Mercurial > repos > fubar > jbrowse2

annotate jbrowse2.xml @ 98:b1260bca5fdc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
author bgruening
date Wed, 05 Jun 2024 10:00:07 +0000
parents 74074746ccd8
children 990291e918c7
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98
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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1 <tool id="jbrowse2" name="JBrowse2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
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2 <description>genome browser</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="edamInc"/>
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7 <xrefs>
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8 <xref type="bio.tools">jbrowse2</xref>
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9 </xrefs>
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10 <expand macro="requirements"/>
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11 <required_files>
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12 <include path="autogenJB2.py"/>
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13 <include path="blastxml_to_gapped_gff3.py"/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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14 <include path="convertMAF.sh"/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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15 <include path="gff3_rebase.py"/>
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16 <include path="jb2_webserver.py"/>
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17 <include path="jbrowse2.py"/>
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18 <include path="maf2bed.py"/>
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19 </required_files>
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20 <version_command>python '${__tool_directory__}/jbrowse2.py' --version</version_command>
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21 <command detect_errors="aggressive"><![CDATA[
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22 mkdir -p '$output.files_path' &&
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23 cp '$trackxml' '$output.files_path/galaxy.xml' &&
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24 export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2 &&
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25 #if $jbgen.ucol.formcoll=="collect":
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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26 python '$__tool_directory__/autogenJB2.py'
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27 #for $key in $autoCollection.keys():
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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28 #if $autoCollection[$key].is_collection:
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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29 #set subCol=$autoCollection[$key]
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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30 #set pafs=[($subCol[x],$subcol[x].ext,x) for x in $subCol.keys() if $subCol[x].ext == 'paf']
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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31 #if len($pafs) > 0:
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32 --pafmeta '$pafs[0]'
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33 #set refs = [($pafs[0][2],$subCol[x],x) for x in $subCol.keys() if $subCol[x].ext == 'fasta']
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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>${jbgen.zipOut}</zipOut>
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77 <analytics>${jbgen.enableAnalytics}</analytics>
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78 <primary_color>${jbgen.primary_color}</primary_color>
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79 <secondary_color>${jbgen.secondary_color}</secondary_color>
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80 <tertiary_color>${jbgen.tertiary_color}</tertiary_color>
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81 <quaternary_color>${jbgen.quaternary_color}</quaternary_color>
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82 <font_size>${jbgen.font_size}</font_size>
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83 <session_name>${jbgen.session_name}</session_name>
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84 </general>
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85 <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl>
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86 </metadata>
62
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87 #if $jbgen.ucol.formcoll=="form":
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88 #for $assembly in $assemblies:
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89 <assembly>
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90 <metadata>
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91 <genomes>
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92 #if str($assembly.reference_genome.genome_type_select) == "uri":
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93 <genome path="${assembly.reference_genome.uri}" label="${assembly.reference_genome.refname}" useuri="yes">
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94 <metadata>
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95 <dataset
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96 dname = "${assembly.reference_genome.refname}" />
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97 </metadata>
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98 </genome>
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99 #else if str($assembly.reference_genome.genome_type_select) == "indexed":
87
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100 <genome path="${assembly.reference_genome.genome.fields.path}" label="${assembly.reference_genome.genome.fields.dbkey}" useuri="no">
62
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101 <metadata>
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102 <dataset
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103 dname = "${assembly.reference_genome.genome.fields.name}" />
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104 </metadata>
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105 </genome>
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106 #else
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107 <genome path="$assembly.reference_genome.genome" label="${assembly.reference_genome.genome.name}" useuri="no">
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108 <metadata>
88
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109
62
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110 <dataset id="${__app__.security.encode_id($assembly.reference_genome.genome.id)}"
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111 hid="${assembly.reference_genome.genome.hid}"
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112 size="${assembly.reference_genome.genome.get_size(nice_size=True)}"
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113 edam_format="${assembly.reference_genome.genome.datatype.edam_format}"
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114 file_ext="${assembly.reference_genome.genome.ext}"
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115 dname = "${assembly.reference_genome.genome.name}"
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116 />
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117 <history
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118 #if $assembly.reference_genome.genome.history.user:
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119 user_email="${assembly.reference_genome.genome.history.user.email}"
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120 user_id="${assembly.reference_genome.genome.history.user_id}"
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121 display_name="${assembly.reference_genome.genome.history.get_display_name()}"/>
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122 #else
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123 user_email="anonymous"
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124 user_id="-1"
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125 display_name="Unnamed History"
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126 #end if
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127 id="${__app__.security.encode_id($assembly.reference_genome.genome.history_id)}"
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128 />
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129 <metadata
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130 #for (key, value) in $assembly.reference_genome.genome.get_metadata().items():
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131 #if "_types" not in $key:
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132 #if isinstance($value, list):
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133 #set value_str = "[%s]" % ','.join([str(val) for val in value])
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134 ${key}="$value_str"
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135 #else
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136 ${key}="${value}"
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137 #end if
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138 #end if
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139 #end for
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140 />
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141 <tool
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142 tool_id="${assembly.reference_genome.genome.creating_job.tool_id}"
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143 tool_version="${assembly.reference_genome.genome.creating_job.tool_version}"
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144 />
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145 </metadata>
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146 </genome>
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147 #end if
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148 </genomes>
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149 </metadata>
0
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150 <tracks>
62
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151 #for $tg in $assembly.track_groups:
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152 #for $track in $tg.data_tracks:
88
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153 #set input_exists = "False"
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154 #if $track.data_format.useuri.insource == "uri":
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155 #if $track.data_format.useuri.annouri:
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156 #set input_exists = "True"
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157 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
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158 <files>
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159 <trackFile path="${track.data_format.useuri.annouri}" ext="${track.data_format.data_format_select}"
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160 label="${track.data_format.useuri.annoname}" useuri="yes">
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161 <metadata>
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162 <dataset id = "${track.data_format.useuri.annouri}" />
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163 </metadata>
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164 </trackFile>
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165 </files>
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166 #end if
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167 #else if $track.data_format.useuri.insource == "history":
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168 #if $track.data_format.useuri.annotation:
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169 #set input_exists = "True"
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170 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
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171 <files>
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172 #for $dataset in $track.data_format.useuri.annotation:
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173 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.name}" useuri="no">
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174 <metadata>
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175 <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}"
