annotate jbrowse.xml @ 30:ca2def38369c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 74554507efb46fb40ce6e12f0b73425e52ec0977
author iuc
date Thu, 11 Apr 2019 09:35:00 -0400
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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 <expand macro="requirements"/>
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7 <version_command>python '${__tool_directory__}/jbrowse.py' --version</version_command>
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8 <command detect_errors="aggressive"><![CDATA[
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9 #if $action.action_select == "create":
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10 mkdir -p $output.files_path &&
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11 #else:
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12 cp -R $action.update_jbrowse.extra_files_path $output.files_path &&
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13 #end if
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14
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15 ## Copy the XML file into the directory, mostly for debugging
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16 ## but nice if users want to reproduce locally
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17 cp $trackxml $output.files_path/galaxy.xml &&
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18
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19 ## Once that's done, we run the python script to handle the real work
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20 python '$__tool_directory__/jbrowse.py'
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22 --jbrowse \${JBROWSE_SOURCE_DIR}
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23 #if str($standalone) == "Complete":
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24 --standalone
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25 #end if
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27 --outdir $output.files_path
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28 $trackxml &&
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29
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30 #if str($standalone) == "Complete":
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31 mv $output.files_path/index.html $output;
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32 #else:
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33 mv $dummyIndex $output;
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34 #end if
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35
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36 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph.
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37 #if str($uglyTestingHack) == "enabled":
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38 mv $trackxml $output
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39 #end if
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40 ]]></command>
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41 <configfiles>
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42 <configfile name="dummyIndex"><![CDATA[
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43 <html>
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44 <head>
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45 </head>
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46 <body>
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47 <h1>JBrowse Data Directory</h1>
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48 <p>
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49 Hi! This is not a full JBrowse instance. JBrowse v0.4(+?)
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50 started shipping with the ability to produce just the
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51 "data" directory from a JBrowse instance, rather than a
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52 complete, standalone instance. This was intended to be used
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53 with the in-development Apollo integration, but may have other
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54 uses as well.
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55 </p>
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56 <p>
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57 <u>This is not usable on its own</u>. The output dataset may be
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58 used with Apollo, or may be passed through the "JBrowse -
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59 Convert to Standalone" tool in Galaxy to "upgrade" to a full
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60 JBrowse instance.
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61 </p>
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62 </body>
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63 </html>
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64 ]]></configfile>
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65 <configfile name="trackxml"><![CDATA[<?xml version="1.0"?>
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66 <root>
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67 <metadata>
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68 <gencode>$gencode</gencode>
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69 <genomes>
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70 #if str($reference_genome.genome_type_select) == "indexed":
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71 <genome path="${reference_genome.genomes.fields.path}">
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72 <metadata />
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73 </genome>s
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74 #else
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75 <genome path="$reference_genome.genome">
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76 <metadata>
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77 <dataset id="${__app__.security.encode_id($reference_genome.genome.id)}" hid="${reference_genome.genome.hid}"
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78 size="${reference_genome.genome.get_size(nice_size=True)}"
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79 edam_format="${reference_genome.genome.datatype.edam_format}"
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80 file_ext="${reference_genome.genome.ext}" />
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81 <history id="${__app__.security.encode_id($reference_genome.genome.history_id)}"
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82 user_email="${reference_genome.genome.history.user.email}"
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83 user_id="${reference_genome.genome.history.user_id}"
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84 display_name="${reference_genome.genome.history.get_display_name()}"/>
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85 <metadata
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86 #for (key, value) in $reference_genome.genome.get_metadata().items():
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87 #if "_types" not in $key:
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88 ${key}="${value}"
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89 #end if
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90 #end for
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91 />
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92 <tool
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93 tool_id="${reference_genome.genome.creating_job.tool_id}"
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94 tool_version="${reference_genome.genome.creating_job.tool_version}"
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95 />
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96 </metadata>
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97 </genome>
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98 #end if
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99 </genomes>
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100 <general>
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101 <defaultLocation>${jbgen.defaultLocation}</defaultLocation>
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102 <trackPadding>${jbgen.trackPadding}</trackPadding>
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103
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104 <shareLink>${jbgen.shareLink}</shareLink>
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105 <aboutDescription>${jbgen.aboutDescription}</aboutDescription>
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106 <show_tracklist>${jbgen.show_tracklist}</show_tracklist>
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107 <show_nav>${jbgen.show_nav}</show_nav>
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108 <show_overview>${jbgen.show_overview}</show_overview>
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109 <show_menu>${jbgen.show_menu}</show_menu>
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110 <hideGenomeOptions>${jbgen.hideGenomeOptions}</hideGenomeOptions>
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111 </general>
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112 <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl>
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113 </metadata>
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114 <tracks>
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115 #for $tg in $track_groups:
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116 #for $track in $tg.data_tracks:
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117 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
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118 #if $track.data_format.data_format_select != "rest" and $track.data_format.data_format_select != "sparql":
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119 <files>
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120 #for $dataset in $track.data_format.annotation:
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121 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}">
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122 <metadata>
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123 <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}"
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124 size="${dataset.get_size(nice_size=True)}"
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125 edam_format="${dataset.datatype.edam_format}"
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126 file_ext="${dataset.ext}" />
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127 <history id="${__app__.security.encode_id($dataset.history_id)}"
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128 user_email="${dataset.history.user.email}"
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129 user_id="${dataset.history.user_id}"
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130 display_name="${dataset.history.get_display_name()}"/>
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131 <metadata
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132 #for (key, value) in $dataset.get_metadata().items():
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133 #if "_types" not in $key and $value is not None and len(str($value)) < 5000:
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134 ${key}="${value}"
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135 #end if
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136 #end for
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137 />
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138 <tool
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139 tool_id="${dataset.creating_job.tool_id}"
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140 tool_version="${dataset.creating_job.tool_version}"
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141 />
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142 </metadata>
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143 </trackFile>
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144 #end for
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145 </files>
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146 #end if
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147
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148 <options>
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149 #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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150 <style>
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151 <overridePlugins>${track.data_format.override_apollo_plugins}</overridePlugins>
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152 <overrideDraggable>${track.data_format.override_apollo_drag}</overrideDraggable>
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153 <className>${track.data_format.jbstyle.style_classname}</className>
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154 <description>${track.data_format.jbstyle.style_description}</description>
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155 <label>${track.data_format.jbstyle.style_label}</label>
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156 <height>${track.data_format.jbstyle.style_height}</height>
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157 <maxHeight>${track.data_format.jbstyle.max_height}</maxHeight>
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158 </style>
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159 <scaling>
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160 #if str($track.data_format.jbcolor_scale.color_score.color_score_select) == "none":
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161 <method>ignore</method>
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162 <scheme>
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163 #if str($track.data_format.jbcolor_scale.color_score.color.color_select) == "automatic":
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164 <color>__auto__</color>
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165 #else
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166 <color>${track.data_format.jbcolor_scale.color_score.color.style_color}</color>
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167 #end if
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168 </scheme>
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169 #else
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170 <method>score</method>
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171 <algo>${track.data_format.jbcolor_scale.color_score.score_scaling}</algo>
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172 <scales>
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173 <type>${track.data_format.jbcolor_scale.color_score.score_scales.scale_select}</type>
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174
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175 #if str($track.data_format.jbcolor_scale.color_score.score_scales.scale_select) == "manual":
