Mercurial > repos > iuc > jbrowse

annotate jbrowse.xml @ 59:e29039f307c4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
author iuc
date Mon, 15 Apr 2019 10:30:46 -0400
parents c8772f1f6a38
children 21585b031a4d
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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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21
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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 #if str($track.data_format.data_format_select) in ["gene_calls", "pileup", "blast", "wiggle", "vcf"]:
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214 <custom_config>
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215 #for $custom_option in $track.data_format.jb_custom_config.option:
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216 <${custom_option.opt_key}>
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217 <${custom_option.opt_value.val_type}>${$custom_option.opt_value.val}</${custom_option.opt_value.val_type}>
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218 </${custom_option.opt_key}>
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219 #end for
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220 </custom_config>
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221 #end if
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222
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223 #if str($track.data_format.data_format_select) == "wiggle":
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224 <wiggle>
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225 <type>${track.data_format.xyplot}</type>
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226 <variance_band>${track.data_format.var_band}</variance_band>
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227 #if str($track.data_format.scaling.scale_select) == "auto_local":
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228 <autoscale>local</autoscale>
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229 #else if str($track.data_format.scaling.scale_select) == "auto_global":
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230 <autoscale>global</autoscale>
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231 #else:
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232 <min>${track.data_format.scaling.minimum}</min>
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233 <max>${track.data_format.scaling.maximum}</max>
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234 #end if
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235 <scale>${track.data_format.scale_select2}</scale>
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236
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237 ## Wiggle tracks need special color config
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238 #if str($track.data_format.jbcolor.color.color_select) != "automatic":
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239 <color_pos>${track.data_format.jbcolor.color.style_pos_color}</color_pos>
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240 <color_neg>${track.data_format.jbcolor.color.style_neg_color}</color_neg>
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241 #else:
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242 <color_pos>__auto__</color_pos>
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243 <color_neg>__auto__</color_neg>
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244 #end if
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245
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246 ## Bicolor pivot config
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247 #if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "zero":
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248 <bicolor_pivot>zero</bicolor_pivot>
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249 #else if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "mean":
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250 <bicolor_pivot>mean</bicolor_pivot>
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251 #else:
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252 <bicolor_pivot>${track.data_format.jbcolor.bicolor_pivot.pivot_point}</bicolor_pivot>
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253 #end if
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254 <multibigwig>${track.data_format.MultiBigWig}</multibigwig>
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255 </wiggle>
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256 #else if str($track.data_format.data_format_select) == "pileup":
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257 <pileup>
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258 <auto_snp>${track.data_format.auto_snp}</auto_snp>
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259 <bam_indices>
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260 #for $dataset in $track.data_format.annotation:
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261 <bam_index>${dataset.metadata.bam_index}</bam_index>
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262 #end for
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263 </bam_indices>
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264 <chunkSizeLimit>${track.data_format.chunkSizeLimit}</chunkSizeLimit>
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265 </pileup>
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266 #else if str($track.data_format.data_format_select) == "blast":
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267 <blast>
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268 #if str($track.data_format.blast_parent) != "":
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269 <parent>${track.data_format.blast_parent}</parent>
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270 #end if
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271 <protein>${track.data_format.is_protein}</protein>
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272 <min_gap>${track.data_format.min_gap}</min_gap>
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273 <index>${track.data_format.index}</index>
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274 </blast>
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275 #else if str($track.data_format.data_format_select) == "gene_calls":
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276 <gff>
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277 <trackType>${track.data_format.track_config.track_class}</trackType>
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278 #if $track.data_format.track_config.track_class in ['JBrowse/View/Track/CanvasFeatures', 'NeatCanvasFeatures/View/Track/NeatFeatures']:
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279 #if str($track.data_format.track_config.canvas_options.transcriptType) != "":
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280 <transcriptType>${track.data_format.track_config.canvas_options.transcriptType}</transcriptType>
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281 #end if
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282 #if str($track.data_format.track_config.canvas_options.subParts) != "":
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283 <subParts>${track.data_format.track_config.canvas_options.subParts}</subParts>
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284 #end if
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285 #if str($track.data_format.track_config.canvas_options.impliedUTRs) != "false":
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286 <impliedUTRs>${track.data_format.track_config.canvas_options.impliedUTRs}</impliedUTRs>
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287 #end if
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288 #else if $track.data_format.track_config.track_class in ['JBrowse/View/Track/HTMLFeatures', 'NeatHTMLFeatures/View/Track/NeatFeatures']:
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289 #if str($track.data_format.track_config.html_options.topLevelFeatures) != "":
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290 <topLevelFeatures>${track.data_format.track_config.html_options.topLevelFeatures}</topLevelFeatures>
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291 #end if
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292 #end if
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293 #if $track.data_format.match_part.match_part_select:
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294 <match>${track.data_format.match_part.name}</match>
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295 #end if
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296 <index>${track.data_format.index}</index>
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297 </gff>
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298 #else if str($track.data_format.data_format_select) == "rest":
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299 <label>${track.data_format.label}</label>
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300 <rest>
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301 <url>${track.data_format.url}</url>
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302 </rest>
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303 #else if str($track.data_format.data_format_select) == "sparql":
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304 <label>${track.data_format.label}</label>
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305 <sparql>
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306 <url>${track.data_format.url}</url>
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307 <query>${track.data_format.query}</query>
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308 </sparql>
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309 #end if
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310 </options>
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311 </track>
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312 #end for
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313 #end for
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314 </tracks>
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315 ## Disable plugins until https://github.com/GMOD/jbrowse/issues/1288 is fixed
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316 ## <plugins
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317 ## ComboTrackSelector="${plugins.ComboTrackSelector}"