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176 size="${dataset.get_size(nice_size=True)}"
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177 edam_format="${dataset.datatype.edam_format}"
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178 file_ext="${dataset.ext}" />
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179 <history id="${__app__.security.encode_id($dataset.history_id)}"
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180 #if $dataset.history.user:
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181 user_email="${dataset.history.user.email}"
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182 user_id="${dataset.history.user_id}"
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183 display_name="${dataset.history.get_display_name()}"/>
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184 #else
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185 user_email="anonymous"
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186 user_id="-1"
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187 display_name="Unnamed History"/>
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188 #end if
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189 <metadata
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190 #for (key, value) in $dataset.get_metadata().items():
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191 #if "_types" not in $key and $value is not None and len(str($value)) < 5000:
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192 #if isinstance($value, list):
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193 #set value_str = "[%s]" % ','.join([str(val) for val in value])
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194 ${key}="$value_str"
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195 #else
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196 ${key}="${value}"
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197 #end if
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198 #end if
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199 #end for
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200 />
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201 <tool
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202 tool_id="${dataset.creating_job.tool_id}"
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203 tool_version="${dataset.creating_job.tool_version}"
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204 />
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205 </metadata>
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206 </trackFile>
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207 #end for
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208 </files>
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209 #end if
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210 #end if
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211 #if $input_exists == "True":
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212 <options>
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213 <style>
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214 #if str($track.data_format.data_format_select) in ["gff", "bed", "maf", "blastxml"]:
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215 <type>${track.data_format.jbstyle.display}</type>
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216 #if str($track.data_format.jbstyle.display) in ["LinearBasicDisplay", "LinearVariantDisplay"]:
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217 <trackShowLabels>${track.data_format.jbstyle.show_labels}</trackShowLabels>
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218 <trackShowDescriptions>${track.data_format.jbstyle.show_descriptions}</trackShowDescriptions>
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219 #end if
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220 #else if str($track.data_format.data_format_select) == "vcf":
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221 <type>${track.data_format.jbstyle.track_style.display}</type>
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222 #if str($track.data_format.jbstyle.track_style.display) in ["LinearBasicDisplay", "LinearVariantDisplay"]:
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223 <trackShowLabels>${track.data_format.jbstyle.track_style.show_labels}</trackShowLabels>
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224 <trackShowDescriptions>${track.data_format.jbstyle.track_style.show_descriptions}</trackShowDescriptions>
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225 #end if
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226
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227 #end if
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228 #if str($track.data_format.data_format_select) in ["bam", "cram"]:
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229 <type>LinearAlignmentsDisplay</type>
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230 #end if
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231 #if str($track.data_format.data_format_select) in ["hic", "cool", "mcool", "scool"]:
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232 <type>LinearHicDisplay</type>
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233 #end if
88
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234 </style>
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235 #if str($track.data_format.data_format_select) == "bam":
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236 <bam>
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237 <bam_index>
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238 #for $dataset in $track.data_format.useuri.annotation:
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239 ${dataset} ~ ${dataset.metadata.bam_index},
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240 #end for
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241 </bam_index>
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242 </bam>
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243 #else if str($track.data_format.data_format_select) == "cram":
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244 <cram>
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245 <cram_index>
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246 #for $dataset in $track.data_format.useuri.annotation:
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247 ${dataset} ~ ${dataset.metadata.cram_index},
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248 #end for
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249 </cram_index>
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250 </cram>
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251 #else if str($track.data_format.data_format_select) == "blastxml":
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252 <blast>
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253 #if str($track.data_format.blast_parent) != "":
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254 <parent>${track.data_format.blast_parent}</parent>
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255 #end if
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256 <protein>${track.data_format.is_protein}</protein>
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257 <min_gap>${track.data_format.min_gap}</min_gap>
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258 </blast>
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259 #else if str($track.data_format.data_format_select) == "gff":
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260 <gff>
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261 #if $track.data_format.match_part.match_part_select == "true":
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262 <match>${track.data_format.match_part.name}</match>
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263 #end if
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264 </gff>
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265 #else if str($track.data_format.data_format_select) == "paf":
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266 <paf>
93
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267 #if str($track.data_format.pafuseuri.insource) == "history":
88
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268 <genome>
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269 #for $anno in $track.data_format.pafuseuri.annotation:
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270 ${anno} ~ ${anno.name},
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271 #end for
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272 </genome>
93
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273 <useuri>
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274 false
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275 </useuri>
88
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276 #else:
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277 <genome>
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278 #for $refgenome in $track.data_format.pafuseuri.refuri:
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279 ${refgenome.annotation} ~ ${refgenome.annoname},
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280 #end for
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281 </genome>
93
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282 <useuri>
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283 true
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284 </useuri>
88
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285 #end if
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286 </paf>
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287 #else if str($track.data_format.data_format_select) == "hic":
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288 <hic>
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289 </hic>
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290 #else if str($track.data_format.data_format_select) == "cool":
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291 <cool>
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292 </cool>
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293 #else if str($track.data_format.data_format_select) == "bed":
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294 <bed>
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295 </bed>
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296 #else if str($track.data_format.data_format_select) == "sparql":
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297 <label>${track.data_format.label}</label>
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298 <sparql>
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299 <url>${track.data_format.url}</url>
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300 <query>${track.data_format.query}</query>
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301 <query_refnames>${track.data_format.query_refnames}</query_refnames>
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302 </sparql>
62
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303 #end if
88
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304 </options>
46
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305 </track>
88
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306 #end if
46
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307 #end for
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308 #end for
0
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309 </tracks>
62
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310 </assembly>
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311 #end for
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312 #end if
0
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313 </root>
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314 ]]></configfile>
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315 </configfiles>
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316 <inputs>
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317 <repeat name="assemblies" min="1" title="Genome reference to provide display coordinates for this set of tracks" help="JBrowse2 can show a set of tracks for each of multiple genome reference fasta files">
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318 <conditional name="reference_genome">
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319 <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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320 <option selected="True" value="indexed">Use a Galaxy server built-in genome</option>
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321 <option value="history">Use a genome fasta file from the current history</option>