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176 <min>${track.data_format.jbcolor_scale.color_score.score_scales.minimum}</min>
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177 <max>${track.data_format.jbcolor_scale.color_score.score_scales.maximum}</max>
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178 #end if
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179 </scales>
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180 <scheme>
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181 <type>${track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme}</type>
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182 ## auto_color
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183 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme) == "opacity":
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184 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.color.color_select) == "automatic":
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185 <color>__auto__</color>
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186 #else
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187 <color>${track.data_format.jbcolor_scale.color_score.color_scheme.color.style_color}</color>
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188 #end if
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189 #end if
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190 </scheme>
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191 #end if
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192 </scaling>
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193 <menus>
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194 #for $menu_item in $track.data_format.jbmenu.track_menu:
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195 <menu>
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196 <action>${menu_item.menu_action}</action>
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197 #if str($menu_item.menu_label) != "":
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198 <label>${menu_item.menu_label}</label>
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199 #end if
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200 #if str($menu_item.menu_title) != "":
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201 <title>${menu_item.menu_title}</title>
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202 #end if
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203 #if str($menu_item.menu_url) != "":
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204 <url>${menu_item.menu_url.replace("&", "&amp;").replace("\"", "&quot;")}</url>
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205 #end if
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206 #if str($menu_item.menu_icon) != "":
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207 <iconClass>${menu_item.menu_icon}</iconClass>
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208 #end if
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209 </menu>
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210 #end for
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211 </menus>
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212 #end if
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213
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214 #if str($track.data_format.data_format_select) == "wiggle":
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215 <wiggle>
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216 <type>${track.data_format.xyplot}</type>
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217 <variance_band>${track.data_format.var_band}</variance_band>
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218 #if str($track.data_format.scaling.scale_select) == "auto_local":
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219 <autoscale>local</autoscale>
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220 #else if str($track.data_format.scaling.scale_select) == "auto_global":
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221 <autoscale>global</autoscale>
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222 #else:
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223 <min>${track.data_format.scaling.minimum}</min>
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224 <max>${track.data_format.scaling.maximum}</max>
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225 #end if
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226 <scale>${track.data_format.scale_select2}</scale>
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227
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228 ## Wiggle tracks need special color config
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229 #if str($track.data_format.jbcolor.color.color_select) != "automatic":
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230 <color_pos>${track.data_format.jbcolor.color.style_pos_color}</color_pos>
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231 <color_neg>${track.data_format.jbcolor.color.style_neg_color}</color_neg>
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232 #else:
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233 <color_pos>__auto__</color_pos>
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234 <color_neg>__auto__</color_neg>
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235 #end if
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236
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237 ## Bicolor pivot config
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238 #if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "zero":
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239 <bicolor_pivot>zero</bicolor_pivot>
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240 #else if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "mean":
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241 <bicolor_pivot>mean</bicolor_pivot>
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242 #else:
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243 <bicolor_pivot>${track.data_format.jbcolor.bicolor_pivot.pivot_point}</bicolor_pivot>
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244 #end if
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245 <multibigwig>${track.data_format.MultiBigWig}</multibigwig>
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246 </wiggle>
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247 #else if str($track.data_format.data_format_select) == "pileup":
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248 <pileup>
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249 <auto_snp>${track.data_format.auto_snp}</auto_snp>
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250 <bam_indices>
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251 #for $dataset in $track.data_format.annotation:
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252 <bam_index>${dataset.metadata.bam_index}</bam_index>
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253 #end for
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254 </bam_indices>
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255 <chunkSizeLimit>${track.data_format.chunkSizeLimit}</chunkSizeLimit>
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256 </pileup>
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257 #else if str($track.data_format.data_format_select) == "blast":
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258 <blast>
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259 #if str($track.data_format.blast_parent) != "":
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260 <parent>${track.data_format.blast_parent}</parent>
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261 #end if
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262 <protein>${track.data_format.is_protein}</protein>
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263 <min_gap>${track.data_format.min_gap}</min_gap>
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264 <index>${track.data_format.index}</index>
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265 </blast>
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266 #else if str($track.data_format.data_format_select) == "gene_calls":
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267 <gff>
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268 <trackType>${track.data_format.track_config.track_class}</trackType>
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269 #if $track.data_format.track_config.track_class in ['JBrowse/View/Track/CanvasFeatures', 'NeatCanvasFeatures/View/Track/NeatFeatures']:
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270 #if str($track.data_format.track_config.canvas_options.transcriptType) != "":
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271 <transcriptType>${track.data_format.track_config.canvas_options.transcriptType}</transcriptType>
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272 #end if
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273 #if str($track.data_format.track_config.canvas_options.subParts) != "":
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274 <subParts>${track.data_format.track_config.canvas_options.subParts}</subParts>
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275 #end if
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276 #if str($track.data_format.track_config.canvas_options.impliedUTRs) != "false":
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277 <impliedUTRs>${track.data_format.track_config.canvas_options.impliedUTRs}</impliedUTRs>
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278 #end if
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279 #else if $track.data_format.track_config.track_class in ['JBrowse/View/Track/HTMLFeatures', 'NeatHTMLFeatures/View/Track/NeatFeatures']:
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280 #if str($track.data_format.track_config.html_options.topLevelFeatures) != "":
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281 <topLevelFeatures>${track.data_format.track_config.html_options.topLevelFeatures}</topLevelFeatures>
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282 #end if
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283 #end if
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284 #if $track.data_format.match_part.match_part_select:
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285 <match>${track.data_format.match_part.name}</match>
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286 #end if
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287 <index>${track.data_format.index}</index>
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288 </gff>
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289 #else if str($track.data_format.data_format_select) == "rest":
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290 <label>${track.data_format.label}</label>
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291 <rest>
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292 <url>${track.data_format.url}</url>
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293 </rest>
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294 #else if str($track.data_format.data_format_select) == "sparql":
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295 <label>${track.data_format.label}</label>
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296 <sparql>
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297 <url>${track.data_format.url}</url>
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298 <query>${track.data_format.query}</query>
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299 </sparql>
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300 #end if
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301 </options>
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302 </track>
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303 #end for
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304 #end for
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305 </tracks>
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306 ## Disable plugins until https://github.com/GMOD/jbrowse/issues/1288 is fixed
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307 ## <plugins
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308 ## ComboTrackSelector="${plugins.ComboTrackSelector}"
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309 ## Bookmarks="${plugins.Bookmarks}"
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310 ## GCContent="${plugins.GCContent}"
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311 ## BlastView="${plugins.BlastView}"
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312 ## theme="${plugins.theme}"
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313 ## />
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314 <plugins
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315 ComboTrackSelector="${plugins.ComboTrackSelector}"
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316 Bookmarks=""
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317 GCContent="${plugins.GCContent}"
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318 BlastView="${plugins.BlastView}"
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319 theme=""
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320 />
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321 </root>]]></configfile>
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322 </configfiles>
0
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323 <inputs>
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324 <conditional name="reference_genome">
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325 <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select">
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326 <option selected="True" value="indexed">Use a built-in genome</option>
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327 <option value="history">Use a genome from history</option>
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328 </param>
8
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329 <when value="indexed">
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330 <param
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331 help="If your genome of interest is not listed, contact the Galaxy team"
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332 label="Select a reference genome"
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333 name="genomes"
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334 type="select"
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335 >
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336 <options from_data_table="all_fasta">
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337 <filter column="2" type="sort_by" />
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338 <validator message="No genomes are available for the selected input dataset" type="no_options" />
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339 </options>
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340 </param>
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341 </when>
