig">BigWig track</option>
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246 <option value="blastxml">Blast XML track - converted to GFF</option>
30
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247 <option value="cool">HiC as cool/mcool/scool format files</option>
0
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248 <option value="cram">CRAM</option>
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249 <option value="gene_calls" selected="true">GFF/GFF3/BED feature track</option>
30
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250 <option value="hic">HiC as juicebox_hic format file. Tabular hic_matrix will NOT work.</option>
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251 <option value="maf">Multiple alignment format. Reference name must match the MAF name exactly to work correctly</option>
21
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252 <option value="paf">PAF - approximate mapping positions between two set of sequences</option>
31
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253 <option value="vcf">VCF SNP</option>
0
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254 </param>
35
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255 <when value="blastxml">
0
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256 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" />
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257
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258 <param label="Features used in Blast Search"
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259 help="in GFF3. This is used so we know where to map features. E.g. where results of which CDS Protein32 match up to. The query IDs in your blast results should MATCH some feature IDs in your GFF3 file. This is an optional field and is most useful if using JBrowse to display protein blast results on a DNA genome. blastn results don't need this, blastp results on a protein sequence don't need this."
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260 format="gff3"
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261 name="blast_parent"
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262 optional="true"
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263 type="data"/>
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264
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265 <param label="Minimum Gap Size"
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266 help="before a new match_part feature is created"
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267 name="min_gap"
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268 type="integer"
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269 value="10"
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270 min="2" />
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271 <param label="Is this a protein blast search?"
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272 type="boolean"
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273 name="is_protein"
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274 truevalue="true"
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275 falsevalue="false" />
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276 <expand macro="track_visibility" />
19
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277 </when>
0
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278 <when value="vcf">
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279 <expand macro="input_conditional" label="SNP Track Data" format="vcf,vcf_bgzip" />
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280 <expand macro="track_styling_vcf"/>
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281 <expand macro="track_visibility" />
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282 </when>
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283 <when value="gene_calls">
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284 <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" />
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285 <conditional name="match_part" label="match/match_part data">
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286 <param help="Match part data selection " label="This is match/match_part data" name="match_part_select" type="select">
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287 <option selected="True" value="false">Not match/match part data</option>
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288 <option value="true">Match/match part data</option>
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289 </param>
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290 <when value="true">
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291 <param label="Match Part Feature Type"
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292 name="name"
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293 type="text"
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294 value="match"
27
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295 help="Match_parts have options for the parent feature type, such as cDNA_match, match, translated_nucleotide_match, etc. Please select the appropriate one here. You can leave empty to try autodetection (only works with CanvasFeatures track type)."
0
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296 optional="True"/>
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297 </when>
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298 <when value="false" />
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299 </conditional>
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300 <expand macro="track_visibility" />
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301 </when>
35
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diff changeset
302 <when value="bam">
0
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303 <expand macro="input_conditional" label="BAM Track Data" format="bam" />
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304 <expand macro="track_visibility" />
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305 </when>
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306 <when value="cram">
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307 <expand macro="input_conditional" label="CRAM Track Data" format="cram" />
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308 <expand macro="track_visibility" />
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309 </when>
19
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diff changeset
310 <when value="maf">
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311 <expand macro="input_conditional" label="MAF Track Data" format="maf" />
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diff changeset
312 <expand macro="track_visibility" />
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313 </when>
35
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diff changeset
314 <when value="bigwig">
0
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315 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" />
7
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diff changeset
316 <expand macro="track_visibility" />
0
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317 </when>
21
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318 <when value="paf">
35
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diff changeset
319 <param label="Comparison genome sequence" help="Paf from these as the reference(s), using the common reference as the reads to map"
0
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320 format="fasta"
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321 name="synteny_genome"
31
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diff changeset
322 type="data"
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diff changeset
323 multiple="True"/>
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324 <expand macro="input_conditional" label="Synteny data" format="paf" help="Make paf with mashmap or minimap2 mapping real reference onto desired syntenic references"/>
0
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325 <expand macro="track_visibility" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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326 </when>
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327
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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328 <when value="hic">
27
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329 <expand macro="input_conditional" label="Binary Juicebox HiC data" format="hic,juicebox_hic" />
0
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330 <expand macro="track_visibility" />
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331 </when>
23
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332 <when value="cool">
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diff changeset
333 <expand macro="input_conditional" label="HiC data in cool/mcool/scool format" format="cool,mcool,scool" />
39b717d934a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty
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334 <expand macro="track_visibility" />
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diff changeset
335 </when>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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336 </conditional>
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337 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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338 </repeat>
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339
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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340 <expand macro="general_options" />
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341
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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342 <param type="hidden" name="uglyTestingHack" value="" />
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343 </inputs>
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344 <outputs>
31
