Mercurial > repos > fubar > jbrowse2

annotate jbrowse2.xml @ 112:56f9a6e0fe80 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 566509061b742b73c8dd1a1db6813fbf6a7a3792
author bgruening
date Thu, 04 Jul 2024 08:40:21 +0000
parents 5d1259b88c27
children 878c27dfea9d
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1 <tool id="jbrowse2" name="JBrowse2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" 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 <required_files>
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12 <include path="autogenJB2.py"/>
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13 <include path="blastxml_to_gapped_gff3.py"/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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14 <include path="convertMAF.sh"/>
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15 <include path="gff3_rebase.py"/>
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16 <include path="jb2_webserver.py"/>
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17 <include path="jbrowse2.py"/>
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18 <include path="maf2bed.py"/>
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19 </required_files>
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20 <version_command>python '${__tool_directory__}/jbrowse2.py' --version</version_command>
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21 <command detect_errors="aggressive"><![CDATA[
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22 mkdir -p '$output.files_path' &&
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23 cp '$trackxml' '$output.files_path/galaxy.xml' &&
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24 export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2 &&
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25 #if $jbgen.ucol.formcoll=="collect":
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26 python '$__tool_directory__/autogenJB2.py'
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27 #for $key in $autoCollection.keys():
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28 #if $autoCollection[$key].is_collection:
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29 #set subCol=$autoCollection[$key]
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30 #set pafs=[($subCol[x],$subcol[x].ext,x) for x in $subCol.keys() if $subCol[x].ext == 'paf']
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31 #set refs=[($subCol[x],$subcol[x].ext,x) for x in $subCol.keys() if $subCol[x].ext in ['fasta.gz','fasta']]
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32 #if len($pafs) > 0:
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33 --pafmeta '$pafs[0]'
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34 #for $ref in $refs:
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35 --pafreferencemeta '$ref'
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36 #end for
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37 #end if
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38 #else if $autoCollection[$key].ext == 'fasta':
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39 --referencemeta '$autoCollection[$key],$autoCollection[$key].ext,$key'
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40 #else if $autoCollection[$key].ext in ['bed', 'bigwig', 'cool', 'gff', 'gff3', 'hic', 'maf', 'mcool', 'scool', 'vcf']
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41 --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key'
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42 #else if $autoCollection[$key].ext in ['bam',]
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43 --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key,$autoCollection[$key].metadata.bam_index'
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44 #else if $autoCollection[$key].ext in ['cram',]
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45 --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key,$autoCollection[$key].metadata.cram_index'
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46 #end if
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47 #end for
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48 --outdir '$output.files_path'
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49 --jbrowse2path \${JBROWSE2_PATH}
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50 --sessName "Autogen JBrowse" &&
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51 #if $jbgen.zipOut == "true":
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52 cd '$output.files_path' &&
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53 zip -r - . > '$output'
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54 #else
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55 cp '$output.files_path/index.html' '$output'
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56 #end if
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57 #else:
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58 python '$__tool_directory__/jbrowse2.py'
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59 --jbrowse2path \${JBROWSE2_PATH}
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60 --outdir '$output.files_path'
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61 --xml '$trackxml' &&
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62 #if $jbgen.zipOut == "true":
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63 cd '$output.files_path' &&
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64 zip -r - . > '$output'
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65 #else
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66 cp '$output.files_path/index.html' '$output'
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67 #end if
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68 #end if
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69 ]]></command>
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70 <configfiles>
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71 <configfile name="trackxml"><![CDATA[<?xml version="1.0"?>
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72 <root>
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73 <metadata>
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74 <general>
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75 <defaultLocation>${jbgen.defaultLocation}</defaultLocation>
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76 <zipOut>${jbgen.zipOut}</zipOut>
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77 <bpPerPx>${jbgen.bpPerPx}</bpPerPx>
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78 <analytics>${jbgen.enableAnalytics}</analytics>
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79 <primary_color>${jbgen.primary_color}</primary_color>
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80 <secondary_color>${jbgen.secondary_color}</secondary_color>
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81 <tertiary_color>${jbgen.tertiary_color}</tertiary_color>
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82 <quaternary_color>${jbgen.quaternary_color}</quaternary_color>
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83 <font_size>${jbgen.font_size}</font_size>
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84 <session_name>${jbgen.session_name}</session_name>
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85 </general>
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86 <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl>
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87 </metadata>
62
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88 #if $jbgen.ucol.formcoll=="form":
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89 #for $assembly in $assemblies:
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90 <assembly>
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91 <metadata>
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92 <genomes>
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93 #if str($assembly.reference_genome.genome_type_select) == "uri":
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94 <genome path="${assembly.reference_genome.uri}" label="${assembly.reference_genome.refname}" useuri="yes">
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95 <metadata>
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96 <dataset
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97 dname = "${assembly.reference_genome.refname}" />
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98 </metadata>
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99 </genome>
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100 #else if str($assembly.reference_genome.genome_type_select) == "indexed":
87
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101 <genome path="${assembly.reference_genome.genome.fields.path}" label="${assembly.reference_genome.genome.fields.dbkey}" useuri="no">
62
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102 <metadata>
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103 <dataset
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104 dname = "${assembly.reference_genome.genome.fields.name}" />
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105 </metadata>
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106 </genome>
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107 #else
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108 <genome path="$assembly.reference_genome.genome" label="${assembly.reference_genome.genome.name}" useuri="no">
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109 <metadata>
88
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110
62
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111 <dataset id="${__app__.security.encode_id($assembly.reference_genome.genome.id)}"
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112 hid="${assembly.reference_genome.genome.hid}"
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113 size="${assembly.reference_genome.genome.get_size(nice_size=True)}"
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114 edam_format="${assembly.reference_genome.genome.datatype.edam_format}"
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115 file_ext="${assembly.reference_genome.genome.ext}"
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116 dname = "${assembly.reference_genome.genome.name}"
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117 />
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118 <history
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119 #if $assembly.reference_genome.genome.history.user:
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120 user_email="${assembly.reference_genome.genome.history.user.email}"
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121 user_id="${assembly.reference_genome.genome.history.user_id}"
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122 display_name="${assembly.reference_genome.genome.history.get_display_name()}"/>
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123 #else
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124 user_email="anonymous"
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125 user_id="-1"
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126 display_name="Unnamed History"
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127 #end if
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128 id="${__app__.security.encode_id($assembly.reference_genome.genome.history_id)}"
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129 />
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130 <metadata
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131 #for (key, value) in $assembly.reference_genome.genome.get_metadata().items():
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132 #if "_types" not in $key:
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133 #if isinstance($value, list):
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134 #set value_str = "[%s]" % ','.join([str(val) for val in value])
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135 ${key}="$value_str"
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136 #else
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137 ${key}="${value}"
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138 #end if
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139 #end if
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140 #end for
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141 />
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142 <tool
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143 tool_id="${assembly.reference_genome.genome.creating_job.tool_id}"
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144 tool_version="${assembly.reference_genome.genome.creating_job.tool_version}"
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145 />
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146 </metadata>
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147 </genome>
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148 #end if
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149 </genomes>
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150 </metadata>
0
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151 <tracks>
62
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152 #for $tg in $assembly.track_groups:
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153 #for $track in $tg.data_tracks:
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154 #set input_exists = "False"
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155 #if $track.data_format.useuri.insource == "uri":
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156 #if $track.data_format.useuri.annouri:
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157 #set input_exists = "True"
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158 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
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159 <files>
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160 <trackFile path="${track.data_format.useuri.annouri}" ext="${track.data_format.data_format_select}"
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161 label="${track.data_format.useuri.annoname}" useuri="yes">
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162 <metadata>
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163 <dataset id = "${track.data_format.useuri.annouri}" />
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164 </metadata>
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165 </trackFile>
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166 </files>
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167 #end if
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168 #else if $track.data_format.useuri.insource == "history":
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169 #if $track.data_format.useuri.annotation:
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170 #set input_exists = "True"
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171 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
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172 <files>
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173 #for $dataset in $track.data_format.useuri.annotation:
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174 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.name}" useuri="no">
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175 <metadata>
