Mercurial > repos > iuc > jbrowse

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 80fbf6800feb0bb02c047d37e97b7a12e9c68f4c"
author iuc
date Fri, 23 Apr 2021 11:36:56 +0000
parents 5c317ff96859
children
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1 <tool id="jbrowse" name="JBrowse" version="@TOOL_VERSION@+@WRAPPER_VERSION@">
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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 <xrefs>
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7 <xref type="bio.tools">jbrowse</xref>
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8 </xrefs>
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9 <expand macro="requirements"/>
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10 <edam_operations>
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11 <edam_operation>operation_0573</edam_operation>
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12 <edam_operation>operation_0564</edam_operation>
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13 </edam_operations>
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14 <edam_topics>
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15 <edam_topic>topic_3307</edam_topic>
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16 <edam_topic>topic_0092</edam_topic>
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17 </edam_topics>
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18 <version_command>python '${__tool_directory__}/jbrowse.py' --version</version_command>
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19 <command detect_errors="aggressive"><![CDATA[
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20 #if $action.action_select == "create":
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21 mkdir -p $output.files_path &&
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22 #else:
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23 cp -R $action.update_jbrowse.extra_files_path $output.files_path &&
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24 #end if
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25
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26 ## Copy the XML file into the directory, mostly for debugging
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27 ## but nice if users want to reproduce locally
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28 cp $trackxml $output.files_path/galaxy.xml &&
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30 export JBROWSE_SOURCE_DIR=\$(dirname \$(which prepare-refseqs.pl))/../opt/jbrowse &&
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31
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32 ## Once that's done, we run the python script to handle the real work
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33 python '$__tool_directory__/jbrowse.py'
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34
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35 --jbrowse \${JBROWSE_SOURCE_DIR}
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36 --standalone '$standalone'
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38 --outdir $output.files_path
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39 $trackxml &&
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41 #if str($standalone) != "data":
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42 cp $output.files_path/index.html $output;
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43 #else:
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44 cp $dummyIndex $output;
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45 #end if
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46
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47 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph.
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48 #if str($uglyTestingHack) == "enabled":
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49 cp $trackxml $output
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50 #end if
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51 ]]></command>
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52 <configfiles>
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53 <configfile name="dummyIndex"><![CDATA[
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54 <html>
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55 <head>
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56 </head>
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57 <body>
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58 <h1>JBrowse Data Directory</h1>
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59 <p>
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60 Hi! This is not a full JBrowse instance. JBrowse v0.4(+?)
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61 started shipping with the ability to produce just the
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62 "data" directory from a JBrowse instance, rather than a
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63 complete, standalone instance. This was intended to be used
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64 with the in-development Apollo integration, but may have other
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65 uses as well.
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66 </p>
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67 <p>
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68 <u>This is not usable on its own</u>. The output dataset may be
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69 used with Apollo, or may be passed through the "JBrowse -
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70 Convert to Standalone" tool in Galaxy to "upgrade" to a full
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71 JBrowse instance.
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72 </p>
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73 </body>
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74 </html>
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75 ]]></configfile>
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76 <configfile name="trackxml"><![CDATA[<?xml version="1.0"?>
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77 <root>
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78 <metadata>
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79 <gencode>$gencode</gencode>
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80 <genomes>
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81 #if str($reference_genome.genome_type_select) == "indexed":
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82 <genome path="${reference_genome.genomes.fields.path}">
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83 <metadata />
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84 </genome>s
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85 #else
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86 <genome path="$reference_genome.genome">
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87 <metadata>
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88 <dataset id="${__app__.security.encode_id($reference_genome.genome.id)}" hid="${reference_genome.genome.hid}"
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89 size="${reference_genome.genome.get_size(nice_size=True)}"
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90 edam_format="${reference_genome.genome.datatype.edam_format}"
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91 file_ext="${reference_genome.genome.ext}" />
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92 <history id="${__app__.security.encode_id($reference_genome.genome.history_id)}"
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93 #if $reference_genome.genome.history.user:
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94 user_email="${reference_genome.genome.history.user.email}"
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95 user_id="${reference_genome.genome.history.user_id}"
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96 display_name="${reference_genome.genome.history.get_display_name()}"/>
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97 #else
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98 user_email="anonymous"
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99 user_id="-1"
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100 display_name="Unnamed History"/>
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101 #end if
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102 <metadata
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103 #for (key, value) in $reference_genome.genome.get_metadata().items():
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104 #if "_types" not in $key:
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105 ${key}="${value}"
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106 #end if
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107 #end for
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108 />
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109 <tool
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110 tool_id="${reference_genome.genome.creating_job.tool_id}"
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111 tool_version="${reference_genome.genome.creating_job.tool_version}"
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112 />
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113 </metadata>
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114 </genome>
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115 #end if
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116 </genomes>
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117 <general>
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118 <defaultLocation>${jbgen.defaultLocation}</defaultLocation>
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119 <trackPadding>${jbgen.trackPadding}</trackPadding>
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120
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121 <shareLink>${jbgen.shareLink}</shareLink>
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122 <aboutDescription>${jbgen.aboutDescription}</aboutDescription>
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123 <show_tracklist>${jbgen.show_tracklist}</show_tracklist>
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124 <show_nav>${jbgen.show_nav}</show_nav>
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125 <show_overview>${jbgen.show_overview}</show_overview>
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126 <show_menu>${jbgen.show_menu}</show_menu>
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127 <hideGenomeOptions>${jbgen.hideGenomeOptions}</hideGenomeOptions>
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128 </general>
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129 <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl>
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130 </metadata>
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131 <tracks>
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132 #for $tg in $track_groups:
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133 #for $track in $tg.data_tracks:
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134 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
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135 #if $track.data_format.data_format_select != "rest" and $track.data_format.data_format_select != "sparql":
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136 <files>
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137 #for $dataset in $track.data_format.annotation:
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138 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}">
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139 <metadata>
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140 <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}"
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141 size="${dataset.get_size(nice_size=True)}"
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142 edam_format="${dataset.datatype.edam_format}"
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143 file_ext="${dataset.ext}" />
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144 <history id="${__app__.security.encode_id($dataset.history_id)}"
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145 #if $dataset.history.user:
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146 user_email="${dataset.history.user.email}"
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147 user_id="${dataset.history.user_id}"
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148 display_name="${dataset.history.get_display_name()}"/>
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149 #else
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150 user_email="anonymous"
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151 user_id="-1"
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152 display_name="Unnamed History"/>
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153 #end if
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154 <metadata
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155 #for (key, value) in $dataset.get_metadata().items():
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156 #if "_types" not in $key and $value is not None and len(str($value)) < 5000:
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157 ${key}="${value}"
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158 #end if
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159 #end for
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160 />
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161 <tool
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162 tool_id="${dataset.creating_job.tool_id}"
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163 tool_version="${dataset.creating_job.tool_version}"
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164 />
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165 </metadata>
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166 </trackFile>
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167 #end for
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168 </files>
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169 #end if
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170
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171 <options>
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172 #if str($track.data_format.data_format_select) == "gene_calls" or str($track.data_format.data_format_select) == "blast" or str($track.data_format.data_format_select) == "rest" or str($track.data_format.data_format_select) == "sparql":
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173 <style>
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174 <overridePlugins>${track.data_format.override_apollo_plugins}</overridePlugins>
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175 <overrideDraggable>${track.data_format.override_apollo_drag}</overrideDraggable>
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176 <className>${track.data_format.jbstyle.style_classname}</className>
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177 <description>${track.data_format.jbstyle.style_description}</description>
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178 <label>${track.data_format.jbstyle.style_label}</label>
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179 <height>${track.data_format.jbstyle.style_height}</height>
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180 <maxHeight>${track.data_format.jbstyle.max_height}</maxHeight>
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181 </style>
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182 <scaling>
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183 #if str($track.data_format.jbcolor_scale.color_score.color_score_select) == "none":
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184 <method>ignore</method>
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185 <scheme>
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186 #if str($track.data_format.jbcolor_scale.color_score.color.color_select) == "automatic":
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187 <color>__auto__</color>
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188 #else
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189 <color>${track.data_format.jbcolor_scale.color_score.color.style_color}</color>
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190 #end if
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191 </scheme>
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192 #else
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193 <method>score</method>
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194 <algo>${track.data_format.jbcolor_scale.color_score.score_scaling}</algo>
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195 <scales>
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196 <type>${track.data_format.jbcolor_scale.color_score.score_scales.scale_select}</type>
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197
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198 #if str($track.data_format.jbcolor_scale.color_score.score_scales.scale_select) == "manual":
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199 <min>${track.data_format.jbcolor_scale.color_score.score_scales.minimum}</min>
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200 <max>${track.data_format.jbcolor_scale.color_score.score_scales.maximum}</max>
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201 #end if
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202 </scales>
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203 <scheme>
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204 <type>${track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme}</type>
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205 ## auto_color
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206 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme) == "opacity":
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207 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.color.color_select) == "automatic":
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208 <color>__auto__</color>
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209 #else
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210 <color>${track.data_format.jbcolor_scale.color_score.color_scheme.color.style_color}</color>
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211 #end if
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212 #end if
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213 </scheme>
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214 #end if
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215 </scaling>
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216 <menus>
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217 #for $menu_item in $track.data_format.jbmenu.track_menu:
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218 <menu>
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219 <action>${menu_item.menu_action}</action>
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220 #if str($menu_item.menu_label) != "":
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221 <label>${menu_item.menu_label}</label>
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222 #end if
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223 #if str($menu_item.menu_title) != "":
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224 <title>${menu_item.menu_title}</title>
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225 #end if
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226 #if str($menu_item.menu_url) != "":
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227 <url>${menu_item.menu_url.replace("&", "&amp;").replace("\"", "&quot;")}</url>
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228 #end if
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229 #if str($menu_item.menu_icon) != "":
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230 <iconClass>${menu_item.menu_icon}</iconClass>
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231 #end if
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232 </menu>
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233 #end for
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234 </menus>
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235 #end if
