Mercurial > repos > fubar > jbrowse2

annotate jbrowse2.xml @ 134:ed3a21033188 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit bb6736899ac3029f73455637a04a006fcd857fc2
author bgruening
date Sun, 20 Oct 2024 07:11:16 +0000
parents cec274db51c0
children 21bb464c1d53
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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">jbrowse_2</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="convertMAF.sh"/>
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14 <include path="jb2_webserver.py"/>
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15 <include path="jbrowse2.py"/>
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16 <include path="maf2bed.py"/>
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17 <include path="bedscoreplugin.js"/>
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18 </required_files>
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19 <version_command>python '${__tool_directory__}/jbrowse2.py' --version</version_command>
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20 <command detect_errors="aggressive"><![CDATA[
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21 export SHELL="/bin/sh" &&
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22 mkdir -p '$output.files_path' &&
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23 cp '$trackxml' '$output.files_path/galaxy.xml' &&
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24 export JBROWSE2_PATH=\$(realpath \$(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":
134
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101 <genome path="${assembly.reference_genome.indexed.fields.path}" label="${assembly.reference_genome.indexed.fields.dbkey}" useuri="no">
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102 <metadata>
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103 <dataset
134
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104 dname = "${assembly.reference_genome.indexed.fields.name}" />
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105 </metadata>
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106 </genome>
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107 #else
116
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108 <genome path="$assembly.reference_genome.genome" label="${assembly.reference_genome.genome.element_identifier}" useuri="no">
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109 <metadata>
88
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110
62
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111 <dataset id="${__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:
88
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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 $track.data_format.useuri.annouri:
88
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157 #set input_exists = "True"
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158 <track cat="${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.element_identifier}" 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 $input_exists == "True":
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213 <options>
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214 <style>
134
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215 #if str($track.data_format.data_format_select) in ["gff", "bed", "maf"]:
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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($track.data_format.data_format_select) == "bam":
134
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247 #if str($track.data_format.useuri.insource) == "history":
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248 <bam>
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249 <bam_index>
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250 #for $dataset in $track.data_format.useuri.annotation:
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251 ${dataset}~~~${dataset.metadata.bam_index},
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252 #end for
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253 </bam_index>
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254 </bam>
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255 #end if
88
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256 #else if str($track.data_format.data_format_select) == "cram":
134
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257 #if str($track.data_format.useuri.insource) == "history":
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258 <cram>
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259 <cram_index>
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260 #for $dataset in $track.data_format.useuri.annotation:
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261 ${dataset}~~~${dataset.metadata.cram_index},
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262 #end for
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263 </cram_index>
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264 </cram>
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265 #end if
88
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266 #else if str($track.data_format.data_format_select) == "gff":
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267 <gff>
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268 #if $track.data_format.match_part.match_part_select == "true":
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269 <match>${track.data_format.match_part.name}</match>
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270 #end if
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271 </gff>
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272 #else if str($track.data_format.data_format_select) == "paf":
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273 <paf>
93
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274 #if str($track.data_format.pafuseuri.insource) == "history":
88
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275 <genome>
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276 #for $anno in $track.data_format.pafuseuri.annotation:
134
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277 #set nospaces = $anno.element_identifier.replace(' ','')
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278 ${anno}~~~${nospaces},
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279 #end for
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280 </genome>
93
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281 <useuri>
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282 false
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283 </useuri>
88
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284 #else:
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285 <genome>
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286 #for $refgenome in $track.data_format.pafuseuri.refuri:
134
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287 #set nospaces = $refgenome.refname.replace(' ','')
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288 ${refgenome.uri}~~~${nospaces},
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289 #end for
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290 </genome>
93
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291 <useuri>
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292 true
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293 </useuri>
88
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294 #end if
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295 </paf>
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296 #else if str($track.data_format.data_format_select) == "hic":
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297 <hic>
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298 </hic>
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299 #else if str($track.data_format.data_format_select) == "cool":
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300 <cool>
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301 </cool>
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302 #else if str($track.data_format.data_format_select) == "bed":
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303 <bed>
108
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304 <usebedscore>${track.data_format.jbstyle.usebedscore}</usebedscore>
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305 </bed>
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306 #else if str($track.data_format.data_format_select) == "sparql":
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307 <label>${track.data_format.label}</label>
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308 <sparql>
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309 <url>${track.data_format.url}</url>
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310 <query>${track.data_format.query}</query>
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311 <query_refnames>${track.data_format.query_refnames}</query_refnames>
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312 </sparql>
62
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313 #end if
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314 </options>
46
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315 </track>
88
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316 #end if
46
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317 #end for
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318 #end for
0
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319 </tracks>
62
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320 </assembly>
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321 #end for
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322 #end if
0
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323 </root>
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324 ]]></configfile>
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325 </configfiles>
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326 <inputs>
99
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327 <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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328 <conditional name="reference_genome">
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329 <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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330 <option selected="True" value="indexed">Use a Galaxy server built-in genome</option>
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331 <option value="history">Use a genome fasta file from the current history</option>
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332 <option value="uri">Provide a URI (e.g. "https://..." for a genome reference as
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333 tabix bgzip with predictable index file URI</option>