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322 <option value="uri">Provide a URI (e.g. "https://..." for a genome reference as
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323 tabix bgzip with predictable index file URI</option>
0
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324 </param>
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325 <when value="indexed">
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326 <param name="genome" type="select" optional="true" label="Select a built in reference genome or custom genome" help="If not listed, add a custom genome, use a history genome or a remote URI tabix genome">
93
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327 <options from_data_table="all_fasta">
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328 <filter column="2" type="sort_by"/>
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329 <validator message="No genomes are available for the selected input dataset" type="no_options"/>
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330 </options>
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331 </param>
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332 </when>
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333 <when value="history">
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334 <param name="genome" type="data" format="fasta" optional="true" label="Select the reference genome"/>
93
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335 </when>
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336 <when value="uri">
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337 <param name="uri" type="text" label="URI pointing to tabix compressed fasta"/>
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338 <param name="refname" type="text" label="Reference dbkey for tracks with this genome, such as hg38 or SacCer4"/>
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339 </when>
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340 </conditional>
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341 <repeat name="track_groups" title="Track Group">
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342 <param name="category" type="text" value="Default" optional="False" label="Track Category" help="Organise your tracks into Categories for a nicer end-user experience. You can use #date# and it will be replaced with the current date in 'yyyy-mm-dd' format, which is very useful for repeatedly updating a JBrowse instance when member databases / underlying tool versions are updated."/>
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343 <repeat name="data_tracks" title="Annotation Track">
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344 <conditional name="data_format" label="Track Data Selection Options">
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345 <param name="data_format_select" type="select" label="Track Type">
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346 <option value="bam">BAM track. Recommend convert to faster BED unless mapping annotation needed</option>
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347 <option value="bed">BED track</option>
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348 <option value="bigwig">BigWig track</option>
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349 <option value="blastxml">Blast XML track (as GFF3)</option>
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350 <option value="cram">CRAM track, we recomment to convert to BED like for BAM</option>
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351 <option value="gff">GFF/GFF3 track</option>
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352 <option value="cool">HiC as cool/mcool/scool format files</option>
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353 <option value="hic">HiC as juicebox_hic format file. Tabular hic_matrix will NOT work.</option>
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354 <option value="maf">Multiple alignment format. Reference name must match the MAF name exactly to work correctly</option>
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355 <option value="paf">PAF - approximate mapping positions between two set of sequences</option>
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356 <option value="vcf">VCF SNP track</option>
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357 </param>
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358 <when value="blastxml">
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359 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml"/>
98
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360 <param name="blast_parent" type="data" format="gff3" optional="true" label="Features used in Blast Search" help="in GFF3. This is used so we know where to map features. E.g. where results of which CDS Protein32 match up to. The query IDs in your blast results should MATCH some feature IDs in your GFF3 file. This is an optional field and is most useful if using JBrowse to display protein blast results on a DNA genome. blastn results don't need this, blastp results on a protein sequence don't need this."/>
97
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361 <param name="min_gap" type="integer" min="2" value="10" label="Minimum Gap Size" help="before a new match_part feature is created"/>
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362 <param name="is_protein" type="boolean" truevalue="true" falsevalue="false" label="Is this a protein blast search?"/>
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363 <expand macro="track_styling_vgp"/>
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364 <expand macro="track_visibility"/>
93
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365 </when>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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366 <when value="vcf">
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367 <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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368 <expand macro="track_styling_vcf"/>
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369 <expand macro="track_visibility"/>
93
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370 </when>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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371 <when value="gff">
97
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372 <expand macro="input_conditional" label="GFF/GFF3 Track Data" format="gff,gff3"/>
93
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373 <conditional name="match_part" label="match/match_part data">
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374 <param name="match_part_select" type="select" label="This is match/match_part data" help="Match part data selection ">
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375 <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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376 <option value="true">Match/match part data</option>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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377 </param>
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378 <when value="true">
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379 <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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380 </when>
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381 <when value="false"/>
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382 </conditional>
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383 <expand macro="track_styling_vgp"/>
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384 <expand macro="track_visibility"/>
93
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385 </when>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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386 <when value="bam">
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387 <expand macro="input_conditional" label="BAM Track Data" format="bam"/>
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388 <expand macro="track_visibility"/>
93
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389 </when>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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390 <when value="bed">
97
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391 <expand macro="input_conditional" label="BED Track Data" format="bed"/>
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392 <expand macro="track_styling_vgp"/>
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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="cram">
97
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396 <expand macro="input_conditional" label="CRAM Track Data" format="cram"/>
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397 <expand macro="track_visibility"/>
93
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398 </when>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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399 <when value="maf">
97
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400 <expand macro="input_conditional" label="MAF Track Data" format="maf"/>
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401 <expand macro="track_styling_vgp"/>
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402 <expand macro="track_visibility"/>
93
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403 </when>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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404 <when value="bigwig">
97
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405 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig"/>
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406 <expand macro="track_visibility"/>
93
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407 </when>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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408 <when value="paf">
97
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409 <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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410 <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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411 <expand macro="track_visibility"/>
93
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412 </when>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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413 <when value="hic">
97
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414 <expand macro="input_conditional" label="Binary Juicebox HiC data" format="hic,juicebox_hic"/>
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415 <expand macro="track_visibility"/>
93
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416 </when>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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417 <when value="cool">
97
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diff changeset
418 <expand macro="input_conditional" label="HiC data in cool/mcool/scool format" format="cool,mcool,scool"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
419 <expand macro="track_visibility"/>
93
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parents: 92
diff changeset
420 </when>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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parents: 92
diff changeset
421 </conditional>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
422 </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:
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423 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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424 </repeat>
97
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parents: 93
diff changeset
425 <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
426 </inputs>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
427 <outputs>
89
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11
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parents: 88
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428 <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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diff changeset
429 <change_format>
97
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parents: 93
diff changeset
430 <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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431 </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
432 </data>
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
433 </outputs>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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434 <tests>
93
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diff changeset