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176 <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}"
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177 size="${dataset.get_size(nice_size=True)}"
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178 edam_format="${dataset.datatype.edam_format}"
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179 file_ext="${dataset.ext}" />
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180 <history id="${__app__.security.encode_id($dataset.history_id)}"
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181 #if $dataset.history.user:
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182 user_email="${dataset.history.user.email}"
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183 user_id="${dataset.history.user_id}"
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184 display_name="${dataset.history.get_display_name()}"/>
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185 #else
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186 user_email="anonymous"
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187 user_id="-1"
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188 display_name="Unnamed History"/>
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189 #end if
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190 <metadata
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191 #for (key, value) in $dataset.get_metadata().items():
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192 #if "_types" not in $key and $value is not None and len(str($value)) < 5000:
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193 #if isinstance($value, list):
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194 #set value_str = "[%s]" % ','.join([str(val) for val in value])
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195 ${key}="$value_str"
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196 #else
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197 ${key}="${value}"
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198 #end if
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199 #end if
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200 #end for
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201 />
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202 <tool
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203 tool_id="${dataset.creating_job.tool_id}"
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204 tool_version="${dataset.creating_job.tool_version}"
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205 />
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206 </metadata>
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207 </trackFile>
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208 #end for
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209 </files>
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210 #end if
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211 #end if
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212 #if $input_exists == "True":
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213 <options>
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214 <style>
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215 #if str($track.data_format.data_format_select) in ["gff", "bed", "maf", "blastxml"]:
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216 <type>${track.data_format.jbstyle.display}</type>
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217 #if str($track.data_format.jbstyle.display) in ["LinearBasicDisplay", "LinearVariantDisplay"]:
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218 <trackShowLabels>${track.data_format.jbstyle.show_labels}</trackShowLabels>
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219 <trackShowDescriptions>${track.data_format.jbstyle.show_descriptions}</trackShowDescriptions>
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220 #end if
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221 #else if str($track.data_format.data_format_select) == "vcf":
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222 <type>${track.data_format.jbstyle.track_style.display}</type>
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223 #if str($track.data_format.jbstyle.track_style.display) in ["LinearBasicDisplay", "LinearVariantDisplay"]:
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224 <trackShowLabels>${track.data_format.jbstyle.track_style.show_labels}</trackShowLabels>
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225 <trackShowDescriptions>${track.data_format.jbstyle.track_style.show_descriptions}</trackShowDescriptions>
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226 #end if
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227 #else if str($track.data_format.data_format_select) == "bigwig":
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228 <type>${track.data_format.jbstyle.track_style.display}</type>
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229 <color>${track.data_format.jbstyle.track_style.color}</color>
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230 <autoscale>${track.data_format.jbstyle.track_style.autoscale}</autoscale>
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231 <resolution>${track.data_format.jbstyle.track_style.resolution}</resolution>
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232 <summaryScoreMode>${track.data_format.jbstyle.track_style.summaryScoreMode}</summaryScoreMode>
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233 <filled>${track.data_format.jbstyle.track_style.filled}</filled>
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234 <scaleType>${track.data_format.jbstyle.track_style.scaleType}</scaleType>
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235 <displayCrossHatches>${track.data_format.jbstyle.track_style.displayCrossHatches}</displayCrossHatches>
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236 <minScore>${track.data_format.jbstyle.track_style.minScore}</minScore>
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237 <maxScore>${track.data_format.jbstyle.track_style.maxScore}</maxScore>
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238 #end if
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239 #if str($track.data_format.data_format_select) in ["bam", "cram"]:
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240 <type>LinearAlignmentsDisplay</type>
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241 #end if
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242 #if str($track.data_format.data_format_select) in ["hic", "cool", "mcool", "scool"]:
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243 <type>LinearHicDisplay</type>
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244 #end if
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245 </style>
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246 #if str($track.data_format.data_format_select) == "bam":
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247 <bam>
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248 <bam_index>
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249 #for $dataset in $track.data_format.useuri.annotation:
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250 ${dataset} ~ ${dataset.metadata.bam_index},
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251 #end for
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252 </bam_index>
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253 </bam>
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254 #else if str($track.data_format.data_format_select) == "cram":
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255 <cram>
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256 <cram_index>
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257 #for $dataset in $track.data_format.useuri.annotation:
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258 ${dataset} ~ ${dataset.metadata.cram_index},
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259 #end for
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260 </cram_index>
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261 </cram>
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262 #else if str($track.data_format.data_format_select) == "blastxml":
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263 <blast>
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264 #if str($track.data_format.blast_parent) != "":
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265 <parent>${track.data_format.blast_parent}</parent>
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266 #end if
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267 <protein>${track.data_format.is_protein}</protein>
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268 <min_gap>${track.data_format.min_gap}</min_gap>
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269 </blast>
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270 #else if str($track.data_format.data_format_select) == "gff":
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271 <gff>
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272 #if $track.data_format.match_part.match_part_select == "true":
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273 <match>${track.data_format.match_part.name}</match>
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274 #end if
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275 </gff>
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276 #else if str($track.data_format.data_format_select) == "paf":
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277 <paf>
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278 #if str($track.data_format.pafuseuri.insource) == "history":
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279 <genome>
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280 #for $anno in $track.data_format.pafuseuri.annotation:
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281 ${anno} ~ ${anno.name},
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282 #end for
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283 </genome>
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284 <useuri>
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285 false
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286 </useuri>
88
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287 #else:
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288 <genome>
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289 #for $refgenome in $track.data_format.pafuseuri.refuri:
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290 ${refgenome.annotation} ~ ${refgenome.annoname},
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291 #end for
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292 </genome>
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293 <useuri>
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294 true
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295 </useuri>
88
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296 #end if
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297 </paf>
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298 #else if str($track.data_format.data_format_select) == "hic":
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299 <hic>
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300 </hic>
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301 #else if str($track.data_format.data_format_select) == "cool":
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302 <cool>
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303 </cool>
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304 #else if str($track.data_format.data_format_select) == "bed":
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305 <bed>
108
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306 <usebedscore>${track.data_format.jbstyle.usebedscore}</usebedscore>
88
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307 </bed>
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308 #else if str($track.data_format.data_format_select) == "sparql":
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309 <label>${track.data_format.label}</label>
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310 <sparql>
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311 <url>${track.data_format.url}</url>
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312 <query>${track.data_format.query}</query>
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313 <query_refnames>${track.data_format.query_refnames}</query_refnames>
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314 </sparql>
62
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315 #end if
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316 </options>
46
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317 </track>
88
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318 #end if
46
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319 #end for
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320 #end for
0
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321 </tracks>
62
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322 </assembly>
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323 #end for
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324 #end if
0
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325 </root>
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326 ]]></configfile>
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327 </configfiles>
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328 <inputs>
99
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329 <repeat name="assemblies" min="1" title="Genome for a set of tracks" help="Tracks will display on this genome coordinates so must all match. Multiple genomes with their own sets of tracks can be added">
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330 <conditional name="reference_genome">
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331 <param name="genome_type_select" type="select" label="Reference genome source" help="Select a built in, history or remote tabix URI for the reference track">
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332 <option selected="True" value="indexed">Use a Galaxy server built-in genome</option>
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333 <option value="history">Use a genome fasta file from the current history</option>
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334 <option value="uri">Provide a URI (e.g. "https://..." for a genome reference as
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335 tabix bgzip with predictable index file URI</option>
0
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336 </param>
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337 <when value="indexed">
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338 <param name="genome" type="select" optional="true" label="Select a built in reference genome or custom genome" help="If not listed, add a custom genome, use a history genome or a remote URI tabix genome">
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339 <options from_data_table="all_fasta">
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340 <filter column="2" type="sort_by"/>
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341 <validator message="No genomes are available for the selected input dataset" type="no_options"/>