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diff changeset
345 <data format="html" name="output" label="JBrowse2 on $reference_genome.genome.name">
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diff changeset
346 <change_format>
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diff changeset
347 <when input="zipOut" value="true" format="zip" />
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348 </change_format>
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diff changeset
349 </data>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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350 </outputs>
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351 <tests>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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352 <test>
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353 <param name="reference_genome|genome_type_select" value="history"/>
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354 <param name="reference_genome|genome" value="merlin.fa"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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355 <repeat name="track_groups">
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356 <param name="category" value="Default" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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357 <repeat name="data_tracks">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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358 <conditional name="data_format">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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359 <param name="data_format_select" value="wiggle"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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360 <param name="annotation" value="bw/merlin.bw"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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361 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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362 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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363 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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364 <param name="uglyTestingHack" value="enabled" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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365 <output name="output">
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366 <assert_contents>
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367 <has_text text="genome path="></has_text>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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368 <has_text text="dataset id="></has_text>
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369 <has_text text="history id="></has_text>
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370 <has_text text="metadata"></has_text>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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371 <has_text text="tool_id"></has_text>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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372 <has_text text="trackFile path="></has_text>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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373 <has_text text="file_ext=&quot;bigwig&quot;"></has_text>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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374 <has_text text="format=&quot;wiggle&quot;"></has_text>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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375 </assert_contents>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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376 </output>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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377 </test>
31
cb4b32ca9968 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
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diff changeset
378
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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379 <test>
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380 <param name="reference_genome|genome_type_select" value="history"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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381 <param name="reference_genome|genome" value="merlin.fa"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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382 <repeat name="track_groups">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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383 <param name="category" value="Default" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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384 <repeat name="data_tracks">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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385 <conditional name="data_format">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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386 <param name="data_format_select" value="vcf"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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387 <param name="annotation" value="vcf/merlin.vcf"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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388 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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389 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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390 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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391 <param name="uglyTestingHack" value="enabled" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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392 <output name="output">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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393 <assert_contents>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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394 <has_text text="genome path="></has_text>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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395 <has_text text="dataset id="></has_text>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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396 <has_text text="history id="></has_text>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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397 <has_text text="metadata"></has_text>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
398 <has_text text="tool_id"></has_text>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
399 <has_text text="trackFile path="></has_text>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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400 <has_text text="ext=&quot;vcf&quot; label=&quot;merlin.vcf&quot;"></has_text>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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401 </assert_contents>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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402 </output>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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403 </test>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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404 <test>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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405 <param name="reference_genome|genome_type_select" value="history"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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406 <param name="reference_genome|genome" value="merlin.fa"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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407 <param name="uglyTestingHack" value="enabled" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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408 <output name="output">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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409 <assert_contents>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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410 <has_text text="genome path="></has_text>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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411 <has_text text="dataset id="></has_text>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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412 <has_text text="history id="></has_text>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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413 <has_text text="metadata"></has_text>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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414 <has_text text="tool_id"></has_text>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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415 </assert_contents>
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416 </output>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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417 </test>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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418 <test>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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419 <param name="reference_genome|genome_type_select" value="history"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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420 <param name="reference_genome|genome" value="merlin.fa"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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421 <repeat name="track_groups">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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422 <param name="category" value="Default" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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423 <repeat name="data_tracks">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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424 <conditional name="data_format">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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425 <param name="data_format_select" value="gene_calls"/>