435 <test>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
436 <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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437 <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
438 <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
439 <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
440 <param name="genome.ext" value="fasta"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
441 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
442 <repeat name="track_groups">
97
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parents: 93
diff changeset
443 <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
444 <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
445 <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
446 <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
447 <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
448 <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
449 <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
450 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
451 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
452 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
453 <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
454 <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
455 <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
456 <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
457 <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
458 <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
459 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
460 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
461 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
462 <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
463 <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
464 <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
465 <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
466 <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
467 <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
468 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
469 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
470 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
471 <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
472 <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
473 <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
474 <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
475 <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
476 <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
477 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
478 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
479 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
480 <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
481 <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
482 <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
483 <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
484 <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
485 <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
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parents: 85
diff changeset
486 </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
487 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
488 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
489 <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
490 <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
491 <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
492 <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
493 <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
494 <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
495 </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
496 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
497 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
498 <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
499 <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
500 <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
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parents: 85
diff changeset
501 <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
502 <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
503 <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
504 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
505 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
506 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
507 <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
508 <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
509 <param name="data_format_select" value="blastxml"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
510 <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
511 <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
512 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlin.blastxml"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
513 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
514 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
515 </repeat>
88
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
516 <repeat name="data_tracks">
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
517 <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
518 <param name="data_format_select" value="bam"/>
88
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
519 <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
520 <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
521 <param name="annotation" value=""/>
88
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
522 </conditional>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
523 </conditional>
efd1d41f11b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents: 87
diff changeset
524 </repeat>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
525 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
526 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
527 <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
528 <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
529 <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
530 <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
531 <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
532 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
533 <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
534 <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
535 <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
536 <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
537 <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
538 <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
539 <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
540 <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
541 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
542 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
543 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
544 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
545 </repeat>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
546 <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
547 <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
548 <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
549 <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
550 <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
551 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
552 <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
553 <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
554 <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
555 <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
556 <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
557 <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
558 <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
559 <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
560 </conditional>
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 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
562 <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
563 <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
564 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
565 </conditional>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
566 </repeat>
91
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents: 90
diff changeset
567 <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
568 <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
569 <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
570 <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
571 <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
572 <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
573 </conditional>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
574 <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
575 <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
576 <repeat name="refuri">
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="annotation" value="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/arabidopsis.fa.gz"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
578 <param name="annoname" 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
579 </repeat>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
580 <repeat name="refuri">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
581 <param name="annotation" value="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Vvinifera1.fa.gz"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
582 <param name="annoname" 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
583 </repeat>
91
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents: 90
diff changeset
584 </conditional>
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents: 90
diff changeset
585 </conditional>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
586 </repeat>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
587 <repeat name="data_tracks">
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588 <conditional name="data_format">
97
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parents: 93
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589 <param name="data_format_select" value="paf"/>
91
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parents: 90
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590 <conditional name="useuri">
97
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parents: 93
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591 <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
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592 <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
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parents: 90
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593 </conditional>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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parents: 92
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594 <conditional name="pafuseuri">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
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595 <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
596 <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
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parents: 93
diff changeset
597 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Vvinifera1.fa"/>
91
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
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parents: 90
diff changeset
598 </conditional>
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
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parents: 90
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599 </conditional>
6246925692cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
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parents: 90
diff changeset
600 </repeat>
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
601 </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
602 </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
603 <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
604 <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
605 <param name="genome_type_select" value="uri"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
606 <param name="uri" value="https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
607 <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
608 </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
609 <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
610 <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
611 <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
612 <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
613 <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