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342 </options>
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343 </param>
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344 </when>
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345 <when value="history">
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346 <param name="genome" type="data" format="fasta" optional="true" label="Select the reference genome"/>
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347 </when>
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348 <when value="uri">
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349 <param name="uri" type="text" label="URI pointing to tabix compressed fasta - must always be on-line"
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350 help="Warning: Requires an internet connection to view. If this URI is not available for any reason, the track will show an error. Saves disk storage">
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351 </param>
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352 <param name="refname" type="text" label="Reference dbkey for tracks with this genome, such as hg38 or SacCer4"/>
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353 </when>
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354 </conditional>
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355 <repeat name="track_groups" title="Track Group">
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356 <param name="category" type="text" value="Default" optional="False" label="Track Category" 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."/>
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357 <repeat name="data_tracks" title="Annotation Track">
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358 <conditional name="data_format" label="Track Data Selection Options">
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359 <param name="data_format_select" type="select" label="Track Type">
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360 <option value="bam">BAM track. Recommend converting to BED/bigWig unless mapping annotation needed</option>
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361 <option value="bed">BED track</option>
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362 <option value="bigwig">BigWig track</option>
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363 <option value="blastxml">Blast XML track (as GFF3)</option>
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364 <option value="cram">CRAM track. Recommend converting to BED/bigWig unless mapping annotation needed</option>
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365 <option value="gff">GFF/GFF3 track</option>
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366 <option value="cool">HiC as cool/mcool/scool format files</option>
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367 <option value="hic">HiC as juicebox_hic format file. Tabular hic_matrix will NOT work.</option>
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368 <option value="maf">Multiple alignment format. Reference name must match the MAF name exactly to work correctly</option>
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369 <option value="paf">PAF - Pairwise approximate mapping positions between two set of sequences</option>
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370 <option value="vcf">VCF SNP track</option>
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371 </param>
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372 <when value="blastxml">
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373 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml"/>
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374 <param name="blast_parent" type="data" format="gff3" optional="true" label="Features used in Blast Search" 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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375 <param name="min_gap" type="integer" min="2" value="10" label="Minimum Gap Size" help="before a new match_part feature is created"/>
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376 <param name="is_protein" type="boolean" truevalue="true" falsevalue="false" label="Is this a protein blast search?"/>
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377 <expand macro="track_styling_vgp"/>
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378 <expand macro="track_visibility"/>
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379 </when>
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380 <when value="vcf">
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381 <expand macro="input_conditional" label="SNP Track Data" format="vcf,vcf_bgzip"/>
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382 <expand macro="track_styling_vcf"/>
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383 <expand macro="track_visibility"/>
93
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384 </when>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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385 <when value="gff">
97
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386 <expand macro="input_conditional" label="GFF/GFF3 Track Data" format="gff,gff3"/>
93
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387 <conditional name="match_part" label="match/match_part data">
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388 <param name="match_part_select" type="select" label="This is match/match_part data" help="Match part data selection ">
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389 <option selected="True" value="false">Not match/match part data</option>
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390 <option value="true">Match/match part data</option>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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391 </param>
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392 <when value="true">
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393 <param name="name" type="text" value="match" optional="True" label="Match Part Feature Type" 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)."/>
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394 </when>
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395 <when value="false"/>
93
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396 </conditional>
97
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397 <expand macro="track_styling_vgp"/>
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398 <expand macro="track_visibility"/>
93
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399 </when>
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400 <when value="bam">
97
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401 <expand macro="input_conditional" label="BAM Track Data" format="bam"/>
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402 <expand macro="track_visibility"/>
93
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403 </when>
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404 <when value="bed">
97
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405 <expand macro="input_conditional" label="BED Track Data" format="bed"/>
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406 <expand macro="track_styling_vgp"/>
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407 <expand macro="track_visibility"/>
93
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408 </when>
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409 <when value="cram">
97
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410 <expand macro="input_conditional" label="CRAM Track Data" format="cram"/>
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411 <expand macro="track_visibility"/>
93
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412 </when>
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413 <when value="maf">
97
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414 <expand macro="input_conditional" label="MAF Track Data" format="maf"/>
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415 <expand macro="track_styling_vgp"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
416 <expand macro="track_visibility"/>
93
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parents: 92
diff changeset
417 </when>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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parents: 92
diff changeset
418 <when value="bigwig">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
419 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
420 <expand macro="track_visibility"/>
99
990291e918c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
fubar
parents: 98
diff changeset
421 <expand macro="track_styling_bigwig"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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parents: 92
diff changeset
422 </when>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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parents: 92
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423 <when value="paf">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
424 <expand macro="input_conditional" label="PAF format synteny mapping data" format="paf" help="PAF made with mashmap or minimap2 mapping the real reference as a query on the comparison genomes as references"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
425 <expand macro="pafref_conditional" label="Comparison genome sequence(s)" format="fasta" help="Paf from these as the reference(s), using the common reference as the reads to map"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
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426 <expand macro="track_visibility"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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parents: 92
diff changeset
427 </when>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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parents: 92
diff changeset
428 <when value="hic">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
429 <expand macro="input_conditional" label="Binary Juicebox HiC data" format="hic,juicebox_hic"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
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430 <expand macro="track_visibility"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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parents: 92
diff changeset
431 </when>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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parents: 92
diff changeset
432 <when value="cool">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
433 <expand macro="input_conditional" label="HiC data in cool/mcool/scool format" format="cool,mcool,scool"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
434 <expand macro="track_visibility"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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parents: 92
diff changeset
435 </when>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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parents: 92
diff changeset
436 </conditional>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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parents: 92
diff changeset
437 </repeat>
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
438 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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439 </repeat>
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
440 <expand macro="general_options"/>
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
441 </inputs>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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442 <outputs>
89
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11
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parents: 88
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443 <data format="html" name="output" label="JBrowse2: ${jbgen.session_name}">
31
cb4b32ca9968 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
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parents: 30
diff changeset
444 <change_format>
97
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parents: 93
diff changeset
445 <when input="zipOut" value="true" format="zip"/>
31
cb4b32ca9968 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
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parents: 30
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446 </change_format>
cb4b32ca9968 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
fubar
parents: 30
diff changeset
447 </data>
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
448 </outputs>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
449 <tests>
93
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450 <test>
86
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parents: 85
diff changeset
451 <repeat name="assemblies">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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diff changeset
452 <conditional name="reference_genome">
97
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parents: 93
diff changeset
453 <param name="genome_type_select" value="history"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
454 <param name="genome" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Merlin"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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diff changeset
455 <param name="genome.ext" value="fasta"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
456 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
457 <repeat name="track_groups">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
458 <param name="category" value="Assembly properties"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
459 <repeat name="data_tracks">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
460 <conditional name="data_format">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
461 <param name="data_format_select" value="gff"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
462 <conditional name="useuri">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
463 <param name="insource" value="history"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
464 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlin.gff3"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
465 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
466 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
467 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
468 <repeat name="data_tracks">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
469 <conditional name="data_format">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
470 <param name="data_format_select" value="bigwig"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
471 <conditional name="useuri">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
472 <param name="insource" value="history"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
473 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlin.bw"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
474 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
475 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
476 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
477 <repeat name="data_tracks">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
478 <conditional name="data_format">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