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236 #if str($track.data_format.data_format_select) in ["gene_calls", "pileup", "blast", "wiggle", "vcf"]:
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237 <custom_config>
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238 #for $custom_option in $track.data_format.jb_custom_config.option:
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239 <${custom_option.opt_key}>
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240 <${custom_option.opt_value.val_type}>${$custom_option.opt_value.val}</${custom_option.opt_value.val_type}>
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241 </${custom_option.opt_key}>
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242 #end for
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243 </custom_config>
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244 #end if
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245
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246 #if str($track.data_format.data_format_select) == "wiggle":
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247 <wiggle>
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248 <type>${track.data_format.xyplot}</type>
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249 <variance_band>${track.data_format.var_band}</variance_band>
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250 #if str($track.data_format.scaling.scale_select) == "auto_local":
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251 <autoscale>local</autoscale>
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252 #else if str($track.data_format.scaling.scale_select) == "auto_global":
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253 <autoscale>global</autoscale>
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254 #else:
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255 <min>${track.data_format.scaling.minimum}</min>
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256 <max>${track.data_format.scaling.maximum}</max>
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257 #end if
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258 <scale>${track.data_format.scale_select2}</scale>
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259
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260 ## Wiggle tracks need special color config
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261 #if str($track.data_format.jbcolor.color.color_select) != "automatic":
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262 <color_pos>${track.data_format.jbcolor.color.style_pos_color}</color_pos>
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263 <color_neg>${track.data_format.jbcolor.color.style_neg_color}</color_neg>
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264 #else:
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265 <color_pos>__auto__</color_pos>
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266 <color_neg>__auto__</color_neg>
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267 #end if
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268
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269 ## Bicolor pivot config
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270 #if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "zero":
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271 <bicolor_pivot>zero</bicolor_pivot>
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272 #else if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "mean":
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273 <bicolor_pivot>mean</bicolor_pivot>
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274 #else:
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275 <bicolor_pivot>${track.data_format.jbcolor.bicolor_pivot.pivot_point}</bicolor_pivot>
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276 #end if
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277 <multibigwig>${track.data_format.MultiBigWig}</multibigwig>
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278 </wiggle>
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279 #else if str($track.data_format.data_format_select) == "pileup":
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280 <pileup>
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281 <auto_snp>${track.data_format.auto_snp}</auto_snp>
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282 <bam_indices>
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283 #for $dataset in $track.data_format.annotation:
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284 <bam_index>${dataset.metadata.bam_index}</bam_index>
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285 #end for
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286 </bam_indices>
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287 <chunkSizeLimit>${track.data_format.chunkSizeLimit}</chunkSizeLimit>
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288 </pileup>
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289 #else if str($track.data_format.data_format_select) == "blast":
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290 <blast>
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291 #if str($track.data_format.blast_parent) != "":
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292 <parent>${track.data_format.blast_parent}</parent>
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293 #end if
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294 <protein>${track.data_format.is_protein}</protein>
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295 <min_gap>${track.data_format.min_gap}</min_gap>
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296 <index>${track.data_format.index}</index>
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297 </blast>
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298 #else if str($track.data_format.data_format_select) == "gene_calls":
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299 <gff>
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300 <trackType>${track.data_format.track_config.track_class}</trackType>
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301 #if $track.data_format.track_config.track_class in ['JBrowse/View/Track/CanvasFeatures', 'NeatCanvasFeatures/View/Track/NeatFeatures']:
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302 #if str($track.data_format.track_config.canvas_options.transcriptType) != "":
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303 <transcriptType>${track.data_format.track_config.canvas_options.transcriptType}</transcriptType>
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304 #end if
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305 #if str($track.data_format.track_config.canvas_options.subParts) != "":
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306 <subParts>${track.data_format.track_config.canvas_options.subParts}</subParts>
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307 #end if
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308 #if str($track.data_format.track_config.canvas_options.impliedUTRs) != "false":
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309 <impliedUTRs>${track.data_format.track_config.canvas_options.impliedUTRs}</impliedUTRs>
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310 #end if
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311 #else if $track.data_format.track_config.track_class in ['JBrowse/View/Track/HTMLFeatures', 'NeatHTMLFeatures/View/Track/NeatFeatures']:
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312 #if str($track.data_format.track_config.html_options.topLevelFeatures) != "":
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313 <topLevelFeatures>${track.data_format.track_config.html_options.topLevelFeatures}</topLevelFeatures>
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314 #end if
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315 #end if
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316 #if $track.data_format.match_part.match_part_select:
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317 <match>${track.data_format.match_part.name}</match>
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318 #end if
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319 <index>${track.data_format.index}</index>
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320 </gff>
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321 #else if str($track.data_format.data_format_select) == "rest":
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322 <label>${track.data_format.label}</label>
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323 <rest>
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324 <url>${track.data_format.url}</url>
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325 </rest>
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326 #else if str($track.data_format.data_format_select) == "sparql":
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327 <label>${track.data_format.label}</label>
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328 <sparql>
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329 <url>${track.data_format.url}</url>
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330 <query>${track.data_format.query}</query>
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331 </sparql>
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332 #end if
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333 </options>
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334 </track>
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335 #end for
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336 #end for
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337 </tracks>
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338 ## Disable plugins until https://github.com/GMOD/jbrowse/issues/1288 is fixed
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339 ## <plugins
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340 ## ComboTrackSelector="${plugins.ComboTrackSelector}"
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341 ## Bookmarks="${plugins.Bookmarks}"
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342 ## GCContent="${plugins.GCContent}"
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343 ## BlastView="${plugins.BlastView}"
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344 ## theme="${plugins.theme}"
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345 ## />
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346 <plugins
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347 ComboTrackSelector="${plugins.ComboTrackSelector}"
53
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348 Bookmarks=""
45
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349 GCContent="${plugins.GCContent}"
53
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350 BlastView="${plugins.BlastView}"
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351 theme=""
45
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352 />
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353 </root>
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354 ]]></configfile>
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355 </configfiles>
0
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356 <inputs>
42
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357 <conditional name="reference_genome">
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358 <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select">
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359 <option selected="True" value="indexed">Use a built-in genome</option>
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360 <option value="history">Use a genome from history</option>
30
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361 </param>
42
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362 <when value="indexed">
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363 <param
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364 help="If your genome of interest is not listed, contact the Galaxy team"
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365 label="Select a reference genome"
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366 name="genomes"
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367 type="select"
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368 >
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369 <options from_data_table="all_fasta">
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370 <filter column="2" type="sort_by" />
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371 <validator message="No genomes are available for the selected input dataset" type="no_options" />
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372 </options>
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373 </param>
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374 </when>
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375 <when value="history">
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376 <param
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377 format="fasta"
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378 label="Select the reference genome"
53
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379 name="genome"
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380 type="data" />
30
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381 </when>
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382 </conditional>
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383
68
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384 <param name="standalone" label="Output JBrowse" type="select">
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385 <option value="complete">Complete, for viewing and further local development (JBrowse, tools, documentation, etc.)</option>
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386 <option value="minimal" selected="true">Minimal for viewing (Documentation removed)</option>
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387 <option value="data">Data directory only (primarily for use with Apollo, requires extra steps to serve as website)</option>
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388 </param>
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389
50
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390 <param name="gencode" type="select" label="Genetic Code">
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391 <option value="1">1. The Standard Code</option>
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392 <option value="2">2. The Vertebrate Mitochondrial Code</option>
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393 <option value="3">3. The Yeast Mitochondrial Code</option>
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394 <option value="4">4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
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395 <option value="5">5. The Invertebrate Mitochondrial Code</option>
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396 <option value="6">6. The Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
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397 <option value="9">9. The Echinoderm and Flatworm Mitochondrial Code</option>
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398 <option value="10">10. The Euplotid Nuclear Code</option>
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399 <option value="11">11. The Bacterial, Archaeal and Plant Plastid Code</option>
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400 <option value="12">12. The Alternative Yeast Nuclear Code</option>
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401 <option value="13">13. The Ascidian Mitochondrial Code</option>
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402 <option value="14">14. The Alternative Flatworm Mitochondrial Code</option>
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403 <option value="16">16. Chlorophycean Mitochondrial Code</option>
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404 <option value="21">21. Trematode Mitochondrial Code</option>
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405 <option value="22">22. Scenedesmus obliquus Mitochondrial Code</option>
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406 <option value="23">23. Thraustochytrium Mitochondrial Code</option>
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407 <option value="24">24. Pterobranchia Mitochondrial Code</option>
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408 <option value="25">25. Candidate Division SR1 and Gracilibacteria Code</option>
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409 </param>
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410
42
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411 <conditional name="action">
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412 <param type="select" label="JBrowse-in-Galaxy Action" name="action_select">
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413 <option value="create">New JBrowse Instance</option>
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414 <option value="update">Update exising JBrowse Instance</option>
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415 </param>
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416 <when value="create" />
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417 <when value="update">
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418 <param name="update_jbrowse" type="data" format="html" label="Previous JBrowse Instance" />
42
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419 </when>
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420 </conditional>
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421
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422 <repeat name="track_groups" title="Track Group">
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423 <param label="Track Category"
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424 name="category"
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425 type="text"
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426 value="Default"
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427 help="Organise your tracks into Categories for a nicer end-user experience. You can use #date# and it will be replaced with the current date in 'yyyy-mm-dd' format, which is very useful for repeatedly updating a JBrowse instance when member databases / underlying tool versions are updated." optional="False"/>
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428 <repeat name="data_tracks" title="Annotation Track">
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429 <conditional name="data_format" label="Track Options">
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430 <param type="select" label="Track Type" name="data_format_select">
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431 <option value="gene_calls">GFF/GFF3/BED Features</option>
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432 <option value="pileup">BAM Pileups</option>
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433 <option value="blast">Blast XML</option>
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434 <option value="wiggle">BigWig XY</option>
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435 <option value="vcf">VCF SNPs</option>
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436 <option value="rest">REST Endpoint</option>
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437 <option value="sparql">SPARQL</option>
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438 </param>
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439 <when value="blast">
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440 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" />
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441
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442 <param label="Features used in Blast Search"
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parents: 15
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443 help="in GFF3. This is used so we know where to map features. E.g. where results of which CDS Protein32 match up to. The query IDs in your blast results should MATCH some feature IDs in your GFF3 file. This is an optional field and is most useful if using JBrowse to display protein blast results on a DNA genome. blastn results don't need this, blastp results on a protein sequence don't need this."