614 <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
615 <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
616 <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
617 <param name="annoname" value="humanhic"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
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618 </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
619 </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
620 </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
621 </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
622 </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
623 <section name="jbgen">
97
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parents: 93
diff changeset
624 <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
625 <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
626 </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
627 <!-- use the following line to generate a ZIP file to inspect it -->
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
628 <!--output name="output" file="jbrowse2_result02.zip" ftype="zip" compare="sim_size"-->
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
629 <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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diff changeset
630 <assert_contents>
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
631 <has_archive_member path=".*" n="637" delta="10"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
632 <has_archive_member path="index.html"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
633 <has_archive_member path="static/media/roboto-latin-400-normal.3f2b9a42f643e62a49b7.woff"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
634 <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
635 <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
636 <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
637 </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
638 <has_archive_member path="galaxy.xml">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
639 <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
640 <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
641 <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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parents: 85
diff changeset
642 </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
643 <has_archive_member path="merlin.gff3_0.gz"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
644 <has_archive_member path="merlin.gff3_0.gz.tbi"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
645 <has_archive_member path="merlin.bw_1"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
646 <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
647 <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
648 <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
fubar
parents: 93
diff changeset
649 <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
650 <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
fubar
parents: 93
diff changeset
651 <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
652 <has_archive_member path="merlin-sample.bam_5.bai"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
653 <has_archive_member path="merlinlastz.maf_6.sorted.bed.gz.tbi"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
654 <has_archive_member path="merlin.blastxml_7.gz"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
655 <has_archive_member path="dm3test.cool_9.hic"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
656 <has_archive_member path="peach-grape-map.paf_10"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
657 <has_archive_member path="arabgrapepeach.paf_11"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
658 <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
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parents: 93
diff changeset
659 <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
660 <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
661 <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
662 <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
663 <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
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parents: 93
diff changeset
664 <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
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parents: 93
diff changeset
665 <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
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parents: 85
diff changeset
666 <has_archive_member path="config.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
667 <has_json_property_with_text property="name" text="Merlin"/>
86
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents: 85
diff changeset
668 </has_archive_member>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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diff changeset
669 </assert_contents>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
670 </output>
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents: 85
diff changeset
671 </test>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
672 <test>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
673 <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
674 <collection type="list" name="merlintest">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
675 <element name="merlin.fa" value="merlin.fa"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
676 <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
677 <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
678 </collection>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
679 </param>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
680 <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
681 <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
682 <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
683 <param name="ucol|formcoll" value="collect"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
684 </section>
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
685 <!-- use the following line to generate a ZIP file to inspect it -->
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
686 <!--output name="output" file="jbrowse2_result01.zip" ftype="zip" compare="sim_size"-->
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
687 <output name="output" ftype="zip">
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
688 <assert_contents>
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
689 <has_archive_member path=".*" n="611" delta="10"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
690 <has_archive_member path="index.html"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
691 <has_archive_member path="static/media/roboto-latin-400-normal.3f2b9a42f643e62a49b7.woff"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
692 <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
693 <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
694 <has_text text="background_color"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
695 </has_archive_member>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
696 <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
697 <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
698 <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
699 <element_text_is path="./metadata/general/session_name" text="Collection test"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
700 </has_archive_member>
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
701 <has_archive_member path="jb2_webserver.py"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
702 <has_archive_member path="merlin.fa.fa.gz.gzi"/>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
703 <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
704 <has_archive_member path="merlin.fa.fa.gz.fai"/>
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
705 <has_archive_member path="merlin.bw"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
706 <has_archive_member path="index.html"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
707 <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
708 <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
709 </assert_contents>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
710 </output>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
711 </test>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
712 <test>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
713 <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
714 <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
715 <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
716 <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
717 <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
718 <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
719 </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
720 <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
721 <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
722 <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
723 <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
724 <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
725 <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
726 <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
727 <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
728 </conditional>
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
729 </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
730 </repeat>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
731 </repeat>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
732 </repeat>
98
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
733 <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
734 <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
735 </section>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
736 <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
737 <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
738 <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
739 <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
740 <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
741 <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
742 <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
743 <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
744 <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
745 <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
746 <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
747 </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
748 </assert_contents>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
749 </output>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
750 </test>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
751 <test>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
752 <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
753 <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
754 <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
755 <param name="genome" 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
756 <param name="genome.ext" value="fasta"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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diff changeset
757 <param name="genome.name" value="Merlin"/>
93
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parents: 92
diff changeset
758 </conditional>
62
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parents: 60
diff changeset
759 <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
760 <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
761 <repeat name="data_tracks">
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
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parents: 60
diff changeset
762 <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
763 <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
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parents: 60
diff changeset
764 <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
765 <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
766 <param name="annotation" value="vcf/merlin.vcf"/>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
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parents: 60
diff changeset
767 </conditional>
46
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parents: 45
diff changeset
768 </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
769 </repeat>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
770 </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
771 </repeat>
98
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bgruening
parents: 97
diff changeset
772 <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
773 <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