34
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diff changeset
426 <param name="annotation" value="bed/test-3.bed"/>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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427 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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428 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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429 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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430 <param name="uglyTestingHack" value="enabled" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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431 <output name="output">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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432 <assert_contents>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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433 <has_text text="genome path="></has_text>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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434 <has_text text="dataset id="></has_text>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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435 <has_text text="history id="></has_text>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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436 <has_text text="metadata"></has_text>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
437 <has_text text="tool_id"></has_text>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
438 <has_text text="trackFile path="></has_text>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
439 <has_text text="ext=&quot;bed&quot; label=&quot;test-3.bed&quot;"></has_text>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
440 </assert_contents>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
441 </output>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
442 </test>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
443 <test>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
444 <param name="reference_genome|genome_type_select" value="history"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
445 <param name="reference_genome|genome" value="merlin.fa"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
446 <repeat name="track_groups">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
447 <param name="category" value="Auto Coloured" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
448 <repeat name="data_tracks">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
449 <conditional name="data_format">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
450 <param name="data_format_select" value="gene_calls"/>
34
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parents: 33
diff changeset
451 <param name="annotation" value="gff3/A.gff"/>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
452 <conditional name="match_part">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff changeset
453 <param name="match_part_select" value="false"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
454 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
455 <section name="jbcolor_scale">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
456 <conditional name="color_score">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
457 <param name="color_score_select" value="none"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
458 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
459 <conditional name="color">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
460 <param name="color_select" value="automatic"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff changeset
461 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff changeset
462 </section>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
463 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
464 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
465 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
466
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
467 <repeat name="track_groups">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
468 <param name="category" value="Ignore Scale" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
469 <repeat name="data_tracks">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
470 <conditional name="data_format">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
471 <param name="data_format_select" value="gene_calls"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
472 <param name="annotation" value="gff3/1.gff"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
473 <conditional name="match_part">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
474 <param name="match_part_select" value="false"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
475 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
476 <section name="jbcolor_scale">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
477 <conditional name="color_score">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
478 <param name="color_score_select" value="none"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
479 <conditional name="color">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
480 <param name="color_select" value="manual"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
481 <param name="style_color" value="#ff00ff"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff changeset
482 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff changeset
483 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
484 </section>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff changeset
485 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
486 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
487 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
488
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
489 <repeat name="track_groups">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
490 <param name="category" value="Scaled Colour" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
491 <repeat name="data_tracks">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
492 <conditional name="data_format">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff changeset
493 <param name="data_format_select" value="gene_calls"/>
34
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fubar
parents: 33
diff changeset
494 <param name="annotation" value="gff3/C.gff"/>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
495 <conditional name="match_part">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
496 <param name="match_part_select" value="false"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
497 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
498 <section name="jbcolor_scale">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
499 <conditional name="color_score">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
500 <param name="color_score_select" value="score"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
501 <param name="score_scaling" value="linear"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
502 <conditional name="score_scales">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
503 <param name="scale_select" value="automatic"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
504 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
505 <conditional name="color_scheme">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
506 <param name="score_scheme" value="opacity"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
507 <conditional name="color">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
508 <param name="color_select" value="automatic"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff changeset
509 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
510 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
511 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
512 </section>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff changeset
513 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
514 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
515 <repeat name="data_tracks">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
516 <conditional name="data_format">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
517 <param name="data_format_select" value="gene_calls"/>
34
2893ef33fba9 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd
fubar
parents: 33
diff changeset
518 <param name="annotation" value="gff3/B.gff"/>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
519 <conditional name="match_part">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
520 <param name="match_part_select" value="false"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
521 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
522 <section name="jbcolor_scale">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
523 <conditional name="color_score">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
524 <param name="color_score_select" value="score"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
525 <param name="score_scaling" value="linear"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
526 <conditional name="score_scales">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
527 <param name="scale_select" value="automatic"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
528 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
529 <conditional name="color_scheme">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
530 <param name="score_scheme" value="opacity"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
531 <conditional name="color">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