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iuc
parents: 15
diff changeset
444 format="gff3"
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iuc
parents: 15
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445 name="blast_parent"
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iuc
parents: 15
diff changeset
446 optional="true"
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iuc
parents: 15
diff changeset
447 type="data"/>
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iuc
parents: 12
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448
16
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iuc
parents: 15
diff changeset
449 <param label="Minimum Gap Size"
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
450 help="before a new match_part feature is created"
318a0aa5075a Uploaded manually
iuc
parents: 15
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451 name="min_gap"
318a0aa5075a Uploaded manually
iuc
parents: 15
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452 type="integer"
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iuc
parents: 15
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453 value="10"
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iuc
parents: 15
diff changeset
454 min="2" />
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iuc
parents: 12
diff changeset
455 <param label="Is this a protein blast search?"
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parents: 15
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456 type="boolean"
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iuc
parents: 15
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457 name="is_protein"
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iuc
parents: 15
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458 truevalue="true"
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iuc
parents: 15
diff changeset
459 falsevalue="false" />
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parents: 15
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460
42
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iuc
parents: 40
diff changeset
461 <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" />
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
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462
16
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iuc
parents: 15
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463 <expand macro="track_styling"
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iuc
parents: 15
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464 classname="feature"
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iuc
parents: 15
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465 label="description"
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iuc
parents: 15
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466 description="Hit_titles"
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iuc
parents: 15
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467 height="600px"/>
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iuc
parents: 15
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468 <expand macro="color_selection"
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iuc
parents: 15
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469 token_scaling_lin_select="false"
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iuc
parents: 15
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470 token_scaling_log_select="true" />
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e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
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471 <expand macro="track_custom_config" />
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iuc
parents: 40
diff changeset
472 <expand macro="track_menu" />
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iuc
parents: 29
diff changeset
473 <expand macro="track_display" />
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iuc
parents: 12
diff changeset
474 </when>
67fb31daef0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 399061eca3a2956704522974446601755503c96d-dirty
iuc
parents: 12
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475 <when value="vcf">
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iuc
parents: 15
diff changeset
476 <expand macro="input_conditional" label="SNP Track Data" format="vcf" />
59
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
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477 <expand macro="track_custom_config" />
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iuc
parents: 29
diff changeset
478 <expand macro="track_display" />
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iuc
parents: 12
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479 </when>
67fb31daef0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 399061eca3a2956704522974446601755503c96d-dirty
iuc
parents: 12
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480 <when value="gene_calls">
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parents: 15
diff changeset
481 <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" />
45
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iuc
parents: 44
diff changeset
482 <conditional name="match_part" label="match/match_part data">
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iuc
parents: 15
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483 <param label="This is match/match_part data"
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iuc
parents: 15
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484 type="boolean"
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parents: 15
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485 name="match_part_select"
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parents: 15
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486 truevalue="true"
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iuc
parents: 15
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487 falsevalue="false" />
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iuc
parents: 15
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488 <when value="true">
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iuc
parents: 15
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489 <param label="Match Part Feature Type"
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iuc
parents: 15
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490 name="name"
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parents: 15
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491 type="text"
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iuc
parents: 15
diff changeset
492 value="match"
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6492c2deb009 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9cac72c004cc7ef57be997e2fdafb3b1839a300f
iuc
parents: 47
diff changeset
493 help="Match_parts have several 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)."
6492c2deb009 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9cac72c004cc7ef57be997e2fdafb3b1839a300f
iuc
parents: 47
diff changeset
494 optional="True"/>
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parents: 15
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495 </when>
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parents: 15
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496 <when value="false" />
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parents: 15
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497 </conditional>
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iuc
parents: 40
diff changeset
498
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
499 <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" />
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
500
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
501 <conditional name="track_config">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
502 <param type="select" label="JBrowse Track Type [Advanced]" name="track_class">
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iuc
parents: 53
diff changeset
503 <option value="NeatHTMLFeatures/View/Track/NeatFeatures" selected="true">Neat HTML Features</option>
b4d512ee2d14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 75f6e483debb4c0d388bf4a54df81ee89af598d5
iuc
parents: 53
diff changeset
504 <option value="NeatCanvasFeatures/View/Track/NeatFeatures">Neat Canvas Features</option>
42
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
505 <option value="JBrowse/View/Track/HTMLFeatures">HTML Features</option>
54
b4d512ee2d14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 75f6e483debb4c0d388bf4a54df81ee89af598d5
iuc
parents: 53
diff changeset
506 <option value="JBrowse/View/Track/CanvasFeatures">Canvas Features</option>
53
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
507 <option value="BlastView/View/Track/CanvasFeatures">Blast Features</option><!-- Disable plugins until https://github.com/GMOD/jbrowse/issues/1288 is fixed -->
42
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
508 </param>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
509 <when value="JBrowse/View/Track/CanvasFeatures">
55
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iuc
parents: 54
diff changeset
510 <expand macro="canvas_options" />
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
511 </when>
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
512 <when value="JBrowse/View/Track/HTMLFeatures">
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
513 <expand macro="html_options" />
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
514 </when>
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
515 <when value="BlastView/View/Track/CanvasFeatures" />
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
516 <when value="NeatHTMLFeatures/View/Track/NeatFeatures">
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
517 <expand macro="html_options" />
54
b4d512ee2d14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 75f6e483debb4c0d388bf4a54df81ee89af598d5
iuc
parents: 53
diff changeset
518 </when>
55
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
519 <when value="NeatCanvasFeatures/View/Track/NeatFeatures">
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
520 <expand macro="canvas_options" />
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
521 </when>
42
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
522 </conditional>
55
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
523 <expand macro="track_styling"
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c8772f1f6a38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 74554507efb46fb40ce6e12f0b73425e52ec0977
iuc
parents: 57
diff changeset
524 classname="feature"
55
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
525 label="product,name,id"
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
526 description="note,description"
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
527 height="10px"/>
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318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
528 <expand macro="color_selection" />
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e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
529 <expand macro="track_custom_config" />
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iuc
parents: 40
diff changeset
530 <expand macro="track_menu" />
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iuc
parents: 29
diff changeset
531 <expand macro="track_display" />
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iuc
parents: 12
diff changeset
532 </when>
67fb31daef0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 399061eca3a2956704522974446601755503c96d-dirty
iuc
parents: 12
diff changeset
533 <when value="pileup">
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parents: 15
diff changeset
534 <expand macro="input_conditional" label="BAM Track Data" format="bam" />
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
535 <param label="Autogenerate SNP Track"
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
536 help="Not recommended for deep coverage BAM files"
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
537 type="boolean"
318a0aa5075a Uploaded manually
iuc
parents: 15
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538 name="auto_snp"
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iuc
parents: 15
diff changeset
539 truevalue="true"
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parents: 15
diff changeset
540 falsevalue="false" />
53
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
541 <param label="Maximum size of BAM chunks"
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
542 name="chunkSizeLimit"
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
543 type="integer"
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
544 help="Maximum size in bytes of BAM chunks that the browser will try to deal with. When this is exceeded, most tracks will display 'Too much data' message."