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318 ## Bookmarks="${plugins.Bookmarks}"
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319 ## GCContent="${plugins.GCContent}"
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320 ## BlastView="${plugins.BlastView}"
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321 ## theme="${plugins.theme}"
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322 ## />
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323 <plugins
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324 ComboTrackSelector="${plugins.ComboTrackSelector}"
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325 Bookmarks=""
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326 GCContent="${plugins.GCContent}"
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327 BlastView="${plugins.BlastView}"
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328 theme=""
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329 />
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diff changeset
330 </root>
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331 ]]></configfile>
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332 </configfiles>
0
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333 <inputs>
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334 <conditional name="reference_genome">
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335 <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select">
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336 <option selected="True" value="indexed">Use a built-in genome</option>
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337 <option value="history">Use a genome from history</option>
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338 </param>
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339 <when value="indexed">
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340 <param
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341 help="If your genome of interest is not listed, contact the Galaxy team"
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342 label="Select a reference genome"
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343 name="genomes"
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344 type="select"
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345 >
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346 <options from_data_table="all_fasta">
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347 <filter column="2" type="sort_by" />
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348 <validator message="No genomes are available for the selected input dataset" type="no_options" />
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349 </options>
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350 </param>
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351 </when>
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352 <when value="history">
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353 <param
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354 format="fasta"
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355 label="Select the reference genome"
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356 name="genome"
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357 type="data" />
30
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358 </when>
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359 </conditional>
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360
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361 <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"/>
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362
50
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363 <param name="gencode" type="select" label="Genetic Code">
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364 <option value="1">1. The Standard Code</option>
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365 <option value="2">2. The Vertebrate Mitochondrial Code</option>
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366 <option value="3">3. The Yeast Mitochondrial Code</option>
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367 <option value="4">4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
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368 <option value="5">5. The Invertebrate Mitochondrial Code</option>
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369 <option value="6">6. The Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
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370 <option value="9">9. The Echinoderm and Flatworm Mitochondrial Code</option>
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371 <option value="10">10. The Euplotid Nuclear Code</option>
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372 <option value="11">11. The Bacterial, Archaeal and Plant Plastid Code</option>
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373 <option value="12">12. The Alternative Yeast Nuclear Code</option>
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374 <option value="13">13. The Ascidian Mitochondrial Code</option>
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375 <option value="14">14. The Alternative Flatworm Mitochondrial Code</option>
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376 <option value="16">16. Chlorophycean Mitochondrial Code</option>
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377 <option value="21">21. Trematode Mitochondrial Code</option>
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378 <option value="22">22. Scenedesmus obliquus Mitochondrial Code</option>
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379 <option value="23">23. Thraustochytrium Mitochondrial Code</option>
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380 <option value="24">24. Pterobranchia Mitochondrial Code</option>
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381 <option value="25">25. Candidate Division SR1 and Gracilibacteria Code</option>
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382 </param>
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383
42
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384 <conditional name="action">
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385 <param type="select" label="JBrowse-in-Galaxy Action" name="action_select">
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386 <option value="create">New JBrowse Instance</option>
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387 <option value="update">Update exising JBrowse Instance</option>
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388 </param>
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389 <when value="create" />
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390 <when value="update">
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391 <param name="update_jbrowse" type="data" format="html" label="Previous JBrowse Instance" />
42
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392 </when>
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393 </conditional>
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394
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395 <repeat name="track_groups" title="Track Group">
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396 <param label="Track Category"
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397 name="category"
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398 type="text"
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399 value="Default"
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400 help="Organise your tracks into Categories for a nicer end-user experience. You can use #date# and it will be replaced with the current date in 'yyyy-mm-dd' format, which is very useful for repeatedly updating a JBrowse instance when member databases / underlying tool versions are updated." optional="False"/>
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401 <repeat name="data_tracks" title="Annotation Track">
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402 <conditional name="data_format" label="Track Options">
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403 <param type="select" label="Track Type" name="data_format_select">
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404 <option value="gene_calls">GFF/GFF3/BED/GBK Features</option>
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405 <option value="pileup">BAM Pileups</option>
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406 <option value="blast">Blast XML</option>
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407 <option value="wiggle">BigWig XY</option>
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408 <option value="vcf">VCF SNPs</option>
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409 <option value="rest">REST Endpoint</option>
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410 <option value="sparql">SPARQL</option>
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411 </param>
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412 <when value="blast">
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413 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" />
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414
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415 <param label="Features used in Blast Search"
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416 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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417 format="gff3"
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418 name="blast_parent"
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419 optional="true"
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420 type="data"/>
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421
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422 <param label="Minimum Gap Size"
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423 help="before a new match_part feature is created"
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424 name="min_gap"
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425 type="integer"
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426 value="10"
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427 min="2" />
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428 <param label="Is this a protein blast search?"