0
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334 </param>
93
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335 <when value="indexed">
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336 <param name="indexed" type="select" optional="false" label="Select a built in reference genome or custom genome"
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337 help="If not listed, add a custom genome, use a history genome or a remote URI tabix genome">
93
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338 <options from_data_table="all_fasta">
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339 <filter column="2" type="sort_by"/>
98
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340 <validator message="No genomes are available for the selected input dataset" type="no_options"/>
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341 </options>
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342 </param>
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343 </when>
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344 <when value="history">
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345 <param name="genome" type="data" format="fasta" optional="false" label="Select the reference genome"/>
93
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346 </when>
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347 <when value="uri">
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348 <param name="uri" type="text" label="URI pointing to tabix compressed fasta - must always be on-line"
990291e918c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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349 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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350 </param>
112
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351 <param name="refname" type="text" label="Reference dbkey for tracks with this genome, such as hg38 or SacCer4"/>
93
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352 </when>
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353 </conditional>
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354 <repeat name="track_groups" title="Track Group">
134
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355 <param name="category" type="text" value="Default" optional="False" label="Track Category"
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356 help="Organise your tracks into Categories for a nicer end-user experience. #date# is replaced with current date"/>
93
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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">
99
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360 <option value="bam">BAM track. Recommend converting to BED/bigWig unless mapping annotation needed</option>
93
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361 <option value="bed">BED track</option>
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362 <option value="bigwig">BigWig track</option>
99
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363 <option value="cram">CRAM track. Recommend converting to BED/bigWig unless mapping annotation needed</option>
93
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364 <option value="gff">GFF/GFF3 track</option>
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365 <option value="cool">HiC as cool/mcool/scool format files</option>
98
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366 <option value="hic">HiC as juicebox_hic format file. Tabular hic_matrix will NOT work.</option>
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367 <option value="maf">Multiple alignment format. Reference name must match the MAF name exactly to work correctly</option>
99
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368 <option value="paf">PAF - Pairwise approximate mapping positions between two set of sequences</option>
93
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369 <option value="vcf">VCF SNP track</option>
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370 </param>
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371 <when value="vcf">
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372 <expand macro="input_conditional" label="SNP Track Data" format="vcf,vcf_bgzip"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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373 <expand macro="track_styling_vcf"/>
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374 <expand macro="track_visibility"/>
93
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375 </when>
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376 <when value="gff">
97
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377 <expand macro="input_conditional" label="GFF/GFF3 Track Data" format="gff,gff3"/>
93
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378 <conditional name="match_part" label="match/match_part data">
97
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379 <param name="match_part_select" type="select" label="This is match/match_part data" help="Match part data selection ">
93
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380 <option selected="True" value="false">Not 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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381 <option value="true">Match/match part data</option>
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382 </param>
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383 <when value="true">
98
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384 <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)."/>
93
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385 </when>
97
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386 <when value="false"/>
93
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387 </conditional>
97
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388 <expand macro="track_styling_vgp"/>
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389 <expand macro="track_visibility"/>
93
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390 </when>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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391 <when value="bam">
97
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392 <expand macro="input_conditional" label="BAM Track Data" format="bam"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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393 <expand macro="track_visibility"/>
93
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394 </when>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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395 <when value="bed">
97
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396 <expand macro="input_conditional" label="BED Track Data" format="bed"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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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>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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400 <when value="cram">
97
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401 <expand macro="input_conditional" label="CRAM Track Data" format="cram"/>
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402 <expand macro="track_visibility"/>
93
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403 </when>
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404 <when value="maf">
97
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405 <expand macro="input_conditional" label="MAF Track Data" format="maf"/>
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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="bigwig">
97
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410 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig"/>
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411 <expand macro="track_visibility"/>
99
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diff changeset
412 <expand macro="track_styling_bigwig"/>
93
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413 </when>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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414 <when value="paf">
97
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415 <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"/>
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416 <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"/>
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417 <expand macro="track_visibility"/>
93
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418 </when>
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419 <when value="hic">
97
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fubar
parents: 93
diff changeset
420 <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
fubar
parents: 93
diff changeset
421 <expand macro="track_visibility"/>
93
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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
fubar
parents: 92
diff changeset
423 <when value="cool">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
424 <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
fubar
parents: 93
diff changeset
425 <expand macro="track_visibility"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
426 </when>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
427 </conditional>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
428 </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
429 </repeat>
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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430 </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
431 <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
432 </inputs>
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
433 <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
diff changeset
434 <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
435 <change_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
436 <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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437 </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
438 </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
439 </outputs>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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440 <tests>
93
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parents: 92
diff changeset
441 <test>
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
442 <repeat name="assemblies">
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
443 <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
444 <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