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342 <when value="history">
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parents: 6
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343 <param
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344 format="fasta"
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345 label="Select the reference genome"
25
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346 name="genome"
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347 type="data" />
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348 </when>
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349 </conditional>
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350
22
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parents: 21
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351 <param name="standalone" type="boolean" truevalue="Complete" falsevalue="Data Directory" checked="true" label="Produce Standalone Instance" help="Produce a full, working JBrowse instance or just the data directory. Data dir mode is experimental and intended to be used with Apollo"/>
3
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parents: 1
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352
22
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353 <param name="gencode" type="select" label="Genetic Code">
3
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parents: 1
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354 <option value="1">1. The Standard Code</option>
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parents: 1
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355 <option value="2">2. The Vertebrate Mitochondrial Code</option>
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parents: 1
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356 <option value="3">3. The Yeast Mitochondrial Code</option>
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parents: 1
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357 <option value="4">4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
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parents: 1
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358 <option value="5">5. The Invertebrate Mitochondrial Code</option>
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parents: 1
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359 <option value="6">6. The Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
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parents: 1
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360 <option value="9">9. The Echinoderm and Flatworm Mitochondrial Code</option>
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parents: 1
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361 <option value="10">10. The Euplotid Nuclear Code</option>
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parents: 1
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362 <option value="11">11. The Bacterial, Archaeal and Plant Plastid Code</option>
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parents: 1
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363 <option value="12">12. The Alternative Yeast Nuclear Code</option>
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parents: 1
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364 <option value="13">13. The Ascidian Mitochondrial Code</option>
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parents: 1
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365 <option value="14">14. The Alternative Flatworm Mitochondrial Code</option>
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parents: 1
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366 <option value="16">16. Chlorophycean Mitochondrial Code</option>
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parents: 1
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367 <option value="21">21. Trematode Mitochondrial Code</option>
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parents: 1
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368 <option value="22">22. Scenedesmus obliquus Mitochondrial Code</option>
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parents: 1
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369 <option value="23">23. Thraustochytrium Mitochondrial Code</option>
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parents: 1
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370 <option value="24">24. Pterobranchia Mitochondrial Code</option>
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parents: 1
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371 <option value="25">25. Candidate Division SR1 and Gracilibacteria Code</option>
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parents: 1
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372 </param>
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373
8
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374 <conditional name="action">
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375 <param type="select" label="JBrowse-in-Galaxy Action" name="action_select">
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376 <option value="create">New JBrowse Instance</option>
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377 <option value="update">Update exising JBrowse Instance</option>
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378 </param>
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parents: 6
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379 <when value="create" />
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380 <when value="update">
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381 <param name="update_jbrowse" type="data" format="html" label="Previous JBrowse Instance" />
8
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382 </when>
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383 </conditional>
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384
3
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parents: 1
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385 <repeat name="track_groups" title="Track Group">
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parents: 1
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386 <param label="Track Category"
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parents: 1
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387 name="category"
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parents: 1
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388 type="text"
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389 value="Default"
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390 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"/>
0
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391 <repeat name="data_tracks" title="Annotation Track">
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parents: 16
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392 <conditional name="data_format" label="Track Options">
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parents: 0
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393 <param type="select" label="Track Type" name="data_format_select">
3
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parents: 1
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394 <option value="gene_calls">GFF/GFF3/BED/GBK Features</option>
1
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parents: 0
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395 <option value="pileup">BAM Pileups</option>
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parents: 0
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396 <option value="blast">Blast XML</option>
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parents: 0
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397 <option value="wiggle">BigWig XY</option>
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parents: 0
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398 <option value="vcf">VCF SNPs</option>
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parents: 16
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399 <option value="rest">REST Endpoint</option>
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parents: 23
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400 <option value="sparql">SPARQL</option>
1
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parents: 0
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401 </param>
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parents: 0
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402 <when value="blast">
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parents: 1
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403 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" />
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parents: 0
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404
3
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parents: 1
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405 <param label="Features used in Blast Search"
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parents: 1
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406 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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407 format="gff3"
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parents: 1
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408 name="blast_parent"
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parents: 1
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409 optional="true"
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parents: 1
diff changeset
410 type="data"/>
1
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parents: 0
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411
3
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parents: 1
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412 <param label="Minimum Gap Size"
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parents: 1
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413 help="before a new match_part feature is created"
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parents: 1
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414 name="min_gap"
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parents: 1
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415 type="integer"
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parents: 1
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416 value="10"
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parents: 1
diff changeset
417 min="2" />
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parents: 0
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418 <param label="Is this a protein blast search?"
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parents: 1
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419 type="boolean"
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parents: 1
diff changeset
420 name="is_protein"
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parents: 1
diff changeset
421 truevalue="true"
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parents: 1
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422 falsevalue="false" />
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423
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parents: 6
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424 <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" />
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425
3
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parents: 1
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426 <expand macro="track_styling"
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parents: 1
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427 classname="feature"
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parents: 1
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428 label="description"
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parents: 1
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429 description="Hit_titles"
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parents: 1
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430 height="600px"/>
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parents: 1
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431 <expand macro="color_selection"
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parents: 1
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432 token_scaling_lin_select="false"
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parents: 1
diff changeset
433 token_scaling_log_select="true" />
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parents: 6
diff changeset
434 <expand macro="track_menu" />
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parents: 3
diff changeset
435 <expand macro="track_display" />
1
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parents: 0
diff changeset
436 </when>
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parents: 0
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437 <when value="vcf">
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parents: 1
diff changeset
438 <expand macro="input_conditional" label="SNP Track Data" format="vcf" />
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parents: 3
diff changeset
439 <expand macro="track_display" />
1
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parents: 0
diff changeset
440 </when>
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parents: 0
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441 <when value="gene_calls">
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parents: 1
diff changeset
442 <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" />
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parents: 16
diff changeset
443 <conditional name="match_part" label="match/match_part data">
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parents: 1
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444 <param label="This is match/match_part data"
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parents: 1
diff changeset
445 type="boolean"
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parents: 1
diff changeset
446 name="match_part_select"
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parents: 1
diff changeset
447 truevalue="true"
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parents: 1
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448 falsevalue="false" />
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parents: 1
diff changeset
449 <when value="true">
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parents: 1
diff changeset
450 <param label="Match Part Feature Type"
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iuc
parents: 1
diff changeset
451 name="name"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
452 type="text"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
453 value="match"
21
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parents: 19
diff changeset
454 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)."