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429 type="boolean"
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430 name="is_protein"
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431 truevalue="true"
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432 falsevalue="false" />
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433
42
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434 <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" />
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435
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436 <expand macro="track_styling"
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437 classname="feature"
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438 label="description"
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439 description="Hit_titles"
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440 height="600px"/>
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441 <expand macro="color_selection"
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442 token_scaling_lin_select="false"
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443 token_scaling_log_select="true" />
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444 <expand macro="track_custom_config" />
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445 <expand macro="track_menu" />
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446 <expand macro="track_display" />
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447 </when>
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448 <when value="vcf">
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449 <expand macro="input_conditional" label="SNP Track Data" format="vcf" />
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450 <expand macro="track_custom_config" />
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451 <expand macro="track_display" />
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452 </when>
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453 <when value="gene_calls">
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454 <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" />
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455 <conditional name="match_part" label="match/match_part data">
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456 <param label="This is match/match_part data"
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457 type="boolean"
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458 name="match_part_select"
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459 truevalue="true"
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460 falsevalue="false" />
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461 <when value="true">
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462 <param label="Match Part Feature Type"
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463 name="name"
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464 type="text"
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465 value="match"
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466 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)."
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467 optional="True"/>
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468 </when>
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parents: 15
diff changeset
469 <when value="false" />
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parents: 15
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470 </conditional>
42
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iuc
parents: 40
diff changeset
471
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
472 <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" />
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
473
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
474 <conditional name="track_config">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
475 <param type="select" label="JBrowse Track Type [Advanced]" name="track_class">
54
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iuc
parents: 53
diff changeset
476 <option value="NeatHTMLFeatures/View/Track/NeatFeatures" selected="true">Neat HTML Features</option>
b4d512ee2d14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 75f6e483debb4c0d388bf4a54df81ee89af598d5
iuc
parents: 53
diff changeset
477 <option value="NeatCanvasFeatures/View/Track/NeatFeatures">Neat Canvas Features</option>
42
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iuc
parents: 40
diff changeset
478 <option value="JBrowse/View/Track/HTMLFeatures">HTML Features</option>
54
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iuc
parents: 53
diff changeset
479 <option value="JBrowse/View/Track/CanvasFeatures">Canvas Features</option>
53
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iuc
parents: 51
diff changeset
480 <option value="BlastView/View/Track/CanvasFeatures">Blast Features</option><!-- Disable plugins until https://github.com/GMOD/jbrowse/issues/1288 is fixed -->
42
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parents: 40
diff changeset
481 </param>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
482 <when value="JBrowse/View/Track/CanvasFeatures">
55
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iuc
parents: 54
diff changeset
483 <expand macro="canvas_options" />
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
484 </when>
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
485 <when value="JBrowse/View/Track/HTMLFeatures">
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
486 <expand macro="html_options" />
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
487 </when>
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
488 <when value="BlastView/View/Track/CanvasFeatures" />
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
489 <when value="NeatHTMLFeatures/View/Track/NeatFeatures">
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
490 <expand macro="html_options" />
54
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iuc
parents: 53
diff changeset
491 </when>
55
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
492 <when value="NeatCanvasFeatures/View/Track/NeatFeatures">
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
493 <expand macro="canvas_options" />
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
494 </when>
42
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
495 </conditional>
55
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
496 <expand macro="track_styling"
58
c8772f1f6a38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 74554507efb46fb40ce6e12f0b73425e52ec0977
iuc
parents: 57
diff changeset
497 classname="feature"
55
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iuc
parents: 54
diff changeset
498 label="product,name,id"
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
499 description="note,description"
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
500 height="10px"/>
16
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
501 <expand macro="color_selection" />
59
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iuc
parents: 58
diff changeset
502 <expand macro="track_custom_config" />
42
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iuc
parents: 40
diff changeset
503 <expand macro="track_menu" />
30
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
504 <expand macro="track_display" />
13
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iuc
parents: 12
diff changeset
505 </when>
67fb31daef0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 399061eca3a2956704522974446601755503c96d-dirty
iuc
parents: 12
diff changeset
506 <when value="pileup">
16
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iuc
parents: 15
diff changeset
507 <expand macro="input_conditional" label="BAM Track Data" format="bam" />
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
508 <param label="Autogenerate SNP Track"
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
509 help="Not recommended for deep coverage BAM files"
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
510 type="boolean"
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
511 name="auto_snp"
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
512 truevalue="true"
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iuc
parents: 15
diff changeset
513 falsevalue="false" />
53
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
514 <param label="Maximum size of BAM chunks"
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
515 name="chunkSizeLimit"
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
516 type="integer"
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
517 help="Maximum size in bytes of BAM chunks that the browser will try to deal with. When this is exceeded, most tracks will display 'Too much data' message."