445 <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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parents: 93
diff changeset
446 <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
447 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
448 <repeat name="track_groups">
97
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parents: 93
diff changeset
449 <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
450 <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
451 <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
452 <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
fubar
parents: 85
diff changeset
453 <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
454 <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
455 <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
fubar
parents: 85
diff changeset
456 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
457 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
458 </repeat>
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
fubar
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
fubar
parents: 93
diff changeset
461 <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
fubar
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.bw"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
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
fubar
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
fubar
parents: 93
diff changeset
470 <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
fubar
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
fubar
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
fubar
parents: 93
diff changeset
473 <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
fubar
parents: 85
diff changeset
474 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
475 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
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
fubar
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
fubar
parents: 93
diff changeset
479 <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
fubar
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
fubar
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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parents: 93
diff changeset
482 <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
fubar
parents: 85
diff changeset
483 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
484 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
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
fubar
parents: 85
diff changeset
487 <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
488 <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
fubar
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
fubar
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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parents: 93
diff changeset
491 <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
492 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
493 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
494 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
495 <repeat name="data_tracks">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
496 <conditional name="data_format">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
497 <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
498 <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
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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parents: 93
diff changeset
500 <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
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="maf"/>
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/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
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>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
514 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
515 <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
516 <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
517 <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
518 <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
519 <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
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 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
522 <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
523 <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
524 <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
525 <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
526 <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
527 <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
528 <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
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 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
531 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
532 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
533 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
534 <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
535 <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
536 <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
537 <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
538 <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
539 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
540 <repeat name="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
541 <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
542 <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
543 <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
544 <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
545 <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
546 <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
547 <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
548 </conditional>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
549 <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
550 <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
551 <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
552 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
553 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
554 </repeat>
91
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents: 90
diff changeset
555 <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
556 <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
557 <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
fubar
parents: 90
diff changeset
558 <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
559 <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
560 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/arabgrapepeach.paf"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
561 </conditional>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
562 <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
563 <param name="insource" value="uri"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
564 <repeat name="refuri">
134
ed3a21033188 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit bb6736899ac3029f73455637a04a006fcd857fc2
bgruening
parents: 133
diff changeset
565 <param name="uri" value="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/arabidopsis.fa.gz"/>
ed3a21033188 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit bb6736899ac3029f73455637a04a006fcd857fc2
bgruening
parents: 133
diff changeset
566 <param name="refname" value="arabidopsis.URI"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
567 </repeat>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
568 <repeat name="refuri">
134
ed3a21033188 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit bb6736899ac3029f73455637a04a006fcd857fc2
bgruening
parents: 133
diff changeset
569 <param name="uri" value="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Vvinifera1.fa.gz"/>
ed3a21033188 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit bb6736899ac3029f73455637a04a006fcd857fc2
bgruening
parents: 133
diff changeset
570 <param name="refname" value="Vvinifera1.URI"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
571 </repeat>
91
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents: 90
diff changeset
572 </conditional>
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents: 90
diff changeset
573 </conditional>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
574 </repeat>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
575 <repeat name="data_tracks">
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="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
577 <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
fubar
parents: 90
diff changeset
578 <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
579 <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
580 <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
581 </conditional>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
582 <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
583 <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
584 <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
585 <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
fubar
parents: 90
diff changeset
586 </conditional>
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents: 90
diff changeset
587 </conditional>
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents: 90
diff changeset
588 </repeat>
86
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parents: 85
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589 </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
590 </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
591 <repeat name="assemblies">
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
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592 <conditional name="reference_genome">
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
593 <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
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594 <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
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595 <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
596 </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
597 <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
598 <param name="category" value="Assembly properties"/>
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
599 <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
600 <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
601 <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
602 <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
603 <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
604 <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
605 <param name="annoname" value="humanhic"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
606 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