479 <param name="data_format_select" value="bed"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
480 <conditional name="useuri">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
481 <param name="insource" value="history"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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diff changeset
482 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/test-6.bed"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
483 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
484 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
485 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
486 <repeat name="data_tracks">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
487 <conditional name="data_format">
97
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parents: 93
diff changeset
488 <param name="data_format_select" value="vcf"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
489 <conditional name="useuri">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
490 <param name="insource" value="history"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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diff changeset
491 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlin.vcf"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
492 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
493 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
494 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
495 <repeat name="data_tracks">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
496 <conditional name="data_format">
97
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parents: 93
diff changeset
497 <param name="data_format_select" value="cram"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
498 <conditional name="useuri">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
499 <param name="insource" value="history"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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diff changeset
500 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlin.cram"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
501 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
502 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
503 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
504 <repeat name="data_tracks">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
505 <conditional name="data_format">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
506 <param name="data_format_select" value="bam"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
507 <conditional name="useuri">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
508 <param name="insource" value="history"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
509 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlin-sample.bam"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
510 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
511 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
512 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
513 <repeat name="data_tracks">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
514 <conditional name="data_format">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
515 <param name="data_format_select" value="maf"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
516 <conditional name="useuri">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
517 <param name="insource" value="history"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
518 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlinlastz.maf"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
519 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
520 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
521 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
522 <repeat name="data_tracks">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
523 <conditional name="data_format">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
524 <param name="data_format_select" value="blastxml"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
525 <conditional name="useuri">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
526 <param name="insource" value="history"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
527 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlin.blastxml"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
528 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
529 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
530 </repeat>
88
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
531 <repeat name="data_tracks">
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
532 <conditional name="data_format">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
533 <param name="data_format_select" value="bam"/>
88
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
534 <conditional name="useuri">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
535 <param name="insource" value="history"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
536 <param name="annotation" value=""/>
88
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
537 </conditional>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
538 </conditional>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
539 </repeat>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
540 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
541 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
542 <repeat name="assemblies">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
543 <conditional name="reference_genome">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
544 <param name="genome_type_select" value="history"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
545 <param name="genome" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/dm3.fa"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
546 <param name="genome.ext" value="fasta"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
547 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
548 <repeat name="track_groups">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
549 <param name="category" value="Assembly properties"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
550 <repeat name="data_tracks">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
551 <conditional name="data_format">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
552 <param name="data_format_select" value="cool"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
553 <conditional name="useuri">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
554 <param name="insource" value="history"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
555 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/dm3test.cool"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
556 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
557 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
558 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
559 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
560 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
561 <repeat name="assemblies">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
562 <conditional name="reference_genome">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
563 <param name="genome_type_select" value="history"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
564 <param name="genome" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Ppersica1.fa"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
565 <param name="genome.ext" value="fasta"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
566 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
567 <repeat name="track_groups">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
568 <param name="category" value="Assembly properties"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
569 <repeat name="data_tracks">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
570 <conditional name="data_format">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
571 <param name="data_format_select" value="paf"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
572 <conditional name="useuri">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
573 <param name="insource" value="history"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
574 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/peach-grape-map.paf"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
575 </conditional>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
576 <conditional name="pafuseuri">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
577 <param name="insource" value="history"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
578 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Vvinifera1.fa"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
579 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
580 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
581 </repeat>
91
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents: 90
diff changeset
582 <repeat name="data_tracks">
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents: 90
diff changeset
583 <conditional name="data_format">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
584 <param name="data_format_select" value="paf"/>
91
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parents: 90
diff changeset
585 <conditional name="useuri">
97
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parents: 93
diff changeset
586 <param name="insource" value="history"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
587 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/arabgrapepeach.paf"/>
93
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parents: 92
diff changeset
588 </conditional>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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parents: 92
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589 <conditional name="pafuseuri">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
590 <param name="insource" value="uri"/>
93
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parents: 92
diff changeset
591 <repeat name="refuri">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
592 <param name="annotation" value="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/arabidopsis.fa.gz"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
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593 <param name="annoname" value="arabidopsis.URI"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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parents: 92
diff changeset
594 </repeat>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
595 <repeat name="refuri">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
596 <param name="annotation" value="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Vvinifera1.fa.gz"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
597 <param name="annoname" value="Vvinifera1.URI"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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parents: 92
diff changeset
598 </repeat>
91
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
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parents: 90
diff changeset
599 </conditional>
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
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parents: 90
diff changeset
600 </conditional>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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parents: 92
diff changeset
601 </repeat>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
602 <repeat name="data_tracks">
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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parents: 92
diff changeset
603 <conditional name="data_format">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
604 <param name="data_format_select" value="paf"/>
91
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
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parents: 90
diff changeset
605 <conditional name="useuri">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
606 <param name="insource" value="history"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
607 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/arabgrapepeach.paf"/>
91
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents: 90
diff changeset
608 </conditional>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
609 <conditional name="pafuseuri">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
610 <param name="insource" value="history"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
611 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/arabidopsis.fa"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
612 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Vvinifera1.fa"/>
91
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
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parents: 90
diff changeset
613 </conditional>
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
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parents: 90
diff changeset
614 </conditional>
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents: 90
diff changeset
615 </repeat>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
616 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
617 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
618 <repeat name="assemblies">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
619 <conditional name="reference_genome">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
620 <param name="genome_type_select" value="uri"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
621 <param name="uri" value="https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
622 <param name="refname" value="hg38"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
623 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
624 <repeat name="track_groups">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
625 <param name="category" value="Assembly properties"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
626 <repeat name="data_tracks">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
627 <conditional name="data_format">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
628 <param name="data_format_select" value="hic"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
629 <conditional name="useuri">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
630 <param name="insource" value="uri"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
631 <param name="annouri" value="https://s3.amazonaws.com/igv.broadinstitute.org/data/hic/intra_nofrag_30.hic"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
632 <param name="annoname" value="humanhic"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
633 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
634 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
635 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
636 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
637 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
638 <section name="jbgen">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
639 <param name="zipOut" value="true"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
640 <param name="session_name" value="New test session"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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diff changeset