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
518 value="5000000" />
59
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
519 <expand macro="track_custom_config" />
30
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iuc
parents: 29
diff changeset
520 <expand macro="track_display" />
13
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iuc
parents: 12
diff changeset
521 </when>
67fb31daef0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 399061eca3a2956704522974446601755503c96d-dirty
iuc
parents: 12
diff changeset
522 <when value="wiggle">
16
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
523 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" />
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
524
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
525 <param label="Use XYPlot"
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
526 help="instead of continuous colored band"
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
527 type="boolean"
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
528 name="xyplot"
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
529 truevalue="JBrowse/View/Track/Wiggle/XYPlot"
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
530 falsevalue="JBrowse/View/Track/Wiggle/Density" />
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
531 <param label="Show variance band"
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
532 help="Only for XYPlots"
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
533 type="boolean"
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
534 name="var_band"
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
535 truevalue="true"
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
536 falsevalue="false" />
13
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iuc
parents: 12
diff changeset
537
45
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iuc
parents: 44
diff changeset
538 <conditional name="scaling" label="Scaling">
13
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iuc
parents: 12
diff changeset
539 <param type="select" label="Track Scaling" name="scale_select">
51
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iuc
parents: 50
diff changeset
540 <option value="auto_local" selected="true">Autoscale (local)</option>
abb1a30d7a5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit cf2c8f3039021b645ac45980a02ffe1f69a3f958
iuc
parents: 50
diff changeset
541 <option value="auto_global">Autoscale (global)</option>
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iuc
parents: 15
diff changeset
542 <option value="fixed">Specify Min/Max</option>
13
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iuc
parents: 12
diff changeset
543 </param>
67fb31daef0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 399061eca3a2956704522974446601755503c96d-dirty
iuc
parents: 12
diff changeset
544 <when value="auto_local"></when>
67fb31daef0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 399061eca3a2956704522974446601755503c96d-dirty
iuc
parents: 12
diff changeset
545 <when value="auto_global"></when>
67fb31daef0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 399061eca3a2956704522974446601755503c96d-dirty
iuc
parents: 12
diff changeset
546 <when value="fixed">
67fb31daef0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 399061eca3a2956704522974446601755503c96d-dirty
iuc
parents: 12
diff changeset
547 <param label="Track minimum" name="minimum"
67fb31daef0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 399061eca3a2956704522974446601755503c96d-dirty
iuc
parents: 12
diff changeset
548 type="integer" value="0" />
67fb31daef0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 399061eca3a2956704522974446601755503c96d-dirty
iuc
parents: 12
diff changeset
549 <param label="Track maximum" name="maximum"
67fb31daef0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 399061eca3a2956704522974446601755503c96d-dirty
iuc
parents: 12
diff changeset
550 type="integer" value="100" />
67fb31daef0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 399061eca3a2956704522974446601755503c96d-dirty
iuc
parents: 12
diff changeset
551 </when>
67fb31daef0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 399061eca3a2956704522974446601755503c96d-dirty
iuc
parents: 12
diff changeset
552 </conditional>
45
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iuc
parents: 44
diff changeset
553 <param type="select" label="Visual Scaling" name="scale_select2">
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
554 <option value="linear" selected="true">Linear</option>
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
555 <option value="log">Logarithmic (Dynamically Calculated)</option>
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
556 </param>
53
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
557
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
558 <param label="Use MultiBigWig Plugin" name="MultiBigWig" truevalue="True" falsevalue="" type="boolean"
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
559 help="MultiBigWig is a plugin to group multiple big-wig tracks in a more aesthetically pleasing format and to show data in a higher density display." />
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
560
16
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
561 <expand macro="color_selection_minmax" />
59
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
562 <expand macro="track_custom_config" />
30
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iuc
parents: 29
diff changeset
563 <expand macro="track_display" />
13
67fb31daef0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 399061eca3a2956704522974446601755503c96d-dirty
iuc
parents: 12
diff changeset
564 </when>
45
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
565 <when value="rest">
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
566 <param type="text" label="REST Endpoint" name="url" />
53
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
567 <param type="text" label="Track Label" name="label" value="REST Genes" />
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
568 <expand macro="track_styling"
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
569 classname="feature"
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
570 label="description"
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents: 51
diff changeset
571 description="Hit_titles"
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
572 height="600px"/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
573 <expand macro="color_selection"
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
574 token_scaling_lin_select="false"
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
575 token_scaling_log_select="true" />
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
576 <expand macro="track_menu" />
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
577 <expand macro="track_display" />
45
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iuc
parents: 44
diff changeset
578 </when>
53
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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579
30
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parents: 29
diff changeset
580 <when value="sparql">
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
581 <param type="text" label="SPARQL Server URL" name="url" />
53
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
582 <param type="text" label="Track Label" name="label" value="SPARQL Genes" />
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
583 <param type="text" label="SPARQL Query" name="query" area="true">
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
584 <sanitizer>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
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585 <mapping initial="galaxy.util.mapped_chars">
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
586 <add source="&#10;" target=" " />
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
587 <add source="&gt;" target="__gt__" />
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
588 <add source="&lt;" target="__lt__" />
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
589 </mapping>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
590 <valid initial="default">
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
591 <add value="|" />
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
592 <add value="#" />
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
593 <add value="{"/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
594 <add value="}"/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
595 <add value="!"/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
596 <add value="?"/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
597 <add value="&amp;"/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
598 <add value="+"/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents: 51
diff changeset
599 <add value="="/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
600 <add value="'"/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
601 <add value='"'/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
602 </valid>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents: 51
diff changeset
603 </sanitizer>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
604 </param>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents: 51