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
545 value="5000000" />
59
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
546 <expand macro="track_custom_config" />
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iuc
parents: 29
diff changeset
547 <expand macro="track_display" />
13
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iuc
parents: 12
diff changeset
548 </when>
67fb31daef0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 399061eca3a2956704522974446601755503c96d-dirty
iuc
parents: 12
diff changeset
549 <when value="wiggle">
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parents: 15
diff changeset
550 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" />
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
551
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
552 <param label="Use XYPlot"
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
553 help="instead of continuous colored band"
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
554 type="boolean"
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iuc
parents: 15
diff changeset
555 name="xyplot"
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
556 truevalue="JBrowse/View/Track/Wiggle/XYPlot"
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
557 falsevalue="JBrowse/View/Track/Wiggle/Density" />
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
558 <param label="Show variance band"
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iuc
parents: 15
diff changeset
559 help="Only for XYPlots"
318a0aa5075a Uploaded manually
iuc
parents: 15
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560 type="boolean"
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
561 name="var_band"
318a0aa5075a Uploaded manually
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diff changeset
562 truevalue="true"
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parents: 15
diff changeset
563 falsevalue="false" />
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parents: 12
diff changeset
564
45
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iuc
parents: 44
diff changeset
565 <conditional name="scaling" label="Scaling">
13
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iuc
parents: 12
diff changeset
566 <param type="select" label="Track Scaling" name="scale_select">
51
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parents: 50
diff changeset
567 <option value="auto_local" selected="true">Autoscale (local)</option>
abb1a30d7a5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit cf2c8f3039021b645ac45980a02ffe1f69a3f958
iuc
parents: 50
diff changeset
568 <option value="auto_global">Autoscale (global)</option>
16
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
569 <option value="fixed">Specify Min/Max</option>
13
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iuc
parents: 12
diff changeset
570 </param>
67fb31daef0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 399061eca3a2956704522974446601755503c96d-dirty
iuc
parents: 12
diff changeset
571 <when value="auto_local"></when>
67fb31daef0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 399061eca3a2956704522974446601755503c96d-dirty
iuc
parents: 12
diff changeset
572 <when value="auto_global"></when>
67fb31daef0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 399061eca3a2956704522974446601755503c96d-dirty
iuc
parents: 12
diff changeset
573 <when value="fixed">
67fb31daef0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 399061eca3a2956704522974446601755503c96d-dirty
iuc
parents: 12
diff changeset
574 <param label="Track minimum" name="minimum"
67fb31daef0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 399061eca3a2956704522974446601755503c96d-dirty
iuc
parents: 12
diff changeset
575 type="integer" value="0" />
67fb31daef0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 399061eca3a2956704522974446601755503c96d-dirty
iuc
parents: 12
diff changeset
576 <param label="Track maximum" name="maximum"
67fb31daef0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 399061eca3a2956704522974446601755503c96d-dirty
iuc
parents: 12
diff changeset
577 type="integer" value="100" />
67fb31daef0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 399061eca3a2956704522974446601755503c96d-dirty
iuc
parents: 12
diff changeset
578 </when>
67fb31daef0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 399061eca3a2956704522974446601755503c96d-dirty
iuc
parents: 12
diff changeset
579 </conditional>
45
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iuc
parents: 44
diff changeset
580 <param type="select" label="Visual Scaling" name="scale_select2">
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
581 <option value="linear" selected="true">Linear</option>
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
582 <option value="log">Logarithmic (Dynamically Calculated)</option>
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
583 </param>
53
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iuc
parents: 51
diff changeset
584
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
585 <param label="Use MultiBigWig Plugin" name="MultiBigWig" truevalue="True" falsevalue="" type="boolean"
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
586 help="MultiBigWig is a plugin to group multiple big-wig tracks in a more aesthetically pleasing format and to show data in a higher density display." />
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
587
16
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
588 <expand macro="color_selection_minmax" />
59
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
589 <expand macro="track_custom_config" />
30
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iuc
parents: 29
diff changeset
590 <expand macro="track_display" />
13
67fb31daef0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 399061eca3a2956704522974446601755503c96d-dirty
iuc
parents: 12
diff changeset
591 </when>
45
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iuc
parents: 44
diff changeset
592 <when value="rest">
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
593 <param type="text" label="REST Endpoint" name="url" />
53
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
594 <param type="text" label="Track Label" name="label" value="REST Genes" />
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
595 <expand macro="track_styling"
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
596 classname="feature"
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
597 label="description"
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
598 description="Hit_titles"
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
599 height="600px"/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
600 <expand macro="color_selection"
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
601 token_scaling_lin_select="false"
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
602 token_scaling_log_select="true" />
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
603 <expand macro="track_menu" />
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
604 <expand macro="track_display" />
45
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iuc
parents: 44
diff changeset
605 </when>
53
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
606
30
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iuc
parents: 29
diff changeset
607 <when value="sparql">
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
608 <param type="text" label="SPARQL Server URL" name="url" />
53
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
609 <param type="text" label="Track Label" name="label" value="SPARQL Genes" />
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
610 <param type="text" label="SPARQL Query" name="query" area="true">
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
611 <sanitizer>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
612 <mapping initial="galaxy.util.mapped_chars">
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
613 <add source="&#10;" target=" " />
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
614 <add source="&gt;" target="__gt__" />
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
615 <add source="&lt;" target="__lt__" />
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
616 </mapping>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
617 <valid initial="default">
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
618 <add value="|" />
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
619 <add value="#" />
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
620 <add value="{"/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
621 <add value="}"/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
622 <add value="!"/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
623 <add value="?"/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
624 <add value="&amp;"/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
625 <add value="+"/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
626 <add value="="/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
627 <add value="'"/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
628 <add value='"'/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
629 </valid>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
630 </sanitizer>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
631 </param>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
632 <expand macro="track_styling"
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
633 classname="feature"
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
634 label="description"
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
635 description="Hit_titles"
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
636 height="600px"/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
637 <expand macro="color_selection"
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
638 token_scaling_lin_select="false"
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
639 token_scaling_log_select="true" />
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
640 <expand macro="track_menu" />
30
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iuc
parents: 29
diff changeset
641 <expand macro="track_display" />
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
642 </when>
13
67fb31daef0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 399061eca3a2956704522974446601755503c96d-dirty
iuc
parents: 12
diff changeset
643 </conditional>
0
c77c1d5baadb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
iuc
parents:
diff changeset
644 </repeat>
16
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
645 </repeat>
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
646
30
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iuc
parents: 29
diff changeset
647 <expand macro="general_options" />
53
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
648 <!-- Disable plugins until https://github.com/GMOD/jbrowse/issues/1288 is fixed -->
45
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iuc
parents: 44
diff changeset
649 <section name="plugins" title="Plugins" expanded="false">
53
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
650
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
651 <param
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
652 label="BlastView" name="BlastView" truevalue="True" falsevalue="" type="boolean" checked="true"
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
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653 help="A JBrowse plugin for viewing blast alignments. This plugin makes MANY assumptions about the format of your data, and may not work without those assumptions: 1) you use protein_match / match_part 2) your features have a Blast_qseq, Blast_mseq, and Blast_sseq attribute in their GFF3 representation." />
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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654
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655 <param
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656 label="Combo Track Selector" name="ComboTrackSelector" truevalue="True" falsevalue="" type="boolean"
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657 help="ComboTrackSelector is a plugin to allow the co-existence of the Hierarchical and Faceted Track selectors in JBrowse, built for/by the Arabidopsis Information Portal (Araport) project" />
53
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658 <!-- No way to disable now that it's built in jbrowse conda package -->
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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659 <!--param
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660 label="Bookmarks" name="Bookmarks" truevalue="True" falsevalue="" type="boolean"
53
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661 help="JBrowse plugin allowing users to manage a persistent list of bookmarks kept in localstorage" /-->
45
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662
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663 <param
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664 label="GC Content" name="GCContent" truevalue="True" falsevalue="" type="boolean"
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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665 help="A JBrowse plugin for plotting GC Content and GC Skew. The plugin consists of a storeClass that automatically calculates the percentage of G/C bases in a region, a track type that derives from the Wiggle XY or density types, and a dialog box to adjust the sliding window size, window step size, and the calculation mode (content or skew)." />
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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666
53
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667 <!--param type="select" label="JBrowse Theme" name="theme">
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668 <option value="" selected="True">Default</option>
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669 <option value="Minimalist">Minimalist</option>
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670 <option value="Dark">Dark</option>
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671 </param-->
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672 </section>
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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673
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674 <param type="hidden" name="uglyTestingHack" value="" />
0
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675 </inputs>
c77c1d5baadb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
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676 <outputs>
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318a0aa5075a Uploaded manually
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677 <data format="html" name="output" label="JBrowse on $on_string - $standalone"/>
0
c77c1d5baadb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
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678 </outputs>
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679 <tests>
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680 <test>
42
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681 <param name="reference_genome|genome_type_select" value="history"/>
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682 <param name="reference_genome|genome" value="merlin.fa"/>
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683 <param name="gencode" value="1" />
68
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684 <param name="standalone" value="data" />
30
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685 <param name="uglyTestingHack" value="enabled" />
70
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686 <output name="output">
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
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687 <assert_contents>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
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688 <has_text text="&lt;gencode&gt;1&lt;/gencode&gt;"></has_text>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
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689 <has_text text="genome path="></has_text>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
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690 <has_text text="dataset id="></has_text>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
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diff changeset
691 <has_text text="history id="></has_text>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
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692 <has_text text="metadata"></has_text>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
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diff changeset
693 <has_text text="tool_id"></has_text>
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694
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
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diff changeset
695 </assert_contents>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
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696 </output>
30
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diff changeset
697 </test>
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698 <test>
42
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diff changeset
699 <param name="reference_genome|genome_type_select" value="history"/>
53
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diff changeset
700 <param name="reference_genome|genome" value="merlin.fa"/>
30
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diff changeset
701 <param name="gencode" value="11" />
68
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diff changeset
702 <param name="standalone" value="data" />
30
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diff changeset
703 <param name="uglyTestingHack" value="enabled" />
70
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diff changeset
704 <output name="output">
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
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diff changeset
705 <assert_contents>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
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parents: 69
diff changeset
706 <has_text text="&lt;gencode&gt;11&lt;/gencode&gt;"></has_text>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
707 <has_text text="genome path="></has_text>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
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diff changeset
708 <has_text text="dataset id="></has_text>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
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diff changeset
709 <has_text text="history id="></has_text>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
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diff changeset
710 <has_text text="metadata"></has_text>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
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diff changeset