641 </section>
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
642 <!-- use the following line to generate a ZIP file to inspect it -->
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
643 <!--output name="output" file="jbrowse2_result02.zip" ftype="zip" compare="sim_size"-->
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
644 <output name="output" ftype="zip">
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
645 <assert_contents>
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
646 <has_archive_member path=".*" n="637" delta="10"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
647 <has_archive_member path="index.html"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
648 <has_archive_member path="static/media/roboto-latin-400-normal.3f2b9a42f643e62a49b7.woff"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
649 <has_archive_member path="manifest.json">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
650 <has_text text="favicon.ico"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
651 <has_text text="background_color"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
652 </has_archive_member>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
653 <has_archive_member path="galaxy.xml">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
654 <is_valid_xml/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
655 <has_n_elements_with_path path="./metadata/general/session_name" n="1"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
656 <element_text_is path="./metadata/general/session_name" text="New test session"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
657 </has_archive_member>
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
658 <has_archive_member path="merlin.gff3_0.gz"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
659 <has_archive_member path="merlin.gff3_0.gz.tbi"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
660 <has_archive_member path="merlin.bw_1"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
661 <has_archive_member path="test-6.bed_2.gz"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
662 <has_archive_member path="merlin.vcf_3"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
663 <has_archive_member path="merlin.vcf_3.tbi"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
664 <has_archive_member path="merlin.cram_4"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
665 <has_archive_member path="merlin.cram_4.crai"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
666 <has_archive_member path="merlin-sample.bam_5"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
667 <has_archive_member path="merlin-sample.bam_5.bai"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
668 <has_archive_member path="merlinlastz.maf_6.sorted.bed.gz.tbi"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
669 <has_archive_member path="merlin.blastxml_7.gz"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
670 <has_archive_member path="dm3test.cool_9.hic"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
671 <has_archive_member path="peach-grape-map.paf_10"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
672 <has_archive_member path="arabgrapepeach.paf_11"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
673 <has_archive_member path="Merlin.fa.gz.fai"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
674 <has_archive_member path="dm3.fa.fa.gz.fai"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
675 <has_archive_member path="Ppersica1.fa.fa.gz"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
676 <has_archive_member path="Ppersica1.fa.fa.gz.fai"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
677 <has_archive_member path="Ppersica1.fa.fa.gz.gzi"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
678 <has_archive_member path="Vvinifera1.fa.fa.gz.fai"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
679 <has_archive_member path="Vvinifera1.fa.fa.gz"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
680 <has_archive_member path="Vvinifera1.fa.fa.gz.gzi"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
681 <has_archive_member path="config.json">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
682 <has_json_property_with_text property="name" text="Merlin"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
683 </has_archive_member>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
684 </assert_contents>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
685 </output>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
686 </test>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
687 <test>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
688 <param name="autoCollection">
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
689 <collection type="list" name="merlintest">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
690 <element name="merlin.fa" value="merlin.fa"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
691 <element name="merlin.bw" value="bw/merlin.bw"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
692 <element name="test-6.bed" value="bed/test-6.bed"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
693 </collection>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
694 </param>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
695 <section name="jbgen">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
696 <param name="zipOut" value="true"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
697 <param name="session_name" value="Collection test"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
698 <param name="ucol|formcoll" value="collect"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
699 </section>
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
700 <!-- use the following line to generate a ZIP file to inspect it -->
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
701 <!--output name="output" file="jbrowse2_result01.zip" ftype="zip" compare="sim_size"-->
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
702 <output name="output" ftype="zip">
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
703 <assert_contents>
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
704 <has_archive_member path=".*" n="611" delta="10"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
705 <has_archive_member path="index.html"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
706 <has_archive_member path="static/media/roboto-latin-400-normal.3f2b9a42f643e62a49b7.woff"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
707 <has_archive_member path="manifest.json">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
708 <has_text text="favicon.ico"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
709 <has_text text="background_color"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
710 </has_archive_member>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
711 <has_archive_member path="galaxy.xml">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
712 <is_valid_xml/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
713 <has_n_elements_with_path path="./metadata/general/session_name" n="1"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
714 <element_text_is path="./metadata/general/session_name" text="Collection test"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
715 </has_archive_member>
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
716 <has_archive_member path="jb2_webserver.py"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
717 <has_archive_member path="merlin.fa.fa.gz.gzi"/>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
718 <has_archive_member path="merlin.fa.fa.gz"/>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
719 <has_archive_member path="merlin.fa.fa.gz.fai"/>
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
720 <has_archive_member path="merlin.bw"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
721 <has_archive_member path="index.html"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
722 <has_archive_member path="test-6.bed.gz"/>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
723 <has_archive_member path="test-6.bed.gz.tbi"/>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
724 </assert_contents>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
725 </output>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
726 </test>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
727 <test>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
728 <repeat name="assemblies">
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
729 <conditional name="reference_genome">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
730 <param name="genome_type_select" value="history"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
731 <param name="genome" value="merlin.fa"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
732 <param name="genome.ext" value="fasta"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
733 <param name="genome.name" value="Merlin"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
734 </conditional>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
735 <repeat name="track_groups">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
736 <param name="category" value="Default"/>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
737 <repeat name="data_tracks">
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
738 <conditional name="data_format">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
739 <param name="data_format_select" value="bigwig"/>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
740 <conditional name="useuri">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
741 <param name="annotation" value="bw/merlin.bw"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
742 <param name="insource" value="history"/>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
743 </conditional>
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
744 </conditional>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
745 </repeat>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
746 </repeat>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
747 </repeat>
98
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
748 <section name="jbgen">
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
749 <param name="zipOut" value="true"/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
750 </section>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
751 <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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752 <assert_contents>
98
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parents: 97
diff changeset
753 <has_archive_member path="galaxy.xml">
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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parents: 97
diff changeset
754 <has_text text="genome path="/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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parents: 97
diff changeset
755 <has_text text="label="/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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parents: 97
diff changeset
756 <has_text text="format="/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
757 <has_text text="metadata"/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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parents: 97
diff changeset
758 <has_text text="useuri="/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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parents: 97
diff changeset
759 <has_text text="trackFile path="/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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parents: 97
diff changeset
760 <has_text text="ext=&quot;bigwig&quot;"/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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parents: 97
diff changeset
761 <has_text text="format=&quot;bigwig&quot;"/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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parents: 97
diff changeset
762 </has_archive_member>
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
763 </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
764 </output>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
765 </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
766 <test>
93
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parents: 92
diff changeset
767 <repeat name="assemblies">
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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parents: 92
diff changeset
768 <conditional name="reference_genome">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
769 <param name="genome_type_select" value="history"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
770 <param name="genome" value="merlin.fa"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
771 <param name="genome.ext" value="fasta"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
772 <param name="genome.name" value="Merlin"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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parents: 92
diff changeset
773 </conditional>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
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parents: 60
diff changeset
774 <repeat name="track_groups">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
775 <param name="category" value="Default"/>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
776 <repeat name="data_tracks">
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
777 <conditional name="data_format">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
778 <param name="data_format_select" value="vcf"/>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
779 <conditional name="useuri">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
780 <param name="insource" value="history"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
781 <param name="annotation" value="vcf/merlin.vcf"/>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
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parents: 60
diff changeset
782 </conditional>
46
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parents: 45
diff changeset
783 </conditional>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
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parents: 60
diff changeset
784 </repeat>
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
785 </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
786 </repeat>
98
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
787 <section name="jbgen">
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
788 <param name="zipOut" value="true"/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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parents: 97
diff changeset
789 </section>
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
790 <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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diff changeset
791 <assert_contents>
98
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
792 <has_archive_member path="galaxy.xml">
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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parents: 97
diff changeset
793 <has_text text="genome path="/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
794 <has_text text="label="/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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parents: 97