diff changeset
605 <expand macro="track_styling"
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
606 classname="feature"
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
607 label="description"
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents: 51
diff changeset
608 description="Hit_titles"
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents: 51
diff changeset
609 height="600px"/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
610 <expand macro="color_selection"
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
611 token_scaling_lin_select="false"
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
612 token_scaling_log_select="true" />
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
613 <expand macro="track_menu" />
30
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iuc
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diff changeset
614 <expand macro="track_display" />
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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diff changeset
615 </when>
13
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diff changeset
616 </conditional>
0
c77c1d5baadb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
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diff changeset
617 </repeat>
16
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618 </repeat>
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diff changeset
619
30
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diff changeset
620 <expand macro="general_options" />
53
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
621 <!-- Disable plugins until https://github.com/GMOD/jbrowse/issues/1288 is fixed -->
45
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iuc
parents: 44
diff changeset
622 <section name="plugins" title="Plugins" expanded="false">
53
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
623
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
624 <param
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
625 label="BlastView" name="BlastView" truevalue="True" falsevalue="" type="boolean" checked="true"
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
626 help="A JBrowse plugin for viewing blast alignments. This plugin makes MANY assumptions about the format of your data, and may not work without those assumptions: 1) you use protein_match / match_part 2) your features have a Blast_qseq, Blast_mseq, and Blast_sseq attribute in their GFF3 representation." />
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
627
45
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diff changeset
628 <param
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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diff changeset
629 label="Combo Track Selector" name="ComboTrackSelector" truevalue="True" falsevalue="" type="boolean"
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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diff changeset
630 help="ComboTrackSelector is a plugin to allow the co-existence of the Hierarchical and Faceted Track selectors in JBrowse, built for/by the Arabidopsis Information Portal (Araport) project" />
53
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
631 <!-- No way to disable now that it's built in jbrowse conda package -->
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
632 <!--param
45
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diff changeset
633 label="Bookmarks" name="Bookmarks" truevalue="True" falsevalue="" type="boolean"
53
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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634 help="JBrowse plugin allowing users to manage a persistent list of bookmarks kept in localstorage" /-->
45
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
635
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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parents: 44
diff changeset
636 <param
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
637 label="GC Content" name="GCContent" truevalue="True" falsevalue="" type="boolean"
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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diff changeset
638 help="A JBrowse plugin for plotting GC Content and GC Skew. The plugin consists of a storeClass that automatically calculates the percentage of G/C bases in a region, a track type that derives from the Wiggle XY or density types, and a dialog box to adjust the sliding window size, window step size, and the calculation mode (content or skew)." />
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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diff changeset
639
53
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents: 51
diff changeset
640 <!--param type="select" label="JBrowse Theme" name="theme">
45
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parents: 44
diff changeset
641 <option value="" selected="True">Default</option>
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
642 <option value="Minimalist">Minimalist</option>
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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diff changeset
643 <option value="Dark">Dark</option>
53
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diff changeset
644 </param-->
45
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parents: 44
diff changeset
645 </section>
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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diff changeset
646
16
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diff changeset
647 <param type="hidden" name="uglyTestingHack" value="" />
0
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648 </inputs>
c77c1d5baadb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
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649 <outputs>
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diff changeset
650 <data format="html" name="output" label="JBrowse on $on_string - $standalone"/>
0
c77c1d5baadb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
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651 </outputs>
30
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parents: 29
diff changeset
652 <tests>
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
653 <test>
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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diff changeset
654 <!-- gencode -->
42
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parents: 40
diff changeset
655 <param name="reference_genome|genome_type_select" value="history"/>
53
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diff changeset
656 <param name="reference_genome|genome" value="merlin.fa"/>
30
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diff changeset
657 <param name="gencode" value="1" />
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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diff changeset
658 <param name="standalone" value="Data Directory" />
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
659 <param name="uglyTestingHack" value="enabled" />
59
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
660 <output name="output" file="gencode/test-1.xml" lines_diff="16"/>
30
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
661 </test>
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
662 <test>
42
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
663 <param name="reference_genome|genome_type_select" value="history"/>
53
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
664 <param name="reference_genome|genome" value="merlin.fa"/>
30
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
665 <param name="gencode" value="11" />
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
666 <param name="standalone" value="Data Directory" />
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
667 <param name="uglyTestingHack" value="enabled" />
59
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
668 <output name="output" file="gencode/test.xml" lines_diff="16"/>
30
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
669 </test>
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
670 <test>
42
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
671 <param name="reference_genome|genome_type_select" value="history"/>
53
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
672 <param name="reference_genome|genome" value="merlin.fa"/>
30
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
673 <param name="gencode" value="11" />
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
674 <param name="standalone" value="Data Directory" />
42
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
675 <repeat name="track_groups">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
676 <param name="category" value="Auto Coloured" />
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
677 <repeat name="data_tracks">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
678 <conditional name="data_format">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
679 <param name="data_format_select" value="gene_calls"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
680 <param name="annotation" value="gff3/A.gff,gff3/B.gff,gff3/C.gff,gff3/D.gff"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
681 <conditional name="match_part">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