711 <has_text text="tool_id"></has_text>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
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parents: 69
diff changeset
712 </assert_contents>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
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diff changeset
713 </output>
30
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parents: 29
diff changeset
714 </test>
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 29
diff changeset
715 <test>
42
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parents: 40
diff changeset
716 <param name="reference_genome|genome_type_select" value="history"/>
53
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parents: 51
diff changeset
717 <param name="reference_genome|genome" value="merlin.fa"/>
30
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diff changeset
718 <param name="gencode" value="11" />
68
17698b85dc47 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
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parents: 67
diff changeset
719 <param name="standalone" value="data" />
42
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diff changeset
720 <repeat name="track_groups">
62
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parents: 61
diff changeset
721 <param name="category" value="Default" />
46cf483e76d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
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parents: 61
diff changeset
722 <repeat name="data_tracks">
46cf483e76d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
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diff changeset
723 <conditional name="data_format">
46cf483e76d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
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parents: 61
diff changeset
724 <param name="data_format_select" value="gene_calls"/>
46cf483e76d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
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parents: 61
diff changeset
725 <param name="annotation" value="bed/test-3.bed,bed/test-6.bed"/>
46cf483e76d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
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diff changeset
726 </conditional>
46cf483e76d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
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parents: 61
diff changeset
727 </repeat>
46cf483e76d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents: 61
diff changeset
728 </repeat>
46cf483e76d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
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parents: 61
diff changeset
729 <param name="uglyTestingHack" value="enabled" />
70
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parents: 69
diff changeset
730 <output name="output">
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parents: 69
diff changeset
731 <assert_contents>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
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parents: 69
diff changeset
732 <has_text text="&lt;gencode&gt;11&lt;/gencode&gt;"></has_text>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
733 <has_text text="genome path="></has_text>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
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diff changeset
734 <has_text text="dataset id="></has_text>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
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diff changeset
735 <has_text text="history id="></has_text>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
736 <has_text text="metadata"></has_text>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
737 <has_text text="tool_id"></has_text>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
738 <has_text text="trackFile path="></has_text>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
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parents: 69
diff changeset
739 <has_text text="ext=&quot;bed&quot; label=&quot;test-3.bed&quot;"></has_text>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
740 <has_text text="NeatHTMLFeatures"></has_text>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
741 </assert_contents>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
742 </output>
62
46cf483e76d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents: 61
diff changeset
743 </test>
46cf483e76d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents: 61
diff changeset
744 <test>
46cf483e76d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents: 61
diff changeset
745 <param name="reference_genome|genome_type_select" value="history"/>
46cf483e76d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents: 61
diff changeset
746 <param name="reference_genome|genome" value="merlin.fa"/>
46cf483e76d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents: 61
diff changeset
747 <param name="gencode" value="11" />
68
17698b85dc47 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
parents: 67
diff changeset
748 <param name="standalone" value="data" />
62
46cf483e76d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents: 61
diff changeset
749 <repeat name="track_groups">
42
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
750 <param name="category" value="Auto Coloured" />
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
751 <repeat name="data_tracks">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
752 <conditional name="data_format">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
753 <param name="data_format_select" value="gene_calls"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
754 <param name="annotation" value="gff3/A.gff,gff3/B.gff,gff3/C.gff,gff3/D.gff"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
755 <conditional name="match_part">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
756 <param name="match_part_select" value="false"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
757 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
758 <section name="jbcolor_scale">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
759 <conditional name="color_score">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
760 <param name="color_score_select" value="none"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
761 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
762 <conditional name="color">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
763 <param name="color_select" value="automatic"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
764 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
765 </section>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
766 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
767 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
768 </repeat>
30
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
769
42
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
770 <repeat name="track_groups">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
771 <param name="category" value="Ignore Scale" />
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
772 <repeat name="data_tracks">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
773 <conditional name="data_format">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
774 <param name="data_format_select" value="gene_calls"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
775 <param name="annotation" value="gff3/1.gff"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
776 <conditional name="match_part">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
777 <param name="match_part_select" value="false"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
778 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
779 <section name="jbcolor_scale">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
780 <conditional name="color_score">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
781 <param name="color_score_select" value="none"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
782 <conditional name="color">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
783 <param name="color_select" value="manual"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
784 <param name="style_color" value="#ff00ff"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
785 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
786 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
787 </section>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
788 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
789 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
790 </repeat>
30
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
791
42
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
792 <repeat name="track_groups">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
793 <param name="category" value="Scaled Colour" />
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
794 <repeat name="data_tracks">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
795 <conditional name="data_format">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
796 <param name="data_format_select" value="gene_calls"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
797 <param name="annotation" value="gff3/1.gff"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
798 <conditional name="match_part">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
799 <param name="match_part_select" value="false"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
800 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
801 <section name="jbcolor_scale">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
802 <conditional name="color_score">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
803 <param name="color_score_select" value="score"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
804 <param name="score_scaling" value="linear"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
805 <conditional name="score_scales">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
806 <param name="scale_select" value="automatic"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
807 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
808 <conditional name="color_scheme">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
809 <param name="score_scheme" value="opacity"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
810 <conditional name="color">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
811 <param name="color_select" value="automatic"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
812 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
813 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
814 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
815 </section>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
816 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
817 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
818 <repeat name="data_tracks">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
819 <conditional name="data_format">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
820 <param name="data_format_select" value="gene_calls"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
821 <param name="annotation" value="gff3/1.gff"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
822 <conditional name="match_part">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
823 <param name="match_part_select" value="false"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
824 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
825 <section name="jbcolor_scale">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
826 <conditional name="color_score">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
827 <param name="color_score_select" value="score"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
828 <param name="score_scaling" value="linear"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
829 <conditional name="score_scales">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
830 <param name="scale_select" value="automatic"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
831 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
832 <conditional name="color_scheme">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
833 <param name="score_scheme" value="opacity"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
834 <conditional name="color">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
835 <param name="color_select" value="manual"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
836 <param name="style_color" value="#0000ff"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
837 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
838 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
839 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
840 </section>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
841 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
842 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
843 <repeat name="data_tracks">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
844 <conditional name="data_format">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
845 <param name="data_format_select" value="gene_calls"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
846 <param name="annotation" value="gff3/1.gff"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
847 <conditional name="match_part">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
848 <param name="match_part_select" value="false"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
849 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
850 <section name="jbcolor_scale">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
851 <conditional name="color_score">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
852 <param name="color_score_select" value="score"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
853 <param name="score_scaling" value="linear"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
854 <conditional name="score_scales">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
855 <param name="scale_select" value="manual"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
856 <param name="minimum" value="0"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
857 <param name="maximum" value="1000"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
858 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
859 <conditional name="color_scheme">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
860 <param name="score_scheme" value="opacity"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
861 <conditional name="color">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
862 <param name="color_select" value="automatic"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
863 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
864 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
865 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
866 </section>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
867 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
868 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
869 <repeat name="data_tracks">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
870 <conditional name="data_format">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
871 <param name="data_format_select" value="gene_calls"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
872 <param name="annotation" value="gff3/1.gff"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
873 <conditional name="match_part">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
874 <param name="match_part_select" value="false"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
875 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
876 <section name="jbcolor_scale">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
877 <conditional name="color_score">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
878 <param name="color_score_select" value="score"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
879 <param name="score_scaling" value="linear"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
880 <conditional name="score_scales">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
881 <param name="scale_select" value="manual"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
882 <param name="minimum" value="0"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
883 <param name="maximum" value="1000"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
884 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
885 <conditional name="color_scheme">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
886 <param name="score_scheme" value="opacity"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
887 <conditional name="color">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
888 <param name="color_select" value="manual"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
889 <param name="style_color" value="#ff0000"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
890 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
891 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
892 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
893 </section>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
894 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
895 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
896 </repeat>
30
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
897
42
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
898 <repeat name="track_groups">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
899 <param name="category" value="Realistic" />
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
900 <repeat name="data_tracks">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
901 <conditional name="data_format">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
902 <param name="data_format_select" value="gene_calls"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
903 <param name="annotation" value="gff3/interpro.gff"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
904 <conditional name="match_part">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
905 <param name="match_part_select" value="false"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
906 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
907 <section name="jbcolor_scale">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
908 <conditional name="color_score">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
909 <param name="color_score_select" value="none"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
910 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
911 <conditional name="color">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
912 <param name="color_select" value="automatic"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
913 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
914 </section>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
915 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
916 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