diff changeset
795 <has_text text="format="/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
796 <has_text text="metadata"/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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parents: 97
diff changeset
797 <has_text text="useuri="/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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parents: 97
diff changeset
798 <has_text text="trackFile path="/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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parents: 97
diff changeset
799 <has_text text="ext=&quot;vcf&quot; label=&quot;merlin.vcf&quot;"/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
800 </has_archive_member>
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
801 </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
802 </output>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
803 </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
804 <test>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
805 <repeat name="assemblies">
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
806 <conditional name="reference_genome">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
807 <param name="genome_type_select" value="history"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
808 <param name="genome" value="merlin.fa"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
809 <param name="genome.ext" value="fasta"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
810 <param name="genome.name" value="Merlin"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
811 </conditional>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
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parents: 60
diff changeset
812 </repeat>
98
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
813 <section name="jbgen">
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
814 <param name="zipOut" value="true"/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
815 </section>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
816 <output name="output">
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
817 <assert_contents>
98
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
818 <has_archive_member path="galaxy.xml">
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
819 <has_text text="genome path="/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
820 <has_text text="label="/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
821 <has_text text="useuri="/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
822 <has_text text="metadata"/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
823 </has_archive_member>
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
824 </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
825 </output>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
826 </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
827 <test>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
828 <repeat name="assemblies">
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
829 <conditional name="reference_genome">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
830 <param name="genome_type_select" value="history"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
831 <param name="genome" value="merlin.fa"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
832 <param name="genome.ext" value="fasta"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
833 <param name="genome.name" value="Merlin"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
834 </conditional>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
835 <repeat name="track_groups">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
836 <param name="category" value="Default"/>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
837 <repeat name="data_tracks">
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
838 <conditional name="data_format">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
839 <param name="data_format_select" value="vcf"/>
62
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fubar
parents: 60
diff changeset
840 <conditional name="useuri">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
841 <param name="insource" value="history"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
842 <param name="annotation" value="vcf/merlin.vcf"/>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
843 </conditional>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
844 </conditional>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
845 </repeat>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
846 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
847 </repeat>
98
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
848 <section name="jbgen">
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
849 <param name="zipOut" value="true"/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
850 </section>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
851 <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
852 <assert_contents>
98
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
853 <has_archive_member path="galaxy.xml">
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
854 <has_text text="genome path="/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
855 <has_text text="label="/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
856 <has_text text="format="/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
857 <has_text text="metadata"/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
858 <has_text text="useuri="/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
859 <has_text text="trackFile path="/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
860 <has_text text="ext=&quot;vcf&quot; label=&quot;merlin.vcf&quot;"/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
861 </has_archive_member>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
862 </assert_contents>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
863 </output>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
864 </test>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
865 <test>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
866 <repeat name="assemblies">
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
867 <conditional name="reference_genome">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
868 <param name="genome_type_select" value="history"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
869 <param name="genome" value="merlin.fa"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
870 <param name="genome.ext" value="fasta"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
871 <param name="genome.name" value="Merlin"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
872 </conditional>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
873 <repeat name="track_groups">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
874 <param name="category" value="Default"/>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
875 <repeat name="data_tracks">
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
876 <conditional name="data_format">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
877 <param name="data_format_select" value="gff"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
878 <conditional name="useuri">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
879 <param name="insource" value="history"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
880 <param name="annotation" value="gff3/A.gff"/>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
881 </conditional>
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
882 </conditional>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
883 <conditional name="match_part">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
884 <param name="match_part_select" value="false"/>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
885 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
886 <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
887 <conditional name="color_score">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
888 <param name="color_score_select" value="none"/>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
889 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
890 <conditional name="color">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
891 <param name="color_select" value="automatic"/>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
892 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
893 </section>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
894 </repeat>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
895 </repeat>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
896 <repeat name="track_groups">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
897 <param name="category" value="Ignore Scale"/>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
898 <repeat name="data_tracks">
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
899 <conditional name="data_format">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
900 <param name="data_format_select" value="gff"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
901 <conditional name="useuri">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
902 <param name="insource" value="history"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
903 <param name="annotation" value="gff3/1.gff"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
904 </conditional>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
905 <conditional name="match_part">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
906 <param name="match_part_select" value="false"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
907 </conditional>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
908 <section name="jbcolor_scale">
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
909 <conditional name="color_score">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
910 <param name="color_score_select" value="none"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
911 <conditional name="color">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
912 <param name="color_select" value="manual"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
913 <param name="style_color" value="#ff00ff"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
914 </conditional>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
915 </conditional>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
916 </section>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
917 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
918 </repeat>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
919 </repeat>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
920 <repeat name="track_groups">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
921 <param name="category" value="Scaled Colour"/>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
922 <repeat name="data_tracks">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
923 <conditional name="data_format">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
924 <param name="data_format_select" value="gff"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
925 <conditional name="useuri">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
926 <param name="insource" value="history"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
927 <param name="annotation" value="gff3/C.gff"/>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
928 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
929 <conditional name="match_part">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
930 <param name="match_part_select" value="false"/>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
931 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
932 <section name="jbcolor_scale">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
933 <conditional name="color_score">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
934 <param name="color_score_select" value="score"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
935 <param name="score_scaling" value="linear"/>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
936 <conditional name="score_scales">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
937 <param name="scale_select" value="automatic"/>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
938 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
939 <conditional name="color_scheme">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
940 <param name="score_scheme" value="opacity"/>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
941 <conditional name="color">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
942 <param name="color_select" value="automatic"/>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
943 </conditional>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
944 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
945 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
946 </section>
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
947 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
948 </repeat>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
949 <repeat name="data_tracks">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
950 <conditional name="data_format">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
951 <param name="data_format_select" value="gff"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
952 <conditional name="useuri">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
953 <param name="annotation" value="gff3/B.gff"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
954 <param name="insource" value="history"/>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
955 </conditional>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
956 <conditional name="match_part">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
957 <param name="match_part_select" value="false"/>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
958 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
959 <section name="jbcolor_scale">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
960 <conditional name="color_score">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
961 <param name="color_score_select" value="score"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
962 <param name="score_scaling" value="linear"/>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
963 <conditional name="score_scales">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
964 <param name="scale_select" value="automatic"/>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
965 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
966 <conditional name="color_scheme">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
967 <param name="score_scheme" value="opacity"/>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
968 <conditional name="color">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
969 <param name="color_select" value="manual"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
970 <param name="style_color" value="#0000ff"/>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
971 </conditional>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
972 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
973 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
974 </section>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