607 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
608 </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
609 </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
610 </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
611 <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
612 <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
613 <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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parents: 85
diff changeset
614 </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
615 <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
616 <assert_contents>
134
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bgruening
parents: 133
diff changeset
617 <has_archive_member path=".*" n="676" delta="10"/>
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
618 <has_archive_member path="index.html"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
619 <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
620 <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
621 <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
622 </has_archive_member>
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 <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
624 <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
625 <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
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parents: 93
diff changeset
626 <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
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diff changeset
627 </has_archive_member>
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 <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
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parents: 93
diff changeset
629 <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
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parents: 93
diff changeset
630 <has_archive_member path="merlin.bw_1"/>
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 <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
632 <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
633 <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
634 <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
635 <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
636 <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
637 <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
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parents: 93
diff changeset
638 <has_archive_member path="merlinlastz.maf_6.sorted.bed.gz.tbi"/>
134
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parents: 133
diff changeset
639 <has_archive_member path="dm3test.cool_7.hic"/>
ed3a21033188 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit bb6736899ac3029f73455637a04a006fcd857fc2
bgruening
parents: 133
diff changeset
640 <has_archive_member path="peach-grape-map.paf_8"/>
ed3a21033188 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit bb6736899ac3029f73455637a04a006fcd857fc2
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parents: 133
diff changeset
641 <has_archive_member path="arabgrapepeach.paf_10"/>
132
1efcc387bef4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b76c8cc45b31e105e6bb51abc5a5728cfd3e3f99
bgruening
parents: 127
diff changeset
642 <has_archive_member path="Merlin.fa.gz.fai"/>
1efcc387bef4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b76c8cc45b31e105e6bb51abc5a5728cfd3e3f99
bgruening
parents: 127
diff changeset
643 <has_archive_member path="dm3.fa.fa.gz.fai"/>
1efcc387bef4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b76c8cc45b31e105e6bb51abc5a5728cfd3e3f99
bgruening
parents: 127
diff changeset
644 <has_archive_member path="Ppersica1.fa.fa.gz"/>
1efcc387bef4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b76c8cc45b31e105e6bb51abc5a5728cfd3e3f99
bgruening
parents: 127
diff changeset
645 <has_archive_member path="Ppersica1.fa.fa.gz.fai"/>
1efcc387bef4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b76c8cc45b31e105e6bb51abc5a5728cfd3e3f99
bgruening
parents: 127
diff changeset
646 <has_archive_member path="Ppersica1.fa.fa.gz.gzi"/>
1efcc387bef4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b76c8cc45b31e105e6bb51abc5a5728cfd3e3f99
bgruening
parents: 127
diff changeset
647 <has_archive_member path="Vvinifera1.fa.fa.gz.fai"/>
1efcc387bef4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b76c8cc45b31e105e6bb51abc5a5728cfd3e3f99
bgruening
parents: 127
diff changeset
648 <has_archive_member path="Vvinifera1.fa.fa.gz"/>
1efcc387bef4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b76c8cc45b31e105e6bb51abc5a5728cfd3e3f99
bgruening
parents: 127
diff changeset
649 <has_archive_member path="Vvinifera1.fa.fa.gz.gzi"/>
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
650 <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
651 <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
652 <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
653 <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
654 <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
655 <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
656 <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
657 <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
658 <has_archive_member path="config.json">
132
1efcc387bef4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b76c8cc45b31e105e6bb51abc5a5728cfd3e3f99
bgruening
parents: 127
diff changeset
659 <has_json_property_with_text property="uri" text="Vvinifera1.fa.fa.gz.fai"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
660 </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
661 </assert_contents>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
662 </output>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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diff changeset
663 </test>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
664 <test>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
665 <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
666 <collection type="list" name="merlintest">
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
667 <element name="merlin.fa" value="merlin.fa"/>
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
668 <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
669 <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
670 </collection>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
671 </param>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
672 <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
673 <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
674 <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
675 <param name="ucol|formcoll" value="collect"/>
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
676 </section>
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
677 <output name="output" ftype="zip">
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
678 <assert_contents>
118
794aecef8327 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7b6920fd88a86cdb48dc4af2c6be77161eb85699-dirty
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parents: 117
diff changeset
679 <has_archive_member path=".*" n="652" delta="10"/>
97
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="index.html"/>
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
681 <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
682 <has_text text="favicon.ico"/>
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
683 <has_text text="background_color"/>
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
684 </has_archive_member>
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
685 <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
686 <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
687 <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
688 <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
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parents: 92
diff changeset
689 </has_archive_member>
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
690 <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
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parents: 92
diff changeset
691 <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
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parents: 92
diff changeset
692 <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
693 <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
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parents: 93
diff changeset
694 <has_archive_member path="merlin.bw"/>
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
695 <has_archive_member path="index.html"/>
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
696 <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
697 <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
698 </assert_contents>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
699 </output>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
700 </test>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
701 <test>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
702 <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
703 <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
704 <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
705 <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
706 <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
707 <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
708 </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
709 <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
710 <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
711 <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
712 <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
713 <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
714 <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
715 <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
716 <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
717 </conditional>
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
718 </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
719 </repeat>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
720 </repeat>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
721 </repeat>
98
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
722 <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
723 <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
724 </section>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
725 <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
726 <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
727 <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
728 <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
729 <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
730 <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