1c718d8b3532 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9cac72c004cc7ef57be997e2fdafb3b1839a300f
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parents: 19
diff changeset
455 optional="True"/>
3
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iuc
parents: 1
diff changeset
456 </when>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
457 <when value="false" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
458 </conditional>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
459
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
460 <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
461
10
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iuc
parents: 8
diff changeset
462 <conditional name="track_config">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
463 <param type="select" label="JBrowse Track Type [Advanced]" name="track_class">
26
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iuc
parents: 25
diff changeset
464 <option value="NeatHTMLFeatures/View/Track/NeatFeatures" selected="true">Neat HTML Features</option>
08776ba76cf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 75f6e483debb4c0d388bf4a54df81ee89af598d5
iuc
parents: 25
diff changeset
465 <option value="NeatCanvasFeatures/View/Track/NeatFeatures">Neat Canvas Features</option>
10
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
466 <option value="JBrowse/View/Track/HTMLFeatures">HTML Features</option>
26
08776ba76cf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 75f6e483debb4c0d388bf4a54df81ee89af598d5
iuc
parents: 25
diff changeset
467 <option value="JBrowse/View/Track/CanvasFeatures">Canvas Features</option>
25
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iuc
parents: 23
diff changeset
468 <option value="BlastView/View/Track/CanvasFeatures">Blast Features</option><!-- Disable plugins until https://github.com/GMOD/jbrowse/issues/1288 is fixed -->
10
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
469 </param>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
470 <when value="JBrowse/View/Track/CanvasFeatures">
27
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iuc
parents: 26
diff changeset
471 <expand macro="canvas_options" />
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 26
diff changeset
472 </when>
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 26
diff changeset
473 <when value="JBrowse/View/Track/HTMLFeatures">
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 26
diff changeset
474 <expand macro="html_options" />
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 26
diff changeset
475 </when>
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 26
diff changeset
476 <when value="BlastView/View/Track/CanvasFeatures" />
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 26
diff changeset
477 <when value="NeatHTMLFeatures/View/Track/NeatFeatures">
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 26
diff changeset
478 <expand macro="html_options" />
26
08776ba76cf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 75f6e483debb4c0d388bf4a54df81ee89af598d5
iuc
parents: 25
diff changeset
479 </when>
27
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 26
diff changeset
480 <when value="NeatCanvasFeatures/View/Track/NeatFeatures">
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 26
diff changeset
481 <expand macro="canvas_options" />
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 26
diff changeset
482 </when>
10
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
483 </conditional>
27
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 26
diff changeset
484 <expand macro="track_styling"
30
ca2def38369c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 74554507efb46fb40ce6e12f0b73425e52ec0977
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parents: 29
diff changeset
485 classname="feature"
27
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 26
diff changeset
486 label="product,name,id"
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 26
diff changeset
487 description="note,description"
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 26
diff changeset
488 height="10px"/>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
489 <expand macro="color_selection" />
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
490 <expand macro="track_menu" />
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
491 <expand macro="track_display" />
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
492 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
493 <when value="pileup">
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
494 <expand macro="input_conditional" label="BAM Track Data" format="bam" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
495 <param label="Autogenerate SNP Track"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
496 help="Not recommended for deep coverage BAM files"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
497 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
498 name="auto_snp"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
499 truevalue="true"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
500 falsevalue="false" />
25
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iuc
parents: 23
diff changeset
501 <param label="Maximum size of BAM chunks"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
502 name="chunkSizeLimit"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
503 type="integer"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
504 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."
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
505 value="5000000" />
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
506 <expand macro="track_display" />
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
507 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
508 <when value="wiggle">
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
509 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
510
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
511 <param label="Use XYPlot"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
512 help="instead of continuous colored band"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
513 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
514 name="xyplot"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
515 truevalue="JBrowse/View/Track/Wiggle/XYPlot"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
516 falsevalue="JBrowse/View/Track/Wiggle/Density" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
517 <param label="Show variance band"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
518 help="Only for XYPlots"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
519 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
520 name="var_band"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
521 truevalue="true"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
522 falsevalue="false" />
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
523
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
524 <conditional name="scaling" label="Scaling">
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
525 <param type="select" label="Track Scaling" name="scale_select">
23
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iuc
parents: 22
diff changeset
526 <option value="auto_local" selected="true">Autoscale (local)</option>
dba3c47e1798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit cf2c8f3039021b645ac45980a02ffe1f69a3f958
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parents: 22
diff changeset
527 <option value="auto_global">Autoscale (global)</option>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
528 <option value="fixed">Specify Min/Max</option>
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
529 </param>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
530 <when value="auto_local"></when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
531 <when value="auto_global"></when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
532 <when value="fixed">
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
533 <param label="Track minimum" name="minimum"
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
534 type="integer" value="0" />
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
535 <param label="Track maximum" name="maximum"
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
536 type="integer" value="100" />
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
537 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
538 </conditional>
17
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iuc
parents: 16
diff changeset
539 <param type="select" label="Visual Scaling" name="scale_select2">
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
540 <option value="linear" selected="true">Linear</option>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
541 <option value="log">Logarithmic (Dynamically Calculated)</option>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
542 </param>
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
543
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
544 <param label="Use MultiBigWig Plugin" name="MultiBigWig" truevalue="True" falsevalue="" type="boolean"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
545 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." />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
546
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
547 <expand macro="color_selection_minmax" />
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
548 <expand macro="track_display" />
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
549 </when>
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
550 <when value="rest">
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
551 <param type="text" label="REST Endpoint" name="url" />
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
552 <param type="text" label="Track Label" name="label" value="REST Genes" />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
553 <expand macro="track_styling"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents: 23
diff changeset
554 classname="feature"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents: 23
diff changeset
555 label="description"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents: 23
diff changeset
556 description="Hit_titles"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
557 height="600px"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
558 <expand macro="color_selection"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
559 token_scaling_lin_select="false"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
560 token_scaling_log_select="true" />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
561 <expand macro="track_menu" />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
562 <expand macro="track_display" />
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
563 </when>
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
564
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
565 <when value="sparql">
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
566 <param type="text" label="SPARQL Server URL" name="url" />
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
567 <param type="text" label="Track Label" name="label" value="SPARQL Genes" />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
568 <param type="text" label="SPARQL Query" name="query" area="true">
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
569 <sanitizer>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
570 <mapping initial="galaxy.util.mapped_chars">
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
571 <add source="&#10;" target=" " />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
572 <add source="&gt;" target="__gt__" />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
573 <add source="&lt;" target="__lt__" />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
574 </mapping>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
575 <valid initial="default">
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
576 <add value="|" />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
577 <add value="#" />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
578 <add value="{"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
579 <add value="}"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
580 <add value="!"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
581 <add value="?"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
582 <add value="&amp;"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
583 <add value="+"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
584 <add value="="/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
585 <add value="'"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
586 <add value='"'/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
587 </valid>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
588 </sanitizer>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
589 </param>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
590 <expand macro="track_styling"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
591 classname="feature"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
592 label="description"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
593 description="Hit_titles"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
594 height="600px"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
595 <expand macro="color_selection"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
596 token_scaling_lin_select="false"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents: 23
diff changeset
597 token_scaling_log_select="true" />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
598 <expand macro="track_menu" />
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
599 <expand macro="track_display" />
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
600 </when>
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
601 </conditional>
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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diff changeset
602 </repeat>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
603 </repeat>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
604
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
605 <expand macro="general_options" />
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