917 <repeat name="data_tracks">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
918 <conditional name="data_format">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
919 <param name="data_format_select" value="gene_calls"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
920 <param name="annotation" value="gff3/2.gff"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
921 <conditional name="match_part">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
922 <param name="match_part_select" value="true"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
923 <param name="name" value="cDNA_match"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
924 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
925 <section name="jbcolor_scale">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
926 <conditional name="color_score">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
927 <param name="color_score_select" value="none"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
928 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
929 <conditional name="color">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
930 <param name="color_select" value="automatic"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
931 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
932 </section>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
933 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
934 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
935 </repeat>
30
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
936
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
937 <param name="uglyTestingHack" value="enabled" />
70
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
938 <output name="output">
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
939 <assert_contents>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
940 <has_text text="Auto Coloured"/>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
941 <has_text text="A.gff"/>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
942 <has_text text="B.gff"/>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
943 <has_text text="C.gff"/>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
944 <has_text text="D.gff"/>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
945 <has_text text="Scaled Colour"/>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
946 <has_text text="1.gff"/>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
947 <has_text text="2.gff"/>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
948 </assert_contents>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
949 </output>
30
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
950 </test>
42
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
951 <test>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
952 <param name="reference_genome|genome_type_select" value="history"/>
53
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
953 <param name="reference_genome|genome" value="merlin.fa"/>
42
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
954 <param name="gencode" value="11" />
68
17698b85dc47 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
parents: 67
diff changeset
955 <param name="standalone" value="data" />
42
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
956
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
957 <repeat name="track_groups">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
958 <param name="category" value="With menu or index" />
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
959 <repeat name="data_tracks">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
960 <conditional name="data_format">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
961 <param name="data_format_select" value="gene_calls"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
962 <param name="annotation" value="gff3/1.gff"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
963 <conditional name="match_part">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
964 <param name="match_part_select" value="false"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
965 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
966 <section name="jbcolor_scale">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
967 <conditional name="color_score">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
968 <param name="color_score_select" value="none"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
969 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
970 <conditional name="color">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
971 <param name="color_select" value="automatic"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
972 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
973 </section>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
974 <section name="jbmenu">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
975 <repeat name="track_menu">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
976 <param name="menu_action" value="iframeDialog"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
977 <param name="menu_label" value="Some menu item"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
978 <param name="menu_title" value="Frame title"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
979 <param name="menu_url" value="https://example.com/#!/?id={name}&amp;q={type}&amp;z=&quot;{end}&quot;"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
980 <param name="menu_icon" value="dijitIconNewTask"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
981 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
982 <repeat name="track_menu">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
983 <param name="menu_action" value="newWindow"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
984 <param name="menu_label" value="Another menu item"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
985 <param name="menu_title" value="Frame title 2"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
986 <param name="menu_url" value="https://example.com/#!/?id={name}&amp;q={type}&amp;z=&quot;{end}&quot;"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
987 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
988 </section>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
989 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
990 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
991 <repeat name="data_tracks">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
992 <conditional name="data_format">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
993 <param name="data_format_select" value="gene_calls"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
994 <param name="annotation" value="gff3/1.gff"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
995 <param name="index" value="true"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
996 <conditional name="match_part">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
997 <param name="match_part_select" value="false"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
998 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
999 <section name="jbcolor_scale">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1000 <conditional name="color_score">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1001 <param name="color_score_select" value="none"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1002 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1003 <conditional name="color">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1004 <param name="color_select" value="automatic"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1005 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1006 </section>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1007 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1008 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1009 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1010
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1011 <param name="uglyTestingHack" value="enabled" />
70
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
1012 <output name="output">
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
1013 <assert_contents>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
1014 <has_text text="With menu or index"/>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
1015 <has_text text="Some menu item"/>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
1016 <has_text text="Frame title"/>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
1017 <has_text text="dijitIconNewTask"/>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
1018 </assert_contents>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
1019 </output>
42
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1020 </test>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1021 <test>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1022 <param name="reference_genome|genome_type_select" value="history"/>
53
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1023 <param name="reference_genome|genome" value="merlin.fa"/>
42
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1024 <param name="gencode" value="11" />
68
17698b85dc47 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
parents: 67
diff changeset
1025 <param name="standalone" value="data" />
42
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1026
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1027 <repeat name="track_groups">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1028 <param name="category" value="With canvas config" />
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1029 <repeat name="data_tracks">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1030 <conditional name="data_format">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1031 <param name="data_format_select" value="gene_calls"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1032 <param name="annotation" value="gff3/1.gff"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1033 <conditional name="match_part">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1034 <param name="match_part_select" value="false"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1035 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1036 <conditional name="track_config">
59
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1037 <param name="track_class" value="JBrowse/View/Track/CanvasFeatures"/>
42
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1038 <section name="canvas_options">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1039 <param name="transcriptType" value="transcript"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1040 <param name="subParts" value="exon"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1041 <param name="impliedUTRs" value="true"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1042 </section>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1043 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1044 <section name="jbcolor_scale">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1045 <conditional name="color_score">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1046 <param name="color_score_select" value="none"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1047 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1048 <conditional name="color">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1049 <param name="color_select" value="automatic"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1050 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1051 </section>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1052 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1053 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1054 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1055
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1056 <param name="uglyTestingHack" value="enabled" />
70
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
1057 <output name="output">
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
1058 <assert_contents>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
1059 <has_text text="With canvas config"></has_text>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
1060 <has_text text="&lt;transcriptType&gt;transcript&lt;/transcriptType&gt;"></has_text>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
1061 <has_text text="&lt;subParts&gt;exon&lt;/subParts&gt;"></has_text>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
1062 </assert_contents>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
1063 </output>
59
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1064 </test>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1065 <test>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1066 <param name="reference_genome|genome_type_select" value="history"/>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1067 <param name="reference_genome|genome" value="merlin.fa"/>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1068 <param name="gencode" value="11" />
68
17698b85dc47 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
parents: 67
diff changeset
1069 <param name="standalone" value="data" />
59
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1070
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1071 <repeat name="track_groups">
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1072 <param name="category" value="With custom track config" />
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1073 <repeat name="data_tracks">
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1074 <conditional name="data_format">
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1075 <param name="data_format_select" value="gene_calls"/>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1076 <param name="annotation" value="gff3/1.gff"/>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1077 <conditional name="match_part">
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1078 <param name="match_part_select" value="false"/>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1079 </conditional>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1080 <section name="jb_custom_config">
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1081 <repeat name="option">
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1082 <param name="opt_key" value="displayMode"/>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1083 <conditional name="opt_value">
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1084 <param name="val_type" value="text"/>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1085 <param name="val" value="collapsed"/>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1086 </conditional>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1087 </repeat>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1088 <repeat name="option">
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1089 <param name="opt_key" value="histograms.height"/>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1090 <conditional name="opt_value">
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1091 <param name="val_type" value="integer"/>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1092 <param name="val" value="150"/>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1093 </conditional>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1094 </repeat>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1095 <repeat name="option">
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1096 <param name="opt_key" value="maxFeatureScreenDensity"/>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1097 <conditional name="opt_value">
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1098 <param name="val_type" value="float"/>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1099 <param name="val" value="0.1"/>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1100 </conditional>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1101 </repeat>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1102 <repeat name="option">
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1103 <param name="opt_key" value="style.strandArrow"/>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1104 <conditional name="opt_value">
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1105 <param name="val_type" value="boolean"/>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1106 <param name="val" value="false"/>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1107 </conditional>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1108 </repeat>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1109 </section>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1110 </conditional>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1111 </repeat>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1112 </repeat>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1113
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1114 <param name="uglyTestingHack" value="enabled" />
70
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
1115 <output name="output">
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
1116 <assert_contents>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
1117 <has_text text="1.gff"/>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
1118 <has_text text="collapsed"/>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
1119 <has_text text="150"/>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
1120 <has_text text="maxFeatureScreenDensity"/>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
1121 <has_text text="style.strandArrow"/>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
1122 </assert_contents>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
1123 </output>
42
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1124 </test>
46
f90c22c8fa7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 45
diff changeset
1125 <test>
47
6b91a500c96d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 46
diff changeset
1126 <param name="reference_genome|genome_type_select" value="history"/>
53
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1127 <param name="reference_genome|genome" value="merlin.fa"/>
47
6b91a500c96d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 46
diff changeset
1128 <param name="gencode" value="11" />
68
17698b85dc47 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
parents: 67
diff changeset
1129 <param name="standalone" value="data" />
47
6b91a500c96d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 46
diff changeset
1130
6b91a500c96d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 46
diff changeset
1131 <repeat name="track_groups">
6b91a500c96d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 46
diff changeset
1132 <param name="category" value="Auto Coloured" />
6b91a500c96d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 46
diff changeset
1133 <repeat name="data_tracks">
6b91a500c96d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 46
diff changeset
1134 <conditional name="data_format">
6b91a500c96d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 46