532 <param name="color_select" value="manual"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
533 <param name="style_color" value="#0000ff"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
534 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
535 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
536 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
537 </section>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
538 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
539 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
540 <repeat name="data_tracks">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
541 <conditional name="data_format">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
542 <param name="data_format_select" value="gene_calls"/>
34
2893ef33fba9 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd
fubar
parents: 33
diff changeset
543 <param name="annotation" value="gff3/A.gff"/>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
544 <conditional name="match_part">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
545 <param name="match_part_select" value="false"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
546 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
547 <section name="jbcolor_scale">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
548 <conditional name="color_score">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
549 <param name="color_score_select" value="score"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
550 <param name="score_scaling" value="linear"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
551 <conditional name="score_scales">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
552 <param name="scale_select" value="manual"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
553 <param name="minimum" value="0"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
554 <param name="maximum" value="1000"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
555 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
556 <conditional name="color_scheme">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
557 <param name="score_scheme" value="opacity"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
558 <conditional name="color">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
559 <param name="color_select" value="automatic"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
560 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
561 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
562 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
563 </section>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
564 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
565 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
566 <repeat name="data_tracks">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
567 <conditional name="data_format">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
568 <param name="data_format_select" value="gene_calls"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
569 <param name="annotation" value="gff3/1.gff"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
570 <conditional name="match_part">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
571 <param name="match_part_select" value="false"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
572 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
573 <section name="jbcolor_scale">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
574 <conditional name="color_score">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
575 <param name="color_score_select" value="score"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
576 <param name="score_scaling" value="linear"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
577 <conditional name="score_scales">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
578 <param name="scale_select" value="manual"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
579 <param name="minimum" value="0"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
580 <param name="maximum" value="1000"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
581 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
582 <conditional name="color_scheme">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
583 <param name="score_scheme" value="opacity"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
584 <conditional name="color">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
585 <param name="color_select" value="manual"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
586 <param name="style_color" value="#ff0000"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
587 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
588 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
589 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
590 </section>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
591 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
592 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
593 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
594
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
595 <repeat name="track_groups">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
596 <param name="category" value="Realistic" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
597 <repeat name="data_tracks">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
598 <conditional name="data_format">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
599 <param name="data_format_select" value="gene_calls"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
600 <param name="annotation" value="gff3/interpro.gff"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
601 <conditional name="match_part">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
602 <param name="match_part_select" value="false"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
603 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
604 <section name="jbcolor_scale">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
605 <conditional name="color_score">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
606 <param name="color_score_select" value="none"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
607 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
608 <conditional name="color">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
609 <param name="color_select" value="automatic"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
610 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
611 </section>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
612 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
613 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
614 <repeat name="data_tracks">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
615 <conditional name="data_format">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
616 <param name="data_format_select" value="gene_calls"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
617 <param name="annotation" value="gff3/2.gff"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
618 <conditional name="match_part">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
619 <param name="match_part_select" value="true"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
620 <param name="name" value="cDNA_match"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
621 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
622 <section name="jbcolor_scale">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
623 <conditional name="color_score">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
624 <param name="color_score_select" value="none"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
625 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
626 <conditional name="color">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
627 <param name="color_select" value="automatic"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
628 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
629 </section>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
630 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
631 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
632 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
633
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
634 <param name="uglyTestingHack" value="enabled" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
635 <output name="output">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
636 <assert_contents>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
637 <has_text text="Auto Coloured"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
638 <has_text text="A.gff"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
639 <has_text text="B.gff"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
640 <has_text text="C.gff"/>
34
2893ef33fba9 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd
fubar
parents: 33
diff changeset
641 <has_text text="interpro.gff"/>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
642 <has_text text="Scaled Colour"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
643 <has_text text="1.gff"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
644 <has_text text="2.gff"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
645 </assert_contents>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
646 </output>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
647 </test>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
648 <test>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
649 <param name="reference_genome|genome_type_select" value="history"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
650 <param name="reference_genome|genome" value="merlin.fa"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
651
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
652 <repeat name="track_groups">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
653 <param name="category" value="With menu or index" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
654 <repeat name="data_tracks">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
655 <conditional name="data_format">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