606 <!-- Disable plugins until https://github.com/GMOD/jbrowse/issues/1288 is fixed -->
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
607 <section name="plugins" title="Plugins" expanded="false">
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
608
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
609 <param
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
610 label="BlastView" name="BlastView" truevalue="True" falsevalue="" type="boolean" checked="true"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents: 23
diff changeset
611 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." />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
612
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
613 <param
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
614 label="Combo Track Selector" name="ComboTrackSelector" truevalue="True" falsevalue="" type="boolean"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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parents: 16
diff changeset
615 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" />
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
616 <!-- No way to disable now that it's built in jbrowse conda package -->
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents: 23
diff changeset
617 <!--param
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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parents: 16
diff changeset
618 label="Bookmarks" name="Bookmarks" truevalue="True" falsevalue="" type="boolean"
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents: 23
diff changeset
619 help="JBrowse plugin allowing users to manage a persistent list of bookmarks kept in localstorage" /-->
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
620
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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parents: 16
diff changeset
621 <param
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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parents: 16
diff changeset
622 label="GC Content" name="GCContent" truevalue="True" falsevalue="" type="boolean"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
623 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)." />
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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parents: 16
diff changeset
624
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents: 23
diff changeset
625 <!--param type="select" label="JBrowse Theme" name="theme">
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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parents: 16
diff changeset
626 <option value="" selected="True">Default</option>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
627 <option value="Minimalist">Minimalist</option>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
628 <option value="Dark">Dark</option>
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents: 23
diff changeset
629 </param-->
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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parents: 16
diff changeset
630 </section>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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parents: 16
diff changeset
631
3
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
632 <param type="hidden" name="uglyTestingHack" value="" />
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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diff changeset
633 </inputs>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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diff changeset
634 <outputs>
3
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iuc
parents: 1
diff changeset
635 <data format="html" name="output" label="JBrowse on $on_string - $standalone"/>
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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diff changeset
636 </outputs>
3
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iuc
parents: 1
diff changeset
637 <tests>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
638 <test>
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
639 <!-- gencode -->
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 6
diff changeset
640 <param name="reference_genome|genome_type_select" value="history"/>
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents: 23
diff changeset
641 <param name="reference_genome|genome" value="merlin.fa"/>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
642 <param name="gencode" value="1" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
643 <param name="standalone" value="Data Directory" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
644 <param name="uglyTestingHack" value="enabled" />
19
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
645 <output name="output" file="gencode/test-1.xml" lines_diff="14"/>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
646 </test>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
647 <test>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
648 <param name="reference_genome|genome_type_select" value="history"/>
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
649 <param name="reference_genome|genome" value="merlin.fa"/>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
650 <param name="gencode" value="11" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
651 <param name="standalone" value="Data Directory" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
652 <param name="uglyTestingHack" value="enabled" />
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
653 <output name="output" file="gencode/test.xml" lines_diff="14"/>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
654 </test>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
655 <test>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
656 <param name="reference_genome|genome_type_select" value="history"/>
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
657 <param name="reference_genome|genome" value="merlin.fa"/>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
658 <param name="gencode" value="11" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
659 <param name="standalone" value="Data Directory" />
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
660 <repeat name="track_groups">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
661 <param name="category" value="Auto Coloured" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
662 <repeat name="data_tracks">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
663 <conditional name="data_format">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
664 <param name="data_format_select" value="gene_calls"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
665 <param name="annotation" value="gff3/A.gff,gff3/B.gff,gff3/C.gff,gff3/D.gff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
666 <conditional name="match_part">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
667 <param name="match_part_select" value="false"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
668 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
669 <section name="jbcolor_scale">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
670 <conditional name="color_score">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
671 <param name="color_score_select" value="none"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
672 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
673 <conditional name="color">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
674 <param name="color_select" value="automatic"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
675 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
676 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
677 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
678 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
679 </repeat>
3
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iuc
parents: 1
diff changeset
680
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
681 <repeat name="track_groups">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
682 <param name="category" value="Ignore Scale" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
683 <repeat name="data_tracks">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
684 <conditional name="data_format">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
685 <param name="data_format_select" value="gene_calls"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
686 <param name="annotation" value="gff3/1.gff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
687 <conditional name="match_part">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
688 <param name="match_part_select" value="false"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
689 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
690 <section name="jbcolor_scale">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
691 <conditional name="color_score">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
692 <param name="color_score_select" value="none"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
693 <conditional name="color">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
694 <param name="color_select" value="manual"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
695 <param name="style_color" value="#ff00ff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
696 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
697 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
698 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
699 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
700 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
701 </repeat>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
702
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
703 <repeat name="track_groups">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
704 <param name="category" value="Scaled Colour" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
705 <repeat name="data_tracks">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
706 <conditional name="data_format">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
707 <param name="data_format_select" value="gene_calls"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
708 <param name="annotation" value="gff3/1.gff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
709 <conditional name="match_part">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
710 <param name="match_part_select" value="false"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
711 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
712 <section name="jbcolor_scale">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
713 <conditional name="color_score">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
714 <param name="color_score_select" value="score"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
715 <param name="score_scaling" value="linear"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
716 <conditional name="score_scales">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
717 <param name="scale_select" value="automatic"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
718 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
719 <conditional name="color_scheme">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
720 <param name="score_scheme" value="opacity"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
721 <conditional name="color">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
722 <param name="color_select" value="automatic"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
723 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
724 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
725 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
726 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
727 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
728 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
729 <repeat name="data_tracks">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
730 <conditional name="data_format">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
731 <param name="data_format_select" value="gene_calls"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
732 <param name="annotation" value="gff3/1.gff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
733 <conditional name="match_part">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
734 <param name="match_part_select" value="false"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
735 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
736 <section name="jbcolor_scale">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
737 <conditional name="color_score">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
738 <param name="color_score_select" value="score"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
739 <param name="score_scaling" value="linear"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
740 <conditional name="score_scales">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
741 <param name="scale_select" value="automatic"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
742 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
743 <conditional name="color_scheme">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
744 <param name="score_scheme" value="opacity"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
745 <conditional name="color">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
746 <param name="color_select" value="manual"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
747 <param name="style_color" value="#0000ff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
748 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
749 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
750 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
751 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
752 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
753 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
754 <repeat name="data_tracks">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
755 <conditional name="data_format">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
756 <param name="data_format_select" value="gene_calls"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
757 <param name="annotation" value="gff3/1.gff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
758 <conditional name="match_part">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