diff changeset
1135 <param name="data_format_select" value="pileup"/>
6b91a500c96d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 46
diff changeset
1136 <param name="annotation" value="bam/merlin-sample.bam"/>
6b91a500c96d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 46
diff changeset
1137 </conditional>
6b91a500c96d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 46
diff changeset
1138 </repeat>
6b91a500c96d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 46
diff changeset
1139 </repeat>
6b91a500c96d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 46
diff changeset
1140
6b91a500c96d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 46
diff changeset
1141 <param name="uglyTestingHack" value="enabled" />
70
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
1142 <output name="output">
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
1143 <assert_contents>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
1144 <has_text text="merlin-sample.bam"/>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
1145 <has_text text="sort_order=&quot;coordinate&quot;"/>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
1146 <has_text text="bam_index"/>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
1147 </assert_contents>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
1148 </output>
47
6b91a500c96d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 46
diff changeset
1149 </test>
6b91a500c96d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 46
diff changeset
1150
6b91a500c96d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 46
diff changeset
1151 <test>
46
f90c22c8fa7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 45
diff changeset
1152 <!-- data_table -->
f90c22c8fa7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 45
diff changeset
1153 <param name="reference_genome|genome_type_select" value="indexed"/>
53
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1154 <param name="reference_genome|genome" value="merlin"/>
46
f90c22c8fa7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 45
diff changeset
1155 <param name="gencode" value="1" />
68
17698b85dc47 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
parents: 67
diff changeset
1156 <param name="standalone" value="data" />
46
f90c22c8fa7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 45
diff changeset
1157 <param name="uglyTestingHack" value="enabled" />
70
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
1158 <output name="output">
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
1159 <assert_contents>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
1160 <has_text text="merlin.fa"/>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
1161 </assert_contents>
5c317ff96859 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents: 69
diff changeset
1162 </output>
46
f90c22c8fa7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 45
diff changeset
1163 </test>
53
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1164
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1165 <test>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1166 <param name="reference_genome|genome_type_select" value="history"/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1167 <param name="reference_genome|genome" value="merlin.fa"/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1168 <param name="gencode" value="11" />
68
17698b85dc47 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
parents: 67
diff changeset
1169 <param name="standalone" value="data" />
53
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1170
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1171 <repeat name="track_groups">
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1172 <param name="category" value="External endpoints" />
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1173 <repeat name="data_tracks">
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1174 <conditional name="data_format">
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1175 <param name="data_format_select" value="rest"/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1176 <param name="url" value="http://example.org.external/rest_api/"/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1177 <param name="label" value="Rest api"/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1178 </conditional>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1179 </repeat>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1180 <repeat name="data_tracks">
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1181 <conditional name="data_format">
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1182 <param name="data_format_select" value="sparql"/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1183 <param name="url" value="http://example.org.external/sparql/"/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1184 <param name="label" value="Sparql endpoint"/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1185 <param name="query" value=" DEFINE sql:select-option 'order'
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1186 prefix rdf: &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#&gt;
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1187 select ?start,
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1188 ?end,
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diff changeset
1189 IF( ?faldo_type = faldo:ForwardStrandPosition,
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
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diff changeset
1190 1,
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1191 IF( ?faldo_type = faldo:ReverseStrandPosition,
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1192 -1,
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iuc
parents: 51
diff changeset
1193 0
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents: 51
diff changeset
1194 )
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents: 51
diff changeset
1195 ) as ?strand,
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents: 51
diff changeset
1196 str(?obj_type_name) as ?type,
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents: 51
diff changeset
1197 str(?label) as ?name,
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents: 51
diff changeset
1198 str(?obj_name) as ?description,
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents: 51
diff changeset
1199 ?obj as ?uniqueID,
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
1200 ?parent as ?parentUniqueID
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
1201 where {
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
1202 values ?faldo_type { faldo:ForwardStrandPosition faldo:ReverseStrandPosition faldo:BothStrandsPosition }
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
1203 }"/>
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1204 </conditional>
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diff changeset
1205 </repeat>
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diff changeset
1206 </repeat>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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1207
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1208 <param name="uglyTestingHack" value="enabled" />
70
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1209 <output name="output">
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1210 <assert_contents>
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1211 <has_text text="http://example.org.external/sparql/"/>
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1212 </assert_contents>
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1213 </output>
53
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1214 </test>
30
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1215 </tests>
0
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parents:
diff changeset
1216 <help><![CDATA[
29
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1217 JBrowse-in-Galaxy
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diff changeset
1218 =================
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diff changeset
1219
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diff changeset
1220 JBrowse-in-Galaxy offers a highly configurable, workflow-compatible
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iuc
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1221 alternative to Trackster.
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diff changeset
1222
45
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diff changeset
1223 Overview
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diff changeset
1224 --------
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parents: 44
diff changeset
1225
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diff changeset
1226 JBrowse is a fast, embeddable genome browser built completely with
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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parents: 44
diff changeset
1227 JavaScript and HTML5.
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parents: 44
diff changeset
1228
29
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parents: 17
diff changeset
1229 The JBrowse-in-Galaxy (JiG) tool was written to help build complex
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iuc
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diff changeset
1230 JBrowse installations straight from Galaxy, taking advantage of the
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iuc
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diff changeset
1231 latest Galaxy features such as dataset collections, sections, and colour
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iuc
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diff changeset
1232 pickers. It allows you to build up a JBrowse instance without worrying
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diff changeset
1233 about how to run the command line tools to format your data, and which
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1234 options need to be supplied and where. Additionally it comes with many
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diff changeset
1235 javascript functions to handle colouring of features which would be
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diff changeset
1236 nearly impossible to write without the assistance of this tool.
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diff changeset
1237
53
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diff changeset
1238 The JBrowse-in-Galaxy tool is maintained by `the Galaxy IUC
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
1239 <https://github.com/galaxyproject/tools-iuc/issues>`__, who you can help you
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
1240 with missing features or bugs in the tool.
29
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diff changeset
1241
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diff changeset
1242 Options
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diff changeset
1243 -------
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1244
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diff changeset
1245 The first option you encounter is the **Fasta Sequence(s)**. This option
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1246 now accepts multiple fasta files, allowing you to build JBrowse
5614cf75bb24 Uploaded
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diff changeset
1247 instances that contain data for multiple genomes or chrosomomes
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diff changeset
1248 (generally known as "landmark features" in gff3 terminology.) Up to 30
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diff changeset
1249 will be shown from the dropdown selector within JBrowse, this is a known
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1250 issue.
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diff changeset
1251
53
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diff changeset
1252 **Standalone Instances** enable you to have either a complete JBrowse instance
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
1253 in a dataset, or just the data directory without JBrowse (e.g. for Apollo).
29
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diff changeset
1254 Currently Galaxy copies the entire JBrowse directory in order to have a
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diff changeset
1255 complete, downloadable file that contains a ready-to-go JBrowse
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diff changeset
1256 instance. This is obviously an anti-feature because users don't want a
53
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diff changeset
1257 complete copy of JBrowse (12Mb) that's duplicated for every JBrowse
29
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parents: 17
diff changeset
1258 dataset in their history, and admins don't want useless copies of
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iuc
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diff changeset
1259 JBrowse on disk. Unfortunately we have not come up with the perfect
5614cf75bb24 Uploaded
iuc
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diff changeset
1260 solution just yet, but we're working on it! In the meantime, users have
5614cf75bb24 Uploaded
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diff changeset
1261 been given the option to produce just the ``data/`` directory. For those
5614cf75bb24 Uploaded
iuc
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diff changeset
1262 unfamiliar with JBrowse, the ``data/`` directory contains processed data
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diff changeset
1263 files, but no way to view them. This feature is additionally implemented
5614cf75bb24 Uploaded
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diff changeset
1264 for upcoming `Apollo <https://github.com/gmod/apollo>`__ integration.
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1265
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diff changeset
1266 **Genetic Code** is a new feature in v0.4 of JiG / v1.12.0 of JBrowse,
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diff changeset
1267 which allows users to specify a non standard genetic code, and have
53
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
1268 JBrowse highlight the correct start and stop codons.
29
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diff changeset
1269
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1270 **Track Groups** represent a set of tracks in a single category. These
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1271 can be used to let your users understand relationships between large
5614cf75bb24 Uploaded
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diff changeset
1272 groups of tracks.
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1273
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diff changeset
1274 .. image:: sections.png
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1275
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diff changeset
1276 Annotation Tracks
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diff changeset
1277 -----------------
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diff changeset
1278
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diff changeset
1279 Within Track Groups, you have one or more **Annotation Tracks**. Each
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diff changeset
1280 Annotation Track is a groups of datasets which have similar styling.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1281 This allows you to rapidly build up JBrowse instances without having to
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iuc
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diff changeset
1282 configure tracks individually. A massive improvement over previous
5614cf75bb24 Uploaded
iuc
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diff changeset
1283 versions. For example, if you have five different GFF3 files from
5614cf75bb24 Uploaded
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diff changeset
1284 various gene callers that you wish to display, you can take advantage of
5614cf75bb24 Uploaded
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1285 this feature to style all of them similarly.
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diff changeset
1286
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diff changeset
1287 There are a few different types of tracks supported, each with their own
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1288 set of options:
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diff changeset
1289
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diff changeset
1290 GFF3/BED
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diff changeset
1291 ~~~~~~~~
29
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diff changeset
1292
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diff changeset
1293 These are your standard feature tracks. They usually highlight genes,
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iuc
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diff changeset
1294 mRNAs and other features of interest along a genomic region. The
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iuc
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diff changeset
1295 underlying tool and this help documentation focus primarily on GFF3
5614cf75bb24 Uploaded
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diff changeset
1296 data, and have not been tested extensively with other formats. Automatic
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diff changeset
1297 min/max detection will fail under BED datasets.
29
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diff changeset
1298
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diff changeset
1299 The data may be of a subclass we call **match/match part** data. This
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iuc
parents: 17
diff changeset
1300 consists of top level ``match`` features, with a child ``match_part``
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diff changeset
1301 feature, and is often used in displaying alignments. (See "Alignments"
5614cf75bb24 Uploaded
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parents: 17
diff changeset
1302 section on the `GFF3
42
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diff changeset
1303 specification <https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md>`__ for more
29
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parents: 17
diff changeset
1304 information). If the data is match/match part, you will need to specify
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diff changeset
1305 the top level match feature name, as it can be one of a few different SO
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diff changeset
1306 terms, and JiG does not yet have the ability to understand SO terms.