656 <param name="data_format_select" value="gene_calls"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
657 <param name="annotation" value="gff3/1.gff"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
658 <conditional name="match_part">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
659 <param name="match_part_select" value="false"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
660 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
661 <section name="jbcolor_scale">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
662 <conditional name="color_score">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
663 <param name="color_score_select" value="none"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
664 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
665 <conditional name="color">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
666 <param name="color_select" value="automatic"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
667 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
668 </section>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
669 <section name="jbmenu">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
670 <repeat name="track_menu">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
671 <param name="menu_action" value="iframeDialog"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
672 <param name="menu_label" value="Some menu item"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
673 <param name="menu_title" value="Frame title"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
674 <param name="menu_url" value="https://example.com/#!/?id={name}&amp;q={type}&amp;z=&quot;{end}&quot;"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
675 <param name="menu_icon" value="dijitIconNewTask"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
676 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
677 <repeat name="track_menu">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
678 <param name="menu_action" value="newWindow"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
679 <param name="menu_label" value="Another menu item"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
680 <param name="menu_title" value="Frame title 2"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
681 <param name="menu_url" value="https://example.com/#!/?id={name}&amp;q={type}&amp;z=&quot;{end}&quot;"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
682 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
683 </section>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
684 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
685 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
686 <repeat name="data_tracks">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
687 <conditional name="data_format">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
688 <param name="data_format_select" value="gene_calls"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
689 <param name="annotation" value="gff3/1.gff"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
690 <conditional name="match_part">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
691 <param name="match_part_select" value="false"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
692 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
693 <section name="jbcolor_scale">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
694 <conditional name="color_score">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
695 <param name="color_score_select" value="none"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
696 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
697 <conditional name="color">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
698 <param name="color_select" value="automatic"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
699 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
700 </section>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
701 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
702 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
703 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
704
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
705 <param name="uglyTestingHack" value="enabled" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
706 <output name="output">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
707 <assert_contents>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff changeset
708 <has_text text="With menu or index"/>
7
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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parents: 5
diff changeset
709 <has_text text="gene_calls"/>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
710 </assert_contents>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
711 </output>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff changeset
712 </test>
31
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parents: 30
diff changeset
713
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff changeset
714 <!-- TODO add a synteny test -->
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff changeset
715 <!-- TODO add a bam and a cram test -->
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff changeset
716 <!-- TODO add an hic test -->
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff changeset
717 <!-- TODO add a vcf_bgzip test -->
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
718 </tests>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
719 <help><![CDATA[
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
720
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
721 JBrowse2-in-Galaxy
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff changeset
722 ==================
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
723
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff changeset
724 JBrowse2-in-Galaxy offers a highly configurable, workflow-compatible
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
725 alternative to JBrowse1-in-Galaxy and Trackster.
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff changeset
726
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
727 Compared to JBrowse1-in-Galaxy, there is no support for alternative codons for unusual genomes,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
728 and detailed track styling is not yet implemented. Send code.
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
729 JBrowse1 development has now ceased in favour of JBrowse2.
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff changeset
730
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
731 Use and local viewing
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
732 =====================
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
733
7
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents: 5
diff changeset
734
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
735 A JBrowse2 history item can be opened by viewing it (the "eye" icon).
7
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents: 5
diff changeset
736
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents: 5
diff changeset
737 The same browser data and setup can also be downloaded as a compressed zip archive by clicking the download ("floppy disk") icon in the history.
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents: 5
diff changeset
738 This can be shared and viewed without Galaxy.
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
739
7
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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parents: 5
diff changeset
740 A replacement application to serve the browser is required without Galaxy. A local python web server can be started using a script included in each archive,
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents: 5
diff changeset
741 assuming that Python3 is already working on your desktop - if not you will have to install it first. Unzip the archive (*unzip [filename].zip*) and change
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents: 5
diff changeset
742 directory to the first level in that zip archive. It contains a file named *jb2_webserver.py*
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
743
7
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents: 5
diff changeset
744 With python3 installed,
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
745
7
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents: 5
diff changeset
746 *python3 jb2_webserver.py*
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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parents: 5
diff changeset
747
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents: 5
diff changeset
748 will serve the unarchived JBrowse2 configuration from the same directory as the python script automatically. If a new browser window does not open,
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents: 5
diff changeset
749 but the script appears to be running, try pointing your web browser to the default of *localhost:8080*
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
750
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
751 Overview
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
752 --------
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
753
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff changeset
754 JBrowse is a fast, embeddable genome browser built completely with
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
755 JavaScript and HTML5.
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
756
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff changeset
757 The JBrowse-in-Galaxy (JiG) tool was written to help build complex
7
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents: 5
diff changeset
758 JBrowse installations straight from Galaxy. It allows you to build up a JBrowse instance without worrying
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff changeset
759 about how to run the command line tools to format your data, and which
7
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents: 5
diff changeset
760 options need to be supplied and where.