731 <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
732 <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
733 <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
734 <has_text text="ext=&quot;bigwig&quot;"/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
735 <has_text text="format=&quot;bigwig&quot;"/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
736 </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
737 </assert_contents>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
738 </output>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
739 </test>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
740 <test>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
741 <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
742 <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
743 <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
744 <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
745 <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
746 <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
747 </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
748 <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
749 <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
750 <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
751 <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
752 <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
753 <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
754 <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
755 <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
756 </conditional>
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
757 </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
758 </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
759 </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
760 </repeat>
98
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bgruening
parents: 97
diff changeset
761 <section name="jbgen">
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 <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
763 </section>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
764 <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
765 <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
766 <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
767 <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
768 <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
769 <has_text text="format="/>
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
770 <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
771 <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
772 <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
773 <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
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parents: 97
diff changeset
774 </has_archive_member>
0
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
775 </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
776 </output>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
777 </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
778 <test>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
779 <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
780 <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
781 <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
782 <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
783 <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
784 <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
785 </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
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
fubar
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
fubar
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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
bgruening
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
bgruening
parents: 97
diff changeset
795 <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
796 <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
797 </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
798 </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
799 </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
800 </test>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
801 <test>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
802 <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
803 <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
804 <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
805 <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
806 <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
807 <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
808 </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
809 <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
810 <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
811 <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
812 <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
813 <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
814 <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
815 <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
816 <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
817 </conditional>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
818 </conditional>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
819 </repeat>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
820 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
821 </repeat>
98
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
822 <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
823 <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
824 </section>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
825 <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
826 <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
827 <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
828 <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
829 <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
830 <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
831 <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
832 <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
833 <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
834 <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
835 </has_archive_member>
0
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
836 </assert_contents>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
837 </output>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
838 </test>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
839 <test>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
840 <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
841 <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
842 <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
843 <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
844 <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
845 <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
846 </conditional>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
847 <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
848 <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
849 <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
850 <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
851 <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
852 <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
853 <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
854 <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
855 </conditional>
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
856 </conditional>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
857 <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
858 <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
859 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
860 <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
861 <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
862 <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
863 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
864 <conditional name="color">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
865 <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
866 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
867 </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
868 </repeat>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
869 </repeat>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
870 <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
871 <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
872 <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
873 <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
874 <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
875 <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
876 <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
877 <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
878 </conditional>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
879 <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
880 <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
881 </conditional>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
882 <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
883 <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
884 <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
885 <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
886 <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
887 <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
888 </conditional>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
889 </conditional>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
890 </section>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
891 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
892 </repeat>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
893 </repeat>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
894 <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
895 <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
896 <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
897 <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
898 <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
899 <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
900 <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
901 <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
902 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
903 <conditional name="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
904 <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
905 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
906 <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
907 <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