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diff changeset
1307
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diff changeset
1308 Next up is the **Styling Options** section, which lets you control a few
5614cf75bb24 Uploaded
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diff changeset
1309 properties on how the track is styled. Most of these you will not need
5614cf75bb24 Uploaded
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diff changeset
1310 to configure and can safely leave on defaults. Occasionally you will
5614cf75bb24 Uploaded
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diff changeset
1311 want to change what information is shown in the end product.
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diff changeset
1312
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diff changeset
1313 .. image:: styling.png
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parents: 17
diff changeset
1314
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diff changeset
1315 In the above image you can see some black text, and some blue text. The
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iuc
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diff changeset
1316 source of the black text is configured with the **style.label** option,
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diff changeset
1317 and the source of the blue text is configured with the
5614cf75bb24 Uploaded
iuc
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diff changeset
1318 **style.description** option.
5614cf75bb24 Uploaded
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parents: 17
diff changeset
1319
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diff changeset
1320 Feature Score Scaling & Colouring Options
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1321 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
5614cf75bb24 Uploaded
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parents: 17
diff changeset
1322
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diff changeset
1323 First, you need to choose between ignoring the score attribute of GFF3
5614cf75bb24 Uploaded
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parents: 17
diff changeset
1324 files, or using it. If you choose to ignore it, all features will be
5614cf75bb24 Uploaded
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diff changeset
1325 coloured with a solid colour. If you choose to use it, features will
5614cf75bb24 Uploaded
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diff changeset
1326 have slightly different colours based on their scores.
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1327
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diff changeset
1328 .. image:: opacity.png
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diff changeset
1329
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diff changeset
1330 If you choose **Ignore score**, you may choose between automatically
5614cf75bb24 Uploaded
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diff changeset
1331 choosing a colour, or manually specifying one. The automatically chosen
5614cf75bb24 Uploaded
iuc
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diff changeset
1332 colours vary along a brewer palette and generally look quite nice with
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1333 no human intervention required. The manual colour choice is somewhat
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1334 self explanatory. Clicking on the small coloured square will bring up a
5614cf75bb24 Uploaded
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parents: 17
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1335 colour palette.
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parents: 17
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1336
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parents: 17
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1337 If you choose **Base on score**, you're faced with a dizzying array of
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iuc
parents: 17
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1338 options. First is the function to map the colour choices to colour
5614cf75bb24 Uploaded
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parents: 17
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1339 values. JiG comes with a few functions built in such as linear scaling,
5614cf75bb24 Uploaded
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parents: 17
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1340 logarithmic scaling, and blast scaling.
5614cf75bb24 Uploaded
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parents: 17
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1341
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parents: 17
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1342 The **linear scaling** method says "take these values, and they map
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1343 directly to a range of output values". **Logarithmic scaling** says
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1344 "please take the log of the score before mapping", and **Blast scaling**
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1345 is further specialised to handle blast data more nicely. These are
5614cf75bb24 Uploaded
iuc
parents: 17
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1346 convenience functions to help transform the wide array of possible
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1347 values in the GFF3 score attribute to more meaningful numbers. If you
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1348 need more comprehensive score scaling, it is recommended that you
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1349 pre-process your GFF3 files somehow.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1350
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1351 Once you've selected a scaling method, you can choose to manually
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1352 specify the minimum and maximum expected values, or you can let JiG
5614cf75bb24 Uploaded
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parents: 17
diff changeset
1353 determine them for you automatically.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1354
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parents: 17
diff changeset
1355 Finally, opacity is the only mapping we currently provide. Future
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1356 iterations will attempt to improve upon this and provide more colour
5614cf75bb24 Uploaded
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parents: 17
diff changeset
1357 scales. The Opacity option maps the highest scoring features to full
5614cf75bb24 Uploaded
iuc
parents: 17
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1358 opacity, and everything else to lower ones.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1359
5614cf75bb24 Uploaded
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parents: 17
diff changeset
1360 BAM Pileups
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1361 ~~~~~~~~~~~
5614cf75bb24 Uploaded
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parents: 17
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1362
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1363 We support BAM files and can automatically generate SNP tracks based on
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1364 that bam data.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1365
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iuc
parents: 17
diff changeset
1366 .. image:: bam.png
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parents: 17
diff changeset
1367
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iuc
parents: 17
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1368 This is *strongly discouraged* for high coverage density datasets.
5614cf75bb24 Uploaded
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parents: 17
diff changeset
1369 Unfortunately there are no other configuration options exposed for bam
53
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1370 files.
29
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1371
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1372 BlastXML
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1373 ~~~~~~~~
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1374
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1375 .. image:: blast.png
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1376
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1377 JiG now supports both blastn and blastp datasets. JiG internally uses a
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1378 blastXML to gapped GFF3 tool to convert your blastxml datasets into a
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12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
1379 format amenable to visualization in JBrowse. This tool is also
29
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1380 available separately from the IUC on the toolshed.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1381
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1382 **Minimum Gap Size** reflects how long a gap must be before it becomes a
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1383 real gap in the processed gff3 file. In the picture above, various sizes
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1384 of gaps can be seen. If the minimum gap size was set much higher, say
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iuc
parents: 17
diff changeset
1385 100nt, many of the smaller gaps would disappear, and the features on
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1386 both sides would be merged into one, longer feature. This setting is
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1387 inversely proportional to runtime and output file size. *Do not set this
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1388 to a low value for large datasets*. By setting this number lower, you
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1389 will have extremely large outputs and extremely long runtimes. The
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1390 default was configured based off of the author's experience, but the
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1391 author only works on small viruses. It is *strongly* recommended that
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1392 you filter your blast results before display, e.g. picking out the top
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1393 10 hits or so.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1394
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1395 **Protein blast search** option merely informs underlying tools that
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1396 they should adjust feature locations by 3x.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1397
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1398 Styling Options
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1399 ^^^^^^^^^^^^^^^
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1400
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1401 Please see the styling options for GFF3 datasets, they are identical.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1402
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1403 Feature Score Scaling & Coloring Options
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1404 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1405
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1406 Please see the score scaling and colouring options for GFF3 datasets,
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1407 they are identical. Remember to set your score scaling to "blast" method
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1408 if you do use it.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1409
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1410 Bigwig XY
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1411 ~~~~~~~~~
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1412
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1413 .. image:: bigwig.png
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1414
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1415 **XYPlot**
5614cf75bb24 Uploaded
iuc
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diff changeset
1416
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1417 BigWig tracks can be displayed as a "density" plot which is continuous
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iuc
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diff changeset
1418 line which varies in colour, or as an "XYplot." XYplots are preferable
29
5614cf75bb24 Uploaded
iuc
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diff changeset
1419 for users to visually identify specific features in a bigwig track,
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1420 however density tracks are more visually compact.
5614cf75bb24 Uploaded
iuc
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diff changeset
1421
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1422 **Variance Band** is an option available to XYPlots, and can be seen in
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1423 the third and fourth tracks in the above picture. This overlays a mean
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1424 line, and 1 and 2 standard deviation areas.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1425
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1426 **Track Scaling** is different from colour scaling, instead it
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1427 configures how the track behaves inside of JBrowse. **Autoscaling
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1428 globally** means that JBrowse will determine the minimum and maximum for
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1429 the track, and fix the bounds of the viewport to that. E.g. if your
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1430 track ranges from 1-1000, and the region you're currently zoomed to only
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1431 goes from 0-50, then the viewport range will still show 1-1000. This is
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1432 good for global genomic context. However you may wish to consider
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1433 **autoscaling locally** instead. In the example of a region which varies
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1434 from 0-50, autoscaling locally would cause the individual track's
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1435 viewport to re-adjust and show just the 0-50 region. If neither of these
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12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
1436 options are palatable, you may manually hardcode the minimum and
29
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1437 maximums for the track to scale to.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1438
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1439 Colour Options
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1440 ^^^^^^^^^^^^^^
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1441
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1442 BigWig tracks have two colours in JBrowse, a positive and a negative
5614cf75bb24 Uploaded
iuc
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diff changeset
1443 colour.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1444
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1445 As always you may manually choose a colour, or let JiG choose for you.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1446
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1447 One of the more interesting options is the **Bicolor pivot**. This
5614cf75bb24 Uploaded
iuc
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diff changeset
1448 option allows you to control the point at which JBrowse switches from
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1449 the positive colour to the negative. In the above graphic, you can see
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1450 this has been configured to "mean" for the first two (orange and blue)
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1451 tracks.
5614cf75bb24 Uploaded
iuc
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diff changeset
1452
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1453 VCFs/SNPs
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1454 ~~~~~~~~~
5614cf75bb24 Uploaded
iuc
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diff changeset
1455
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1456 These tracks do not support any special configuration.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1457
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1458 Known Issues
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1459 ------------
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1460
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1461 - More than 30 landmark features cannot be listed in the manual
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1462 selector.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1463 - Non GFF3 likely has issue with automatically determined min/max
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1464 scores. Manually specify minimum and maximum score attributes, or do
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1465 not use varied colours based on scores to avoid this issue.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1466
5
b55fad376d87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents: 4
diff changeset
1467 @ATTRIBUTION@
0
c77c1d5baadb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
iuc
parents:
diff changeset
1468 ]]></help>
42
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
1469 <expand macro="citations"/>
0
c77c1d5baadb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
iuc
parents:
diff changeset
1470 </tool>