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff changeset
761
17
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents: 16
diff changeset
762 The JBrowse-in-Galaxy tool has been rejected by `a Galaxy IUC
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents: 16
diff changeset
763 <https://github.com/galaxyproject/tools-iuc/issues>`__, reviewer.
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents: 16
diff changeset
764 It is maintained by https://github.com/fubar2 who you can help you
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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parents: 16
diff changeset
765 with missing features or bugs in the tool. For the record, he remains unconvinced by the reviewer's logic,
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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parents: 16
diff changeset
766 and disturbed by the distinctly coercive approach to introducing new code,
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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parents: 16
diff changeset
767 compared to the more usual method of providing a working PR.
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
768
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff changeset
769 Options
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
770 -------
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
771
17
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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parents: 16
diff changeset
772 **Reference or Assembly**
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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parents: 16
diff changeset
773
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents: 16
diff changeset
774 Choose either a built-in or select one from your history.
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
775
17
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents: 16
diff changeset
776 Track coordinates and contig names *must* match this reference precisely
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents: 16
diff changeset
777 or they will not display.
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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parents: 16
diff changeset
778
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents: 16
diff changeset
779 **Track Groups** represent a set of tracks in a single category.
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff changeset
780
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff changeset
781 Annotation Tracks
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
782 -----------------
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
783
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff changeset
784 GFF3/BED
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff changeset
785 ~~~~~~~~
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
786
17
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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parents: 16
diff changeset
787 Standard feature tracks. They usually highlight genes, mRNAs and other features of interest along a genomic region.
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
788
5
efc64d8f4b72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9
fubar
parents: 3
diff changeset
789 When these contain tens of millions of features, such as repeat regions from a VGP assembly, displaying one at a time leads
efc64d8f4b72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9
fubar
parents: 3
diff changeset
790 to extremely slow loading times when a large region is in view, unless the "LinearPileupDisplay" display option is
efc64d8f4b72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9
fubar
parents: 3
diff changeset
791 selected for that track in the styling options section. The default is LinearBasicDisplay, which shows all details and works
17
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents: 16
diff changeset
792 well for relatively sparse bed files. A better option is to make a bigwig track using a set of windows based on the
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents: 16
diff changeset
793 lengths of each assembly or reference contig.
5
efc64d8f4b72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9
fubar
parents: 3
diff changeset
794
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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795 BAM Pileups
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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796 ~~~~~~~~~~~
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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797
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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798 We support BAM files and can automatically generate SNP tracks based on
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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799 that bam data.
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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800
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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801
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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802 BlastXML
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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803 ~~~~~~~~
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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804
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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805 JiG now supports both blastn and blastp datasets. JiG internally uses a
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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806 blastXML to gapped GFF3 tool to convert your blastxml datasets into a
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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807 format amenable to visualization in JBrowse. This tool is also
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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808 available separately from the IUC on the toolshed.
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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809
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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810 **Minimum Gap Size** reflects how long a gap must be before it becomes a
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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811 real gap in the processed gff3 file. In the picture above, various sizes
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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812 of gaps can be seen. If the minimum gap size was set much higher, say
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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813 100nt, many of the smaller gaps would disappear, and the features on
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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814 both sides would be merged into one, longer feature. This setting is
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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815 inversely proportional to runtime and output file size. *Do not set this
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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816 to a low value for large datasets*. By setting this number lower, you
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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817 will have extremely large outputs and extremely long runtimes. The
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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818 default was configured based off of the author's experience, but the
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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819 author only works on small viruses. It is *strongly* recommended that
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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820 you filter your blast results before display, e.g. picking out the top
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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821 10 hits or so.
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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822
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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823 **Protein blast search** option merely informs underlying tools that
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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824 they should adjust feature locations by 3x.
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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825
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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826
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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827 @ATTRIBUTION@
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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828 ]]></help>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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829 <expand macro="citations"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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830 </tool>