774 </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
775 <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
776 <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
777 <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
778 <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
779 <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
780 <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
781 <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
782 <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
783 <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
784 <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
785 </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
786 </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
787 </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
788 </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
789 <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
790 <repeat name="assemblies">
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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parents: 92
diff changeset
791 <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
792 <param name="genome_type_select" value="history"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
793 <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
794 <param name="genome.ext" value="fasta"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
795 <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
796 </conditional>
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
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parents: 60
diff changeset
797 </repeat>
98
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
798 <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
799 <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
800 </section>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
801 <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
802 <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
803 <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
804 <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
805 <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
806 <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
807 <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
808 </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
809 </assert_contents>
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
810 </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
811 </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
812 <test>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
813 <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
814 <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
815 <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
816 <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
817 <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
818 <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
819 </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
820 <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
821 <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
822 <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
823 <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
824 <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
825 <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
826 <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
827 <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
828 </conditional>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
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parents: 60
diff changeset
829 </conditional>
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
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parents: 60
diff changeset
830 </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
831 </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
832 </repeat>
98
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
833 <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
834 <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
835 </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
836 <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
837 <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
838 <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
839 <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
840 <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
841 <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
842 <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
843 <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
844 <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
845 <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
846 </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
847 </assert_contents>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
848 </output>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
849 </test>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
850 <test>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
851 <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
852 <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
853 <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
854 <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
855 <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
856 <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
857 </conditional>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
858 <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
859 <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
860 <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
861 <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
862 <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
863 <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
864 <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
865 <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
866 </conditional>
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
867 </conditional>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
868 <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
869 <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
870 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
871 <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
872 <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
873 <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
874 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
875 <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
876 <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
877 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
878 </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
879 </repeat>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
880 </repeat>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
881 <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
882 <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
883 <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
884 <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
885 <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
886 <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
887 <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
888 <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
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 <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
891 <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
892 </conditional>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
893 <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
894 <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
895 <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
896 <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
897 <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
898 <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
899 </conditional>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
900 </conditional>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
901 </section>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
902 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
903 </repeat>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
904 </repeat>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
905 <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
906 <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
907 <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
908 <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
909 <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
910 <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
911 <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
912 <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
913 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
914 <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
915 <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
916 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
917 <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
918 <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
919 <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
920 <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
921 <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
922 <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
923 </conditional>
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="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
925 <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
926 <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
927 <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
928 </conditional>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
929 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
930 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
931 </section>
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 45
diff changeset
932 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
933 </repeat>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
934 <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
935 <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
936 <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
937 <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
938 <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
939 <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
940 </conditional>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
941 <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
942 <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
943 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
944 <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
945 <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
946 <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
947 <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
948 <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
949 <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
950 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
951 <conditional name="color_scheme">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents: 93
diff changeset
952 <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
953 <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
954 <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
955 <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
956 </conditional>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
957 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
958 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
959 </section>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
960 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
961 </repeat>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
962 <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
963 <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
964 <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
965 <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
966 <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
967 <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
968 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
969 <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
970 <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
971 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
972 <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
973 <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
974 <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
975 <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
976 <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
977 <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