759 <param name="match_part_select" value="false"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
760 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
761 <section name="jbcolor_scale">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
762 <conditional name="color_score">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
763 <param name="color_score_select" value="score"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
764 <param name="score_scaling" value="linear"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
765 <conditional name="score_scales">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
766 <param name="scale_select" value="manual"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
767 <param name="minimum" value="0"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
768 <param name="maximum" value="1000"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
769 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
770 <conditional name="color_scheme">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
771 <param name="score_scheme" value="opacity"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
772 <conditional name="color">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
773 <param name="color_select" value="automatic"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
774 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
775 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
776 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
777 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
778 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
779 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
780 <repeat name="data_tracks">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
781 <conditional name="data_format">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
782 <param name="data_format_select" value="gene_calls"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
783 <param name="annotation" value="gff3/1.gff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
784 <conditional name="match_part">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
785 <param name="match_part_select" value="false"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
786 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
787 <section name="jbcolor_scale">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
788 <conditional name="color_score">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
789 <param name="color_score_select" value="score"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
790 <param name="score_scaling" value="linear"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
791 <conditional name="score_scales">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
792 <param name="scale_select" value="manual"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
793 <param name="minimum" value="0"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
794 <param name="maximum" value="1000"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
795 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
796 <conditional name="color_scheme">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
797 <param name="score_scheme" value="opacity"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
798 <conditional name="color">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
799 <param name="color_select" value="manual"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
800 <param name="style_color" value="#ff0000"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
801 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
802 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
803 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
804 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
805 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
806 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
807 </repeat>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
808
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
809 <repeat name="track_groups">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
810 <param name="category" value="Realistic" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
811 <repeat name="data_tracks">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
812 <conditional name="data_format">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
813 <param name="data_format_select" value="gene_calls"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
814 <param name="annotation" value="gff3/interpro.gff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
815 <conditional name="match_part">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
816 <param name="match_part_select" value="false"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
817 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
818 <section name="jbcolor_scale">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
819 <conditional name="color_score">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
820 <param name="color_score_select" value="none"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
821 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
822 <conditional name="color">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
823 <param name="color_select" value="automatic"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
824 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
825 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
826 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
827 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
828 <repeat name="data_tracks">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
829 <conditional name="data_format">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
830 <param name="data_format_select" value="gene_calls"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
831 <param name="annotation" value="gff3/2.gff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
832 <conditional name="match_part">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
833 <param name="match_part_select" value="true"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
834 <param name="name" value="cDNA_match"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
835 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
836 <section name="jbcolor_scale">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
837 <conditional name="color_score">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
838 <param name="color_score_select" value="none"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
839 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
840 <conditional name="color">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
841 <param name="color_select" value="automatic"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
842 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
843 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
844 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
845 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
846 </repeat>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
847
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
848 <param name="uglyTestingHack" value="enabled" />
19
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
849 <output name="output" file="gff3/test.xml" lines_diff="256" />
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
850 </test>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
851 <test>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
852 <param name="reference_genome|genome_type_select" value="history"/>
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
853 <param name="reference_genome|genome" value="merlin.fa"/>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
854 <param name="gencode" value="11" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
855 <param name="standalone" value="Data Directory" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
856
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
857 <repeat name="track_groups">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
858 <param name="category" value="With menu or index" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
859 <repeat name="data_tracks">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
860 <conditional name="data_format">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
861 <param name="data_format_select" value="gene_calls"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
862 <param name="annotation" value="gff3/1.gff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
863 <conditional name="match_part">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
864 <param name="match_part_select" value="false"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
865 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
866 <section name="jbcolor_scale">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
867 <conditional name="color_score">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
868 <param name="color_score_select" value="none"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
869 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
870 <conditional name="color">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
871 <param name="color_select" value="automatic"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
872 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
873 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
874 <section name="jbmenu">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
875 <repeat name="track_menu">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
876 <param name="menu_action" value="iframeDialog"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
877 <param name="menu_label" value="Some menu item"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
878 <param name="menu_title" value="Frame title"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
879 <param name="menu_url" value="https://example.com/#!/?id={name}&amp;q={type}&amp;z=&quot;{end}&quot;"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
880 <param name="menu_icon" value="dijitIconNewTask"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
881 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
882 <repeat name="track_menu">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
883 <param name="menu_action" value="newWindow"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
884 <param name="menu_label" value="Another menu item"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
885 <param name="menu_title" value="Frame title 2"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
886 <param name="menu_url" value="https://example.com/#!/?id={name}&amp;q={type}&amp;z=&quot;{end}&quot;"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
887 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
888 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
889 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
890 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
891 <repeat name="data_tracks">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
892 <conditional name="data_format">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
893 <param name="data_format_select" value="gene_calls"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
894 <param name="annotation" value="gff3/1.gff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
895 <param name="index" value="true"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
896 <conditional name="match_part">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
897 <param name="match_part_select" value="false"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
898 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
899 <section name="jbcolor_scale">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
900 <conditional name="color_score">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
901 <param name="color_score_select" value="none"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
902 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
903 <conditional name="color">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
904 <param name="color_select" value="automatic"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
905 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
906 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
907 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
908 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
909 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
910
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
911 <param name="uglyTestingHack" value="enabled" />
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
912 <output name="output" file="menus/test.xml" lines_diff="24"/>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
913 </test>
10
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
914 <test>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
915 <param name="reference_genome|genome_type_select" value="history"/>
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
916 <param name="reference_genome|genome" value="merlin.fa"/>
10
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
917 <param name="gencode" value="11" />
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
918 <param name="standalone" value="Data Directory" />
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
919
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
920 <repeat name="track_groups">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
921 <param name="category" value="With canvas config" />
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
922 <repeat name="data_tracks">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
923 <conditional name="data_format">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
924 <param name="data_format_select" value="gene_calls"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
925 <param name="annotation" value="gff3/1.gff"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
926 <conditional name="match_part">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
927 <param name="match_part_select" value="false"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
928 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
929 <conditional name="track_config">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