908 <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
909 <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
910 <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
911 <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
912 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
913 <conditional name="color_scheme">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
914 <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
915 <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
916 <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
917 </conditional>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
918 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
919 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
920 </section>
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
921 </conditional>
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>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
923 <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
924 <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
925 <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
926 <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
927 <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
928 <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
929 </conditional>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
930 <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
931 <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
932 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
933 <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
934 <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
935 <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
936 <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
937 <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
938 <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
939 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
940 <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
941 <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
942 <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
943 <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
944 <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
945 </conditional>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
946 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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 </section>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
949 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
950 </repeat>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
951 <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
952 <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
953 <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
954 <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
955 <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
956 <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
957 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
958 <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
959 <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
960 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
961 <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
962 <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
963 <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
964 <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
965 <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
966 <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
967 <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
968 <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
969 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
970 <conditional name="color_scheme">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
971 <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
972 <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
973 <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
974 </conditional>
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>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
976 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
977 </section>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
978 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
979 </repeat>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
980 <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
981 <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
982 <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
983 <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
984 <param name="annotation" value="gff3/1.gff"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
985 <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
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 <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
988 <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
989 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
990 <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
991 <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
992 <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
993 <param name="score_scaling" value="linear"/>
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
994 <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
995 <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
996 <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
997 <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
998 </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
999 <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
1000 <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
1001 <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
1002 <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
1003 <param name="style_color" value="#ff0000"/>
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
1004 </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
1005 </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
1006 </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
1007 </section>
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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parents: 45
diff changeset
1008 </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
1009 </repeat>
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
1010 </repeat>
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
1011 <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
1012 <param name="category" value="Realistic"/>
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
1013 <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
1014 <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
1015 <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
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parents: 62
diff changeset
1016 <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
1017 <param name="annotation" value="gff3/interpro.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
1018 <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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diff changeset
1019 </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
1020 <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
1021 <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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diff changeset
1022 </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
1023 <section name="jbcolor_scale">
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
1024 <conditional name="color_score">
97
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parents: 93
diff changeset
1025 <param name="color_score_select" value="none"/>
63
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parents: 62
diff changeset
1026 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1027 <conditional name="color">
97
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parents: 93
diff changeset
1028 <param name="color_select" value="automatic"/>
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
1029 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1030 </section>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1031 </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
1032 </repeat>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1033 <repeat name="data_tracks">
93
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fubar
parents: 92
diff changeset
1034 <conditional name="data_format">
97
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fubar
parents: 93
diff changeset
1035 <param name="data_format_select" value="gff"/>
93
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fubar
parents: 92
diff changeset
1036 <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
1037 <param name="annotation" value="gff3/2.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
1038 <param name="insource" value="history"/>
93
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parents: 92
diff changeset
1039 </conditional>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
1040 <conditional name="match_part">
97
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fubar
parents: 93
diff changeset
1041 <param name="match_part_select" 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
1042 <param name="name" value="cDNA_match"/>
93
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parents: 92
diff changeset
1043 </conditional>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
1044 <section name="jbcolor_scale">
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
1045 <conditional name="color_score">
97
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parents: 93
diff changeset
1046 <param name="color_score_select" value="none"/>
93
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parents: 92
diff changeset
1047 </conditional>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
1048 <conditional name="color">
97
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parents: 93
diff changeset
1049 <param name="color_select" value="automatic"/>
93
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parents: 92
diff changeset
1050 </conditional>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
1051 </section>
0
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parents:
diff changeset
1052 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1053 </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
1054 </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
1055 </repeat>
98
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parents: 97
diff changeset
1056 <section name="jbgen">
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
1057 <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
1058 </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
1059 <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