975 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
976 </repeat>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
977 <repeat name="data_tracks">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
978 <conditional name="data_format">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
979 <param name="data_format_select" value="gff"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
980 <conditional name="useuri">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
981 <param name="annotation" value="gff3/A.gff"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
982 <param name="insource" value="history"/>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
983 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
984 <conditional name="match_part">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
985 <param name="match_part_select" value="false"/>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
986 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
987 <section name="jbcolor_scale">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
988 <conditional name="color_score">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
989 <param name="color_score_select" value="score"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
990 <param name="score_scaling" value="linear"/>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
991 <conditional name="score_scales">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
992 <param name="scale_select" value="manual"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
993 <param name="minimum" value="0"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
994 <param name="maximum" value="1000"/>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
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parents: 62
diff changeset
995 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
996 <conditional name="color_scheme">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
997 <param name="score_scheme" value="opacity"/>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
998 <conditional name="color">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
999 <param name="color_select" value="automatic"/>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1000 </conditional>
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
1001 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
1002 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
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parents: 62
diff changeset
1003 </section>
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
1004 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
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parents: 62
diff changeset
1005 </repeat>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1006 <repeat name="data_tracks">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
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parents: 62
diff changeset
1007 <conditional name="data_format">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
1008 <param name="data_format_select" value="gff"/>
63
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parents: 62
diff changeset
1009 <conditional name="useuri">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
1010 <param name="annotation" value="gff3/1.gff"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
1011 <param name="insource" value="history"/>
63
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parents: 62
diff changeset
1012 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
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parents: 62
diff changeset
1013 <conditional name="match_part">
97
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parents: 93
diff changeset
1014 <param name="match_part_select" value="false"/>
63
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diff changeset
1015 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1016 <section name="jbcolor_scale">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1017 <conditional name="color_score">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
1018 <param name="color_score_select" value="score"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
1019 <param name="score_scaling" value="linear"/>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1020 <conditional name="score_scales">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
1021 <param name="scale_select" value="manual"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
1022 <param name="minimum" value="0"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
1023 <param name="maximum" value="1000"/>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1024 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1025 <conditional name="color_scheme">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
1026 <param name="score_scheme" value="opacity"/>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
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parents: 62
diff changeset
1027 <conditional name="color">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
1028 <param name="color_select" value="manual"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
1029 <param name="style_color" value="#ff0000"/>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1030 </conditional>
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
1031 </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
1032 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1033 </section>
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
1034 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1035 </repeat>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1036 </repeat>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1037 <repeat name="track_groups">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
1038 <param name="category" value="Realistic"/>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1039 <repeat name="data_tracks">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
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parents: 62
diff changeset
1040 <conditional name="data_format">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
1041 <param name="data_format_select" value="gff"/>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1042 <conditional name="useuri">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
1043 <param name="annotation" value="gff3/interpro.gff"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
1044 <param name="insource" value="history"/>
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
1045 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
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parents: 62
diff changeset
1046 <conditional name="match_part">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
1047 <param name="match_part_select" value="false"/>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff changeset
1048 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1049 <section name="jbcolor_scale">
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1050 <conditional name="color_score">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
1051 <param name="color_score_select" value="none"/>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1052 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1053 <conditional name="color">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
1054 <param name="color_select" value="automatic"/>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1055 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1056 </section>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1057 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1058 </repeat>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1059 <repeat name="data_tracks">
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
1060 <conditional name="data_format">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
1061 <param name="data_format_select" value="gff"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
1062 <conditional name="useuri">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
1063 <param name="annotation" value="gff3/2.gff"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
1064 <param name="insource" value="history"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
1065 </conditional>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
1066 <conditional name="match_part">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
1067 <param name="match_part_select" value="true"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
1068 <param name="name" value="cDNA_match"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
1069 </conditional>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
1070 <section name="jbcolor_scale">
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
1071 <conditional name="color_score">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
1072 <param name="color_score_select" value="none"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
1073 </conditional>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
1074 <conditional name="color">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
1075 <param name="color_select" value="automatic"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
1076 </conditional>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
1077 </section>
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
1078 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1079 </repeat>
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
1080 </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
1081 </repeat>
98
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bgruening
parents: 97
diff changeset
1082 <section name="jbgen">
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
1083 <param name="zipOut" value="true"/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
1084 </section>
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
1085 <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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parents:
diff changeset
1086 <assert_contents>
98
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
1087 <has_archive_member path="A.gff"/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
1088 <has_archive_member path="B.gff"/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
1089 <has_archive_member path="C.gff"/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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parents: 97
diff changeset
1090 <has_archive_member path="interpro.gff"/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
1091 <has_archive_member path="1.gff"/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
1092 <has_archive_member path="2.gff"/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
1093 <has_archive_member path="galaxy.xml">
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
1094 <is_valid_xml/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
1095 <has_n_elements_with_path path="./metadata/general/session_name" n="1"/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
1096 <element_text_is path="./metadata/general/session_name" text="New JBrowse2 session"/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
1097 </has_archive_member>
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
1098 </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
1099 </output>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
1100 </test>
98
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
1101 <test>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
1102 <repeat name="assemblies">
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
1103 <conditional name="reference_genome">
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1104 <param name="genome_type_select" value="history"/>
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1105 <param name="genome" value="merlin.fa"/>
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1106 </conditional>
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1107 <repeat name="track_groups">
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1108 <param name="category" value="Auto Coloured"/>
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1109 <repeat name="data_tracks">
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1110 <conditional name="data_format">
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1111 <param name="data_format_select" value="cram"/>
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1112 <param name="annotation" value="cram/merlin-sample.cram"/>
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1113 </conditional>
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1114 </repeat>
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1115 </repeat>
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1116 </repeat>
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1117 <section name="jbgen">
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1118 <param name="zipOut" value="true"/>
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1119 </section>
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1120 <output name="output" ftype="zip">
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1121 <assert_contents>
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1122 <!-- roughly 590 files in an archive -->
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1123 <has_archive_member path=".*" n="608" delta="30"/>
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1124 <has_archive_member path="index.html"/>
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1125 <has_archive_member path="static/media/roboto-latin-400-normal.3f2b9a42f643e62a49b7.woff"/>
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1126 <has_archive_member path="manifest.json">
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1127 <has_text text="favicon.ico"/>
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1128 <has_text text="background_color"/>
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1129 </has_archive_member>
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1130 <has_archive_member path="merlin.fa.fa.gz.fai"/>
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1131 <has_archive_member path="galaxy.xml">
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1132 <is_valid_xml/>
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1133 <has_n_elements_with_path path="./metadata/general/session_name" n="1"/>
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1134 <element_text_is path="./metadata/general/session_name" text="New JBrowse2 session"/>
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1135 </has_archive_member>
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1136 </assert_contents>
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1137 </output>
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1138 </test>
0
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1139 </tests>
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1140 <help><![CDATA[
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1141
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1142 JBrowse2-in-Galaxy
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1143 ==================
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1144
98
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1145 JBrowse2-in-Galaxy offers a highly configurable, workflow-compatible Genome viewer.