978 <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
979 <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
980 </conditional>
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="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
982 <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
983 <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
984 <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
985 </conditional>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
986 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
987 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
988 </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
989 </conditional>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
990 </repeat>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
991 <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
992 <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
993 <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
994 <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
995 <param name="annotation" value="gff3/1.gff"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
996 <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
997 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
998 <conditional name="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
999 <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
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parents: 62
diff changeset
1000 </conditional>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1001 <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
1002 <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
1003 <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
1004 <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
1005 <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
1006 <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
1007 <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
1008 <param name="maximum" value="1000"/>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
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parents: 62
diff changeset
1009 </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
1010 <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
1011 <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
1012 <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
1013 <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
1014 <param name="style_color" value="#ff0000"/>
63
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1015 </conditional>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff changeset
1016 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff changeset
1017 </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
1018 </section>
46
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diff changeset
1019 </conditional>
63
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diff changeset
1020 </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
1021 </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
1022 <repeat name="track_groups">
97
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diff changeset
1023 <param name="category" value="Realistic"/>
63
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parents: 62
diff changeset
1024 <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
1025 <conditional name="data_format">
97
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parents: 93
diff changeset
1026 <param name="data_format_select" value="gff"/>
63
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parents: 62
diff changeset
1027 <conditional name="useuri">
97
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parents: 93
diff changeset
1028 <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
1029 <param name="insource" value="history"/>
0
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diff changeset
1030 </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
1031 <conditional name="match_part">
97
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parents: 93
diff changeset
1032 <param name="match_part_select" value="false"/>
0
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diff changeset
1033 </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
1034 <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
1035 <conditional name="color_score">
97
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parents: 93
diff changeset
1036 <param name="color_score_select" value="none"/>
63
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parents: 62
diff changeset
1037 </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
1038 <conditional name="color">
97
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parents: 93
diff changeset
1039 <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
1040 </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
1041 </section>
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
1042 </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
1043 </repeat>
ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents: 62
diff changeset
1044 <repeat name="data_tracks">
93
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parents: 92
diff changeset
1045 <conditional name="data_format">
97
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parents: 93
diff changeset
1046 <param name="data_format_select" value="gff"/>
93
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parents: 92
diff changeset
1047 <conditional name="useuri">
97
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
1048 <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
1049 <param name="insource" value="history"/>
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
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parents: 92
diff changeset
1051 <conditional name="match_part">
97
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parents: 93
diff changeset
1052 <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
1053 <param name="name" value="cDNA_match"/>
93
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parents: 92
diff changeset
1054 </conditional>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
1055 <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
1056 <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
1057 <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
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parents: 92
diff changeset
1058 </conditional>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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parents: 92
diff changeset
1059 <conditional name="color">
97
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parents: 93
diff changeset
1060 <param name="color_select" value="automatic"/>
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
1061 </conditional>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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parents: 92
diff changeset
1062 </section>
0
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diff changeset
1063 </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
1064 </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
1065 </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
1066 </repeat>
98
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parents: 97
diff changeset
1067 <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
1068 <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
1069 </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
1070 <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
1071 <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
1072 <has_archive_member path="A.gff"/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
1073 <has_archive_member path="B.gff"/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
1074 <has_archive_member path="C.gff"/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
1075 <has_archive_member path="interpro.gff"/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
1076 <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
1077 <has_archive_member path="2.gff"/>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
1078 <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
1079 <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
1080 <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
1081 <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
1082 </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
1083 </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
1084 </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
1085 </test>
98
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
1086 <test>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
1087 <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
1088 <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
1089 <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
1090 <param name="genome" value="merlin.fa"/>
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 </conditional>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
1092 <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
1093 <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
1094 <repeat name="data_tracks">
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
1095 <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
1096 <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
1097 <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
1098 </conditional>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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diff changeset
1099 </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
1100 </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
1101 </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
1102 <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
1103 <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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diff changeset
1104 </section>
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
1105 <output name="output" ftype="zip">
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
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diff changeset
1106 <assert_contents>
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
1107 <!-- roughly 590 files in an archive -->
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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diff changeset
1108 <has_archive_member path=".*" n="608" delta="30"/>
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1109 <has_archive_member path="index.html"/>
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1110 <has_archive_member path="static/media/roboto-latin-400-normal.3f2b9a42f643e62a49b7.woff"/>
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1111 <has_archive_member path="manifest.json">
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1112 <has_text text="favicon.ico"/>
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1113 <has_text text="background_color"/>
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1114 </has_archive_member>
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1115 <has_archive_member path="merlin.fa.fa.gz.fai"/>
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1116 <has_archive_member path="galaxy.xml">
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1117 <is_valid_xml/>
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1118 <has_n_elements_with_path path="./metadata/general/session_name" n="1"/>
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1119 <element_text_is path="./metadata/general/session_name" text="New JBrowse2 session"/>
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1120 </has_archive_member>
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1121 </assert_contents>
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1122 </output>
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1123 </test>
0
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1124 </tests>
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1125 <help><![CDATA[
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1126
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1127 JBrowse2-in-Galaxy
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1128 ==================
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1129
98
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1130 JBrowse2-in-Galaxy offers a highly configurable, workflow-compatible Genome viewer.
0
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1131
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1132 Compared to JBrowse1-in-Galaxy, there is no support for alternative codons for unusual genomes,
98
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1133 and detailed track styling is not yet implemented. Please contact us if you are missing features.