682 <param name="match_part_select" value="false"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
683 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
684 <section name="jbcolor_scale">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
685 <conditional name="color_score">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
686 <param name="color_score_select" value="none"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
687 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
688 <conditional name="color">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
689 <param name="color_select" value="automatic"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
690 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
691 </section>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
692 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
693 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
694 </repeat>
30
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
695
42
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
696 <repeat name="track_groups">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
697 <param name="category" value="Ignore Scale" />
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
698 <repeat name="data_tracks">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
699 <conditional name="data_format">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
700 <param name="data_format_select" value="gene_calls"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
701 <param name="annotation" value="gff3/1.gff"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
702 <conditional name="match_part">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
703 <param name="match_part_select" value="false"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
704 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
705 <section name="jbcolor_scale">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
706 <conditional name="color_score">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
707 <param name="color_score_select" value="none"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
708 <conditional name="color">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
709 <param name="color_select" value="manual"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
710 <param name="style_color" value="#ff00ff"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
711 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
712 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
713 </section>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
714 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
715 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
716 </repeat>
30
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
717
42
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
718 <repeat name="track_groups">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
719 <param name="category" value="Scaled Colour" />
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
720 <repeat name="data_tracks">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
721 <conditional name="data_format">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
722 <param name="data_format_select" value="gene_calls"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
723 <param name="annotation" value="gff3/1.gff"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
724 <conditional name="match_part">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
725 <param name="match_part_select" value="false"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
726 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
727 <section name="jbcolor_scale">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
728 <conditional name="color_score">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
729 <param name="color_score_select" value="score"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
730 <param name="score_scaling" value="linear"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
731 <conditional name="score_scales">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
732 <param name="scale_select" value="automatic"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
733 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
734 <conditional name="color_scheme">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
735 <param name="score_scheme" value="opacity"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
736 <conditional name="color">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
737 <param name="color_select" value="automatic"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
738 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
739 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
740 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
741 </section>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
742 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
743 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
744 <repeat name="data_tracks">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
745 <conditional name="data_format">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
746 <param name="data_format_select" value="gene_calls"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
747 <param name="annotation" value="gff3/1.gff"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
748 <conditional name="match_part">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
749 <param name="match_part_select" value="false"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
750 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
751 <section name="jbcolor_scale">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
752 <conditional name="color_score">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
753 <param name="color_score_select" value="score"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
754 <param name="score_scaling" value="linear"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
755 <conditional name="score_scales">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
756 <param name="scale_select" value="automatic"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
757 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
758 <conditional name="color_scheme">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
759 <param name="score_scheme" value="opacity"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
760 <conditional name="color">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
761 <param name="color_select" value="manual"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
762 <param name="style_color" value="#0000ff"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
763 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
764 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
765 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
766 </section>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
767 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
768 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
769 <repeat name="data_tracks">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
770 <conditional name="data_format">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
771 <param name="data_format_select" value="gene_calls"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
772 <param name="annotation" value="gff3/1.gff"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
773 <conditional name="match_part">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
774 <param name="match_part_select" value="false"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
775 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
776 <section name="jbcolor_scale">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
777 <conditional name="color_score">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
778 <param name="color_score_select" value="score"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
779 <param name="score_scaling" value="linear"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
780 <conditional name="score_scales">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
781 <param name="scale_select" value="manual"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
782 <param name="minimum" value="0"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
783 <param name="maximum" value="1000"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
784 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
785 <conditional name="color_scheme">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
786 <param name="score_scheme" value="opacity"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
787 <conditional name="color">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
788 <param name="color_select" value="automatic"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
789 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
790 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
791 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
792 </section>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
793 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
794 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