1060 <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
1061 <has_archive_member path="A.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
1062 <has_archive_member path="B.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
1063 <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
1064 <has_archive_member path="interpro.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
1065 <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
1066 <has_archive_member path="2.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
1067 <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
1068 <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
1069 <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
1070 <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
1071 </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
1072 </assert_contents>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff changeset
1073 </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
1074 </test>
98
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
1075 <test>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
1076 <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
1077 <conditional name="reference_genome">
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
1078 <param name="genome_type_select" value="history"/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
1079 <param name="genome" value="merlin.fa"/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
1080 </conditional>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
1081 <repeat name="track_groups">
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
1082 <param name="category" value="Auto Coloured"/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
1083 <repeat name="data_tracks">
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
1084 <conditional name="data_format">
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
1085 <param name="data_format_select" value="cram"/>
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
1086 <param name="annotation" value="cram/merlin-sample.cram"/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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diff changeset
1087 </conditional>
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
1088 </repeat>
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
1089 </repeat>
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 </repeat>
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
1091 <section name="jbgen">
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
1092 <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
1093 </section>
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
1094 <output name="output" ftype="zip">
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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diff changeset
1095 <assert_contents>
118
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parents: 117
diff changeset
1096 <has_archive_member path=".*" n="649" delta="30"/>
98
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
1097 <has_archive_member path="index.html"/>
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
1098 <has_archive_member path="manifest.json">
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
1099 <has_text text="favicon.ico"/>
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
1100 <has_text text="background_color"/>
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
1101 </has_archive_member>
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
1102 <has_archive_member path="merlin.fa.fa.gz.fai"/>
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
1103 <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
1104 <is_valid_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
1105 <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
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parents: 97
diff changeset
1106 <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
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diff changeset
1107 </has_archive_member>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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diff changeset
1108 </assert_contents>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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diff changeset
1109 </output>
125
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diff changeset
1110 </test>
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1111 <test>
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1112 <repeat name="assemblies">
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1113 <conditional name="reference_genome">
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1114 <param name="genome_type_select" value="history"/>
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1115 <param name="genome" value="merlin.fa"/>
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1116 <param name="genome.ext" value="fasta"/>
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1117 <param name="genome.name" value="Merlin"/>
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1118 </conditional>
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1119 <repeat name="track_groups">
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1120 <param name="category" value="Default"/>
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1121 <repeat name="data_tracks">
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1122 <conditional name="data_format">
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1123 <param name="data_format_select" value="bigwig"/>
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1124 <conditional name="useuri">
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1125 <param name="annotation" value="bw/m:e.r.l .i-n.bw"/>
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1126 <param name="insource" value="history"/>
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1127 </conditional>
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1128 </conditional>
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1129 </repeat>
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1130 </repeat>
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1131 </repeat>
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1132 <section name="jbgen">
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1133 <param name="zipOut" value="true"/>
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1134 </section>
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1135 <output name="output">
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1136 <assert_contents>
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1137 <has_archive_member path="config.json">
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1138 <has_text text="QuantitativeTrack"/>
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1139 <has_text text="trackId"/>
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1140 <has_text text="me.r.l.i-n.bw_0"/>
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1141 <has_text text="name"/>
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1142 <has_text text="Default"/>
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diff changeset
1143 <has_text text="name"/>
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diff changeset
1144 <has_text text="assemblyName"/>
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1145 <has_text text="merlin.fa"/>
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1146 </has_archive_member>
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1147 </assert_contents>
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1148 </output>
98
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diff changeset
1149 </test>
0
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1150 </tests>
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diff changeset
1151 <help><![CDATA[
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1152
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diff changeset
1153 JBrowse2-in-Galaxy
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1154 ==================
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1155
98
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diff changeset
1156 JBrowse2-in-Galaxy offers a highly configurable, workflow-compatible Genome viewer.
0
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1157
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1158
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diff changeset
1159 Use and local viewing
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1160 =====================
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1161
107
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diff changeset
1162 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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diff changeset
1163
112
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diff changeset
1164 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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diff changeset
1165 used to generate the data:
990291e918c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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1166
114
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diff changeset
1167 ::
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diff changeset
1168
99
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diff changeset
1169 bam
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diff changeset
1170 bed
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diff changeset
1171 bigwig
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diff changeset
1172 cram
990291e918c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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diff changeset
1173 gff3
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diff changeset
1174 hic
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diff changeset
1175 maf
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diff changeset
1176 paf
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diff changeset
1177 vcf
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diff changeset
1178
134
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diff changeset
1179 Blastxml was deprecated in JBrowse 2.15.4 because the emitted GFF fails validation and will not display
107
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diff changeset
1180 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
1181 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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1182
0
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1183 A JBrowse2 history item can be opened by viewing it (the "eye" icon).