0
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1134
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1135 Use and local viewing
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1136 =====================
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1137
7
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1138
0
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1139 A JBrowse2 history item can be opened by viewing it (the "eye" icon).
7
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1140
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diff changeset
1141 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.
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diff changeset
1142 This can be shared and viewed without Galaxy.
0
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1143
7
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1144 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,
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diff changeset
1145 assuming that Python3 is already working on your desktop - if not you will have to install it first. Unzip the archive (*unzip [filename].zip*) and change
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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diff changeset
1146 directory to the first level in that zip archive. It contains a file named *jb2_webserver.py*
0
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1147
7
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diff changeset
1148 With python3 installed,
0
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1149
7
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diff changeset
1150 *python3 jb2_webserver.py*
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diff changeset
1151
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diff changeset
1152 will serve the unarchived JBrowse2 configuration from the same directory as the python script automatically. If a new browser window does not open,
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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diff changeset
1153 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
1154
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diff changeset
1155 Overview
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1156 --------
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1157
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diff changeset
1158 JBrowse is a fast, embeddable genome browser built completely with
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
1159 JavaScript and HTML5.
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diff changeset
1160
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diff changeset
1161 The JBrowse-in-Galaxy (JiG) tool was written to help build complex
7
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diff changeset
1162 JBrowse installations straight from Galaxy. It allows you to build up a JBrowse instance without worrying
0
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diff changeset
1163 about how to run the command line tools to format your data, and which
7
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diff changeset
1164 options need to be supplied and where.
0
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diff changeset
1165
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diff changeset
1166 Options
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1167 -------
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1168
17
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diff changeset
1169 **Reference or Assembly**
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diff changeset
1170
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diff changeset
1171 Choose either a built-in or select one from your history.
0
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diff changeset
1172
17
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diff changeset
1173 Track coordinates and contig names *must* match this reference precisely
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diff changeset
1174 or they will not display.
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diff changeset
1175
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diff changeset
1176 **Track Groups** represent a set of tracks in a single category.
0
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1177
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diff changeset
1178 Annotation Tracks
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1179 -----------------
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1180
86
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diff changeset
1181 MAF
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diff changeset
1182 ~~~
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diff changeset
1183
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diff changeset
1184 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
1185 because it becomes the "dbkey" for that reference. So, it must be exactly the same as the genome name (dbkey) used
0fae1d68347f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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diff changeset
1186 when making the MAF, typically in the Lastz tool.
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diff changeset
1187
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diff changeset
1188 If you used "hg38" as the reference in Lastz, that is exactly what the reference fasta should be named for any MAF track.
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diff changeset
1189 Change it using the "pencil" icon on the reference data in your history. Any other name, such as "hg38.fasta"
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diff changeset
1190 will cause the MAF track to show no data since there are no matches with that reference dbkey.
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diff changeset
1191
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diff changeset
1192
0
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1193 GFF3/BED
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1194 ~~~~~~~~
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1195
17
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1196 Standard feature tracks. They usually highlight genes, mRNAs and other features of interest along a genomic region.
0
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1197
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1198 When these contain tens of millions of features, such as repeat regions from a VGP assembly, displaying one at a time leads
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1199 to extremely slow loading times when a large region is in view, unless the "LinearPileupDisplay" display option is
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1200 selected for that track in the styling options section. The default is LinearBasicDisplay, which shows all details and works
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1201 well for relatively sparse bed files. A better option is to make a bigwig track using a set of windows based on the
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1202 lengths of each assembly or reference contig.
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1203
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1204 BAM Pileups
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1205 ~~~~~~~~~~~
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1206
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1207 We support BAM files and can automatically generate SNP tracks based on
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1208 that bam data.
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1209
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1210
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1211 BlastXML
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1212 ~~~~~~~~
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1213
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1214 JiG now supports both blastn and blastp datasets. JiG internally uses a
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1215 blastXML to gapped GFF3 tool to convert your blastxml datasets into a
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1216 format amenable to visualization in JBrowse. This tool is also
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1217 available separately from the IUC on the toolshed.
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1218
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1219 **Minimum Gap Size** reflects how long a gap must be before it becomes a
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1220 real gap in the processed gff3 file. In the picture above, various sizes
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1221 of gaps can be seen. If the minimum gap size was set much higher, say
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1222 100nt, many of the smaller gaps would disappear, and the features on
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1223 both sides would be merged into one, longer feature. This setting is
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1224 inversely proportional to runtime and output file size. *Do not set this
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1225 to a low value for large datasets*. By setting this number lower, you
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1226 will have extremely large outputs and extremely long runtimes. The
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1227 default was configured based off of the author's experience, but the
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1228 author only works on small viruses. It is *strongly* recommended that
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1229 you filter your blast results before display, e.g. picking out the top
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1230 10 hits or so.
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1231
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1232 **Protein blast search** option merely informs underlying tools that
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1233 they should adjust feature locations by 3x.
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1234
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1235
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1236 ]]></help>
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1237 <expand macro="citations"/>
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1238 <expand macro="creators"/>
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1239 </tool>