930 <section name="canvas_options">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
931 <param name="transcriptType" value="transcript"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
932 <param name="subParts" value="exon"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
933 <param name="impliedUTRs" value="true"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
934 </section>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
935 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
936 <section name="jbcolor_scale">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
937 <conditional name="color_score">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
938 <param name="color_score_select" value="none"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
939 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
940 <conditional name="color">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
941 <param name="color_select" value="automatic"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
942 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
943 </section>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
944 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
945 </repeat>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
946 </repeat>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
947
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
948 <param name="uglyTestingHack" value="enabled" />
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
949 <output name="output" file="track_config/test.xml" lines_diff="26"/>
10
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
950 </test>
18
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 17
diff changeset
951 <test>
19
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
952 <param name="reference_genome|genome_type_select" value="history"/>
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
953 <param name="reference_genome|genome" value="merlin.fa"/>
19
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
954 <param name="gencode" value="11" />
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
955 <param name="standalone" value="Data Directory" />
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
956
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
957 <repeat name="track_groups">
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
958 <param name="category" value="Auto Coloured" />
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
959 <repeat name="data_tracks">
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
960 <conditional name="data_format">
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
961 <param name="data_format_select" value="pileup"/>
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
962 <param name="annotation" value="bam/merlin-sample.bam"/>
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
963 </conditional>
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
964 </repeat>
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
965 </repeat>
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
966
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
967 <param name="uglyTestingHack" value="enabled" />
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
968 <output name="output" file="bam/test.xml" lines_diff="48"/>
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
969 </test>
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
970
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
971 <test>
18
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 17
diff changeset
972 <!-- data_table -->
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 17
diff changeset
973 <param name="reference_genome|genome_type_select" value="indexed"/>
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
974 <param name="reference_genome|genome" value="merlin"/>
18
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 17
diff changeset
975 <param name="gencode" value="1" />
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 17
diff changeset
976 <param name="standalone" value="Data Directory" />
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 17
diff changeset
977 <param name="uglyTestingHack" value="enabled" />
19
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
978 <output name="output" file="gencode/test-data_table.xml" lines_diff="6" />
18
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 17
diff changeset
979 </test>
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
980
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
981 <test>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
982 <param name="reference_genome|genome_type_select" value="history"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
983 <param name="reference_genome|genome" value="merlin.fa"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
984 <param name="gencode" value="11" />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
985 <param name="standalone" value="Data Directory" />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
986
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
987 <repeat name="track_groups">
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
988 <param name="category" value="External endpoints" />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
989 <repeat name="data_tracks">
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
990 <conditional name="data_format">
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
991 <param name="data_format_select" value="rest"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
992 <param name="url" value="http://example.org.external/rest_api/"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
993 <param name="label" value="Rest api"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
994 </conditional>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
995 </repeat>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
996 <repeat name="data_tracks">
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
997 <conditional name="data_format">
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
998 <param name="data_format_select" value="sparql"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
999 <param name="url" value="http://example.org.external/sparql/"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1000 <param name="label" value="Sparql endpoint"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1001 <param name="query" value=" DEFINE sql:select-option 'order'
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1002 prefix rdf: &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#&gt;
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1003 select ?start,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1004 ?end,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1005 IF( ?faldo_type = faldo:ForwardStrandPosition,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1006 1,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1007 IF( ?faldo_type = faldo:ReverseStrandPosition,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1008 -1,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1009 0
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1010 )
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1011 ) as ?strand,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1012 str(?obj_type_name) as ?type,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1013 str(?label) as ?name,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1014 str(?obj_name) as ?description,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1015 ?obj as ?uniqueID,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1016 ?parent as ?parentUniqueID
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1017 where {
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1018 values ?faldo_type { faldo:ForwardStrandPosition faldo:ReverseStrandPosition faldo:BothStrandsPosition }
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1019 }"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1020 </conditional>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1021 </repeat>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1022 </repeat>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents: 23
diff changeset
1023
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents: 23
diff changeset
1024 <param name="uglyTestingHack" value="enabled" />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
1025 <output name="output" file="endpoints/test.xml" lines_diff="48"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
1026 </test>
3
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parents: 1
diff changeset
1027 </tests>
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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parents:
diff changeset
1028 <help><![CDATA[
3
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parents: 1
diff changeset
1029 JBrowse-in-Galaxy
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1030 =================
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1031
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1032 JBrowse-in-Galaxy offers a highly configurable, workflow-compatible
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1033 alternative to Trackster.
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1034
17
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parents: 16
diff changeset
1035 Overview
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parents: 16
diff changeset
1036 --------
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parents: 16
diff changeset
1037
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parents: 16
diff changeset
1038 JBrowse is a fast, embeddable genome browser built completely with
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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parents: 16
diff changeset
1039 JavaScript and HTML5.
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1040
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1041 The JBrowse-in-Galaxy (JiG) tool was written to help build complex
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1042 JBrowse installations straight from Galaxy, taking advantage of the
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1043 latest Galaxy features such as dataset collections, sections, and colour
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1044 pickers. It allows you to build up a JBrowse instance without worrying
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1045 about how to run the command line tools to format your data, and which
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1046 options need to be supplied and where. Additionally it comes with many
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1047 javascript functions to handle colouring of features which would be
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1048 nearly impossible to write without the assistance of this tool.
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1049
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents: 23
diff changeset
1050 The JBrowse-in-Galaxy tool is maintained by `the Galaxy IUC
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents: 23
diff changeset
1051 <https://github.com/galaxyproject/tools-iuc/issues>`__, who you can help you
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1052 with missing features or bugs in the tool.
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1053
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1054 Options
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1055 -------
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1056
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1057 The first option you encounter is the **Fasta Sequence(s)**. This option
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1058 now accepts multiple fasta files, allowing you to build JBrowse
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1059 instances that contain data for multiple genomes or chrosomomes
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1060 (generally known as "landmark features" in gff3 terminology.) Up to 30
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1061 will be shown from the dropdown selector within JBrowse, this is a known
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1062 issue.
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1063
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
1064 **Standalone Instances** enable you to have either a complete JBrowse instance
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents: 23
diff changeset
1065 in a dataset, or just the data directory without JBrowse (e.g. for Apollo).
3
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1066 Currently Galaxy copies the entire JBrowse directory in order to have a
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1067 complete, downloadable file that contains a ready-to-go JBrowse
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1068 instance. This is obviously an anti-feature because users don't want a
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents: 23
diff changeset
1069 complete copy of JBrowse (12Mb) that's duplicated for every JBrowse
3
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1070 dataset in their history, and admins don't want useless copies of
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1071 JBrowse on disk. Unfortunately we have not come up with the perfect
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1072 solution just yet, but we're working on it! In the meantime, users have
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1073 been given the option to produce just the ``data/`` directory. For those
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1074 unfamiliar with JBrowse, the ``data/`` directory contains processed data
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1075 files, but no way to view them. This feature is additionally implemented
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1076 for upcoming `Apollo <https://github.com/gmod/apollo>`__ integration.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1077
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1078 **Genetic Code** is a new feature in v0.4 of JiG / v1.12.0 of JBrowse,
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1079 which allows users to specify a non standard genetic code, and have