795 <repeat name="data_tracks">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
796 <conditional name="data_format">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
797 <param name="data_format_select" value="gene_calls"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
798 <param name="annotation" value="gff3/1.gff"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
799 <conditional name="match_part">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
800 <param name="match_part_select" value="false"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
801 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
802 <section name="jbcolor_scale">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
803 <conditional name="color_score">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
804 <param name="color_score_select" value="score"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
805 <param name="score_scaling" value="linear"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
806 <conditional name="score_scales">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
807 <param name="scale_select" value="manual"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
808 <param name="minimum" value="0"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
809 <param name="maximum" value="1000"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
810 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
811 <conditional name="color_scheme">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
812 <param name="score_scheme" value="opacity"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
813 <conditional name="color">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
814 <param name="color_select" value="manual"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
815 <param name="style_color" value="#ff0000"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
816 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
817 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
818 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
819 </section>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
820 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
821 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
822 </repeat>
30
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
823
42
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
824 <repeat name="track_groups">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
825 <param name="category" value="Realistic" />
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
826 <repeat name="data_tracks">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
827 <conditional name="data_format">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
828 <param name="data_format_select" value="gene_calls"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
829 <param name="annotation" value="gff3/interpro.gff"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
830 <conditional name="match_part">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
831 <param name="match_part_select" value="false"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
832 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
833 <section name="jbcolor_scale">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
834 <conditional name="color_score">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
835 <param name="color_score_select" value="none"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
836 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
837 <conditional name="color">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
838 <param name="color_select" value="automatic"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
839 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
840 </section>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
841 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
842 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
843 <repeat name="data_tracks">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
844 <conditional name="data_format">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
845 <param name="data_format_select" value="gene_calls"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
846 <param name="annotation" value="gff3/2.gff"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
847 <conditional name="match_part">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
848 <param name="match_part_select" value="true"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
849 <param name="name" value="cDNA_match"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
850 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
851 <section name="jbcolor_scale">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
852 <conditional name="color_score">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
853 <param name="color_score_select" value="none"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
854 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
855 <conditional name="color">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
856 <param name="color_select" value="automatic"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
857 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
858 </section>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
859 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
860 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
861 </repeat>
30
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
862
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
863 <param name="uglyTestingHack" value="enabled" />
59
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
864 <output name="output" file="gff3/test.xml" lines_diff="170" />
30
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
865 </test>
42
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
866 <test>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
867 <param name="reference_genome|genome_type_select" value="history"/>
53
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
868 <param name="reference_genome|genome" value="merlin.fa"/>
42
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
869 <param name="gencode" value="11" />
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
870 <param name="standalone" value="Data Directory" />
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
871
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
872 <repeat name="track_groups">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
873 <param name="category" value="With menu or index" />
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
874 <repeat name="data_tracks">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
875 <conditional name="data_format">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
876 <param name="data_format_select" value="gene_calls"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
877 <param name="annotation" value="gff3/1.gff"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
878 <conditional name="match_part">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
879 <param name="match_part_select" value="false"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
880 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
881 <section name="jbcolor_scale">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
882 <conditional name="color_score">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
883 <param name="color_score_select" value="none"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
884 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
885 <conditional name="color">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
886 <param name="color_select" value="automatic"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
887 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
888 </section>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
889 <section name="jbmenu">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
890 <repeat name="track_menu">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
891 <param name="menu_action" value="iframeDialog"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
892 <param name="menu_label" value="Some menu item"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
893 <param name="menu_title" value="Frame title"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
894 <param name="menu_url" value="https://example.com/#!/?id={name}&amp;q={type}&amp;z=&quot;{end}&quot;"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
895 <param name="menu_icon" value="dijitIconNewTask"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
896 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
897 <repeat name="track_menu">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
898 <param name="menu_action" value="newWindow"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
899 <param name="menu_label" value="Another menu item"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
900 <param name="menu_title" value="Frame title 2"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
901 <param name="menu_url" value="https://example.com/#!/?id={name}&amp;q={type}&amp;z=&quot;{end}&quot;"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
902 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
903 </section>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