0
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1146
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1147
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1148 Use and local viewing
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1149 =====================
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1150
107
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diff changeset
1151 Browser tracks need a coordinate system, based on the reference genome, so that must be chosen before adding groups of tracks.
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1152
112
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diff changeset
1153 Many Galaxy datatypes can be turned into a track for display - in all cases, the selected reference genome must have been
99
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1154 used to generate the data:
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1155
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diff changeset
1156 bam
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diff changeset
1157 bed
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1158 bigwig
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diff changeset
1159 blastxml
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diff changeset
1160 cram
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1161 gff3
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1162 hic
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1163 maf
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1164 paf
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diff changeset
1165 vcf
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1166
107
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diff changeset
1167 Note that cram and bam will be large, so very slow amd are only recommended if you need the cigar annotation. Otherwise conversion to bed is recommended to slim them down.
99
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diff changeset
1168 Unfortunately if you have millions of rows in a bed, it will also be very slow - in which case a bigwig is recommended.
7
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1169
0
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1170 A JBrowse2 history item can be opened by viewing it (the "eye" icon).
7
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1171
0
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diff changeset
1172 Overview
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1173 --------
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1174
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1175 JBrowse is a fast, embeddable genome browser built completely with
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1176 JavaScript and HTML5.
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1177
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1178 The JBrowse-in-Galaxy (JiG) tool was written to help build complex
7
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diff changeset
1179 JBrowse installations straight from Galaxy. It allows you to build up a JBrowse instance without worrying
0
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1180 about how to run the command line tools to format your data, and which
7
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diff changeset
1181 options need to be supplied and where.
0
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1182
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diff changeset
1183 Options
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1184 -------
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1185
17
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1186 **Reference or Assembly**
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1187
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1188 Choose either a built-in or select one from your history.
0
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1189
17
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1190 Track coordinates and contig names *must* match this reference precisely
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diff changeset
1191 or they will not display.
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1192
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diff changeset
1193 **Track Groups** represent a set of tracks in a single category.
0
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1194
99
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diff changeset
1195
0
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1196 Annotation Tracks
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1197 -----------------
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1198
112
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1199
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diff changeset
1200 BED
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diff changeset
1201 ~~~
56f9a6e0fe80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 566509061b742b73c8dd1a1db6813fbf6a7a3792
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diff changeset
1202
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diff changeset
1203 Bed feature annotation usually requires clicking on the feature.
56f9a6e0fe80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 566509061b742b73c8dd1a1db6813fbf6a7a3792
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diff changeset
1204
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diff changeset
1205 Bed files created by the *Bigwig extremes to bed features* tool have the score in column 5
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diff changeset
1206 set to *1* for regions above the quantile and *-1* for regions below. It is possible to set an advanced option for each bed track, to use the bed score in column 5
56f9a6e0fe80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 566509061b742b73c8dd1a1db6813fbf6a7a3792
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diff changeset
1207 for the feature colour, giving red and blue using a JBrowse2 plugin, so they are easy to distinguish in a combined track.
56f9a6e0fe80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 566509061b742b73c8dd1a1db6813fbf6a7a3792
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diff changeset
1208
56f9a6e0fe80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 566509061b742b73c8dd1a1db6813fbf6a7a3792
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diff changeset
1209
86
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diff changeset
1210 MAF
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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diff changeset
1211 ~~~
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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diff changeset
1212
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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diff changeset
1213 For history references, the name of the reference genome dataset in your history is very important for MAF tracks,
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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diff changeset
1214 because it becomes the "dbkey" for that reference. So, it must be exactly the same as the genome name (dbkey) used
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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diff changeset
1215 when making the MAF, typically in the Lastz tool.
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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diff changeset
1216
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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diff changeset
1217 If you used "hg38" as the reference in Lastz, that is exactly what the reference fasta should be named for any MAF track.
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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diff changeset
1218 Change it using the "pencil" icon on the reference data in your history. Any other name, such as "hg38.fasta"
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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diff changeset
1219 will cause the MAF track to show no data since there are no matches with that reference dbkey.
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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diff changeset
1220
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diff changeset
1221
0
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diff changeset
1222 GFF3/BED
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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1223 ~~~~~~~~
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1224
17
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diff changeset
1225 Standard feature tracks. They usually highlight genes, mRNAs and other features of interest along a genomic region.
0
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1226
5
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diff changeset
1227 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
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diff changeset
1228 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
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diff changeset
1229 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
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diff changeset
1230 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
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diff changeset
1231 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
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diff changeset
1232
0
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diff changeset
1233 BAM Pileups
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1234 ~~~~~~~~~~~
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1235
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diff changeset
1236 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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diff changeset
1237 that bam data.
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diff changeset
1238
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diff changeset
1239
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diff changeset
1240 BlastXML
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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1241 ~~~~~~~~
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
1242
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diff changeset
1243 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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diff changeset
1244 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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diff changeset
1245 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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diff changeset
1246 available separately from the IUC on the toolshed.
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diff changeset
1247
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diff changeset
1248 **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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diff changeset
1249 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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diff changeset
1250 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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diff changeset
1251 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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parents:
diff changeset
1252 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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parents:
diff changeset
1253 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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diff changeset
1254 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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parents:
diff changeset
1255 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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parents:
diff changeset
1256 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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diff changeset
1257 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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diff changeset
1258 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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diff changeset
1259 10 hits or so.
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diff changeset
1260
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diff changeset
1261 **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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diff changeset
1262 they should adjust feature locations by 3x.
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diff changeset
1263
99
990291e918c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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diff changeset
1264 Local viewing
990291e918c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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diff changeset
1265 =============
990291e918c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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diff changeset
1266
990291e918c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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parents: 98
diff changeset
1267 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.
990291e918c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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diff changeset
1268 This can be shared and viewed without Galaxy.
990291e918c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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diff changeset
1269
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diff changeset
1270 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,
990291e918c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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parents: 98
diff changeset
1271 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
990291e918c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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parents: 98
diff changeset
1272 directory to the first level in that zip archive. It contains a file named *jb2_webserver.py*
990291e918c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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parents: 98
diff changeset
1273
990291e918c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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parents: 98
diff changeset
1274 With python3 installed,
990291e918c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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diff changeset
1275
990291e918c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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diff changeset
1276 *python3 jb2_webserver.py*
990291e918c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
fubar
parents: 98
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1277
990291e918c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
fubar
parents: 98
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1278 will serve the unarchived JBrowse2 configuration from the same directory as the python script automatically. If a new browser window does not open,
990291e918c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
fubar
parents: 98
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1279 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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parents:
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1280
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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1281 ]]></help>
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
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1282 <expand macro="citations"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
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1283 <expand macro="creators"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
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1284 </tool>