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents: 23
diff changeset
1080 JBrowse highlight the correct start and stop codons.
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1081
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1082 **Track Groups** represent a set of tracks in a single category. These
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1083 can be used to let your users understand relationships between large
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1084 groups of tracks.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1085
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1086 .. image:: sections.png
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1087
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1088 Annotation Tracks
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1089 -----------------
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1090
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1091 Within Track Groups, you have one or more **Annotation Tracks**. Each
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1092 Annotation Track is a groups of datasets which have similar styling.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1093 This allows you to rapidly build up JBrowse instances without having to
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1094 configure tracks individually. A massive improvement over previous
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1095 versions. For example, if you have five different GFF3 files from
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1096 various gene callers that you wish to display, you can take advantage of
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1097 this feature to style all of them similarly.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1098
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1099 There are a few different types of tracks supported, each with their own
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1100 set of options:
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1101
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1102 GFF3/BED/GBK
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1103 ~~~~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1104
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1105 These are your standard feature tracks. They usually highlight genes,
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1106 mRNAs and other features of interest along a genomic region. The
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1107 underlying tool and this help documentation focus primarily on GFF3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1108 data, and have not been tested extensively with other formats. Automatic
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1109 min/max detection will likely fail under BED and GBK datasets.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1110
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1111 The data may be of a subclass we call **match/match part** data. This
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1112 consists of top level ``match`` features, with a child ``match_part``
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1113 feature, and is often used in displaying alignments. (See "Alignments"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1114 section on the `GFF3
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
1115 specification <https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md>`__ for more
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1116 information). If the data is match/match part, you will need to specify
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1117 the top level match feature name, as it can be one of a few different SO
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1118 terms, and JiG does not yet have the ability to understand SO terms.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1119
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1120 Next up is the **Styling Options** section, which lets you control a few
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1121 properties on how the track is styled. Most of these you will not need
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1122 to configure and can safely leave on defaults. Occasionally you will
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1123 want to change what information is shown in the end product.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1124
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1125 .. image:: styling.png
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1126
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1127 In the above image you can see some black text, and some blue text. The
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1128 source of the black text is configured with the **style.label** option,
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1129 and the source of the blue text is configured with the
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1130 **style.description** option.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1131
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1132 Feature Score Scaling & Colouring Options
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1133 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1134
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1135 First, you need to choose between ignoring the score attribute of GFF3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1136 files, or using it. If you choose to ignore it, all features will be
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1137 coloured with a solid colour. If you choose to use it, features will
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1138 have slightly different colours based on their scores.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1139
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1140 .. image:: opacity.png
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1141
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1142 If you choose **Ignore score**, you may choose between automatically
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1143 choosing a colour, or manually specifying one. The automatically chosen
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1144 colours vary along a brewer palette and generally look quite nice with
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1145 no human intervention required. The manual colour choice is somewhat
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1146 self explanatory. Clicking on the small coloured square will bring up a
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1147 colour palette.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1148
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1149 If you choose **Base on score**, you're faced with a dizzying array of
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1150 options. First is the function to map the colour choices to colour
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1151 values. JiG comes with a few functions built in such as linear scaling,
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1152 logarithmic scaling, and blast scaling.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1153
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1154 The **linear scaling** method says "take these values, and they map
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1155 directly to a range of output values". **Logarithmic scaling** says
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1156 "please take the log of the score before mapping", and **Blast scaling**
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1157 is further specialised to handle blast data more nicely. These are
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1158 convenience functions to help transform the wide array of possible
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1159 values in the GFF3 score attribute to more meaningful numbers. If you
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1160 need more comprehensive score scaling, it is recommended that you
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1161 pre-process your GFF3 files somehow.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1162
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1163 Once you've selected a scaling method, you can choose to manually
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1164 specify the minimum and maximum expected values, or you can let JiG
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1165 determine them for you automatically.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1166
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1167 Finally, opacity is the only mapping we currently provide. Future
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1168 iterations will attempt to improve upon this and provide more colour
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1169 scales. The Opacity option maps the highest scoring features to full
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1170 opacity, and everything else to lower ones.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1171
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1172 BAM Pileups
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1173 ~~~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1174
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1175 We support BAM files and can automatically generate SNP tracks based on
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1176 that bam data.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1177
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1178 .. image:: bam.png
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1179
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1180 This is *strongly discouraged* for high coverage density datasets.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1181 Unfortunately there are no other configuration options exposed for bam
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1182 files.
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1183
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1184 BlastXML
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1185 ~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1186
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1187 .. image:: blast.png
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1188
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1189 JiG now supports both blastn and blastp datasets. JiG internally uses a
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1190 blastXML to gapped GFF3 tool to convert your blastxml datasets into a
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1191 format amenable to visualization in JBrowse. This tool is also
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1192 available separately from the IUC on the toolshed.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1193
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1194 **Minimum Gap Size** reflects how long a gap must be before it becomes a
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1195 real gap in the processed gff3 file. In the picture above, various sizes
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1196 of gaps can be seen. If the minimum gap size was set much higher, say
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1197 100nt, many of the smaller gaps would disappear, and the features on
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1198 both sides would be merged into one, longer feature. This setting is
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1199 inversely proportional to runtime and output file size. *Do not set this
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1200 to a low value for large datasets*. By setting this number lower, you
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1201 will have extremely large outputs and extremely long runtimes. The
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1202 default was configured based off of the author's experience, but the
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1203 author only works on small viruses. It is *strongly* recommended that
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1204 you filter your blast results before display, e.g. picking out the top
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1205 10 hits or so.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1206
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1207 **Protein blast search** option merely informs underlying tools that
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1208 they should adjust feature locations by 3x.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1209
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1210 Styling Options
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1211 ^^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1212
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1213 Please see the styling options for GFF3 datasets, they are identical.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1214
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1215 Feature Score Scaling & Coloring Options
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1216 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1217
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1218 Please see the score scaling and colouring options for GFF3 datasets,
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1219 they are identical. Remember to set your score scaling to "blast" method
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1220 if you do use it.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1221
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1222 Bigwig XY
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1223 ~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1224
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1225 .. image:: bigwig.png
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1226
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1227 **XYPlot**
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1228
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1229 BigWig tracks can be displayed as a "density" plot which is continuous
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1230 line which varies in colour, or as an "XYplot." XYplots are preferable
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1231 for users to visually identify specific features in a bigwig track,
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1232 however density tracks are more visually compact.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1233
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1234 **Variance Band** is an option available to XYPlots, and can be seen in
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1235 the third and fourth tracks in the above picture. This overlays a mean
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1236 line, and 1 and 2 standard deviation areas.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1237
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1238 **Track Scaling** is different from colour scaling, instead it
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1239 configures how the track behaves inside of JBrowse. **Autoscaling
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1240 globally** means that JBrowse will determine the minimum and maximum for
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1241 the track, and fix the bounds of the viewport to that. E.g. if your
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1242 track ranges from 1-1000, and the region you're currently zoomed to only
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1243 goes from 0-50, then the viewport range will still show 1-1000. This is
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1244 good for global genomic context. However you may wish to consider
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1245 **autoscaling locally** instead. In the example of a region which varies
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1246 from 0-50, autoscaling locally would cause the individual track's
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1247 viewport to re-adjust and show just the 0-50 region. If neither of these
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1248 options are palatable, you may manually hardcode the minimum and
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1249 maximums for the track to scale to.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1250
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1251 Colour Options
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1252 ^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1253
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1254 BigWig tracks have two colours in JBrowse, a positive and a negative
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1255 colour.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1256
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1257 As always you may manually choose a colour, or let JiG choose for you.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1258
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1259 One of the more interesting options is the **Bicolor pivot**. This
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1260 option allows you to control the point at which JBrowse switches from
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1261 the positive colour to the negative. In the above graphic, you can see
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1262 this has been configured to "mean" for the first two (orange and blue)
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1263 tracks.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1264
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1265 VCFs/SNPs
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1266 ~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1267
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1268 These tracks do not support any special configuration.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1269
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1270 Known Issues
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1271 ------------
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1272
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1273 - More than 30 landmark features cannot be listed in the manual
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1274 selector.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1275 - Non GFF3 likely has issue with automatically determined min/max
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1276 scores. Manually specify minimum and maximum score attributes, or do
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1277 not use varied colours based on scores to avoid this issue.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1278
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
1279 @ATTRIBUTION@
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
1280 ]]></help>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
1281 <expand macro="citations"/>
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
1282 </tool>