7
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1184
0
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diff changeset
1185 Overview
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1186 --------
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1187
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diff changeset
1188 JBrowse is a fast, embeddable genome browser built completely with
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diff changeset
1189 JavaScript and HTML5.
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1190
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diff changeset
1191 The JBrowse-in-Galaxy (JiG) tool was written to help build complex
7
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diff changeset
1192 JBrowse installations straight from Galaxy. It allows you to build up a JBrowse instance without worrying
0
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1193 about how to run the command line tools to format your data, and which
7
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1194 options need to be supplied and where.
0
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1195
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1196 Options
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1197 -------
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1198
17
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diff changeset
1199 **Reference or Assembly**
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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1200
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diff changeset
1201 Choose either a built-in or select one from your history.
0
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1202
17
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diff changeset
1203 Track coordinates and contig names *must* match this reference precisely
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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diff changeset
1204 or they will not display.
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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diff changeset
1205
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diff changeset
1206 **Track Groups** represent a set of tracks in a single category.
0
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1207
99
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diff changeset
1208
0
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diff changeset
1209 Annotation Tracks
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
1210 -----------------
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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1211
112
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diff changeset
1212
56f9a6e0fe80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 566509061b742b73c8dd1a1db6813fbf6a7a3792
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diff changeset
1213 BED
56f9a6e0fe80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 566509061b742b73c8dd1a1db6813fbf6a7a3792
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1214 ~~~
56f9a6e0fe80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 566509061b742b73c8dd1a1db6813fbf6a7a3792
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diff changeset
1215
56f9a6e0fe80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 566509061b742b73c8dd1a1db6813fbf6a7a3792
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diff changeset
1216 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
1217
56f9a6e0fe80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 566509061b742b73c8dd1a1db6813fbf6a7a3792
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diff changeset
1218 Bed files created by the *Bigwig extremes to bed features* tool have the 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
1219 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
1220 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
1221
56f9a6e0fe80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 566509061b742b73c8dd1a1db6813fbf6a7a3792
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diff changeset
1222
86
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diff changeset
1223 MAF
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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diff changeset
1224 ~~~
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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diff changeset
1225
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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diff changeset
1226 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
1227 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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parents: 85
diff changeset
1228 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
1229
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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diff changeset
1230 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
1231 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
1232 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
1233
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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diff changeset
1234
0
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diff changeset
1235 GFF3/BED
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
1236 ~~~~~~~~
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
17
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diff changeset
1238 Standard feature tracks. They usually highlight genes, mRNAs and other features of interest along a genomic region.
0
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diff changeset
1239
5
efc64d8f4b72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9
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diff changeset
1240 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
1241 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
1242 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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parents: 16
diff changeset
1243 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
1244 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
1245
0
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diff changeset
1246 BAM Pileups
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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1247 ~~~~~~~~~~~
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
1248
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 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
1250 that bam data.
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
1251
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diff changeset
1252
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
1253 BlastXML
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 ~~~~~~~~
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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1255
134
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diff changeset
1256 Deprecated in 2.15.4 because the new GFF parser rejects the output of the
ed3a21033188 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit bb6736899ac3029f73455637a04a006fcd857fc2
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diff changeset
1257 original JBrowse1 blastxml to gff converter.
0
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diff changeset
1258
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
1259 Local viewing
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
1260 =============
990291e918c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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diff changeset
1261
990291e918c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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diff changeset
1262 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
1263 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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parents: 98
diff changeset
1264
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 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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diff changeset
1266 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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diff changeset
1267 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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diff changeset
1268
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
1269 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
1270
990291e918c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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diff changeset
1271 *python3 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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diff changeset
1272
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 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
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parents: 98
diff changeset
1274 but the script appears to be running, try pointing your web browser to the default of *localhost:8080*
0
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diff changeset
1275
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diff changeset
1276 ]]></help>
97
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diff changeset
1277 <expand macro="citations"/>
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diff changeset
1278 <expand macro="creators"/>
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diff changeset
1279 </tool>