904 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
905 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
906 <repeat name="data_tracks">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
907 <conditional name="data_format">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
908 <param name="data_format_select" value="gene_calls"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
909 <param name="annotation" value="gff3/1.gff"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
910 <param name="index" value="true"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
911 <conditional name="match_part">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
912 <param name="match_part_select" value="false"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
913 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
914 <section name="jbcolor_scale">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
915 <conditional name="color_score">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
916 <param name="color_score_select" value="none"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
917 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
918 <conditional name="color">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
919 <param name="color_select" value="automatic"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
920 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
921 </section>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
922 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
923 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
924 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
925
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
926 <param name="uglyTestingHack" value="enabled" />
59
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
927 <output name="output" file="menus/test.xml" lines_diff="44"/>
42
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
928 </test>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
929 <test>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
930 <param name="reference_genome|genome_type_select" value="history"/>
53
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
931 <param name="reference_genome|genome" value="merlin.fa"/>
42
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
932 <param name="gencode" value="11" />
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
933 <param name="standalone" value="Data Directory" />
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
934
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
935 <repeat name="track_groups">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
936 <param name="category" value="With canvas config" />
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
937 <repeat name="data_tracks">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
938 <conditional name="data_format">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
939 <param name="data_format_select" value="gene_calls"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
940 <param name="annotation" value="gff3/1.gff"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
941 <conditional name="match_part">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
942 <param name="match_part_select" value="false"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
943 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
944 <conditional name="track_config">
59
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
945 <param name="track_class" value="JBrowse/View/Track/CanvasFeatures"/>
42
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
946 <section name="canvas_options">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
947 <param name="transcriptType" value="transcript"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
948 <param name="subParts" value="exon"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
949 <param name="impliedUTRs" value="true"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
950 </section>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
951 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
952 <section name="jbcolor_scale">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
953 <conditional name="color_score">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
954 <param name="color_score_select" value="none"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
955 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
956 <conditional name="color">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
957 <param name="color_select" value="automatic"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
958 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
959 </section>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
960 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
961 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
962 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
963
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
964 <param name="uglyTestingHack" value="enabled" />
59
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
965 <output name="output" file="track_config/test.xml" lines_diff="30"/>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
966 </test>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
967 <test>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
968 <param name="reference_genome|genome_type_select" value="history"/>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
969 <param name="reference_genome|genome" value="merlin.fa"/>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
970 <param name="gencode" value="11" />
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
971 <param name="standalone" value="Data Directory" />
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
972
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
973 <repeat name="track_groups">
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
974 <param name="category" value="With custom track config" />
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
975 <repeat name="data_tracks">
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
976 <conditional name="data_format">
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
977 <param name="data_format_select" value="gene_calls"/>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
978 <param name="annotation" value="gff3/1.gff"/>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
979 <conditional name="match_part">
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
980 <param name="match_part_select" value="false"/>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
981 </conditional>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
982 <section name="jb_custom_config">
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
983 <repeat name="option">
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
984 <param name="opt_key" value="displayMode"/>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
985 <conditional name="opt_value">
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
986 <param name="val_type" value="text"/>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
987 <param name="val" value="collapsed"/>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
988 </conditional>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
989 </repeat>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
990 <repeat name="option">
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
991 <param name="opt_key" value="histograms.height"/>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
992 <conditional name="opt_value">
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
993 <param name="val_type" value="integer"/>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
994 <param name="val" value="150"/>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
995 </conditional>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
996 </repeat>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
997 <repeat name="option">
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
998 <param name="opt_key" value="maxFeatureScreenDensity"/>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
999 <conditional name="opt_value">
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1000 <param name="val_type" value="float"/>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1001 <param name="val" value="0.1"/>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1002 </conditional>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1003 </repeat>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1004 <repeat name="option">
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1005 <param name="opt_key" value="style.strandArrow"/>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1006 <conditional name="opt_value">
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1007 <param name="val_type" value="boolean"/>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1008 <param name="val" value="false"/>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1009 </conditional>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1010 </repeat>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1011 </section>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1012 </conditional>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1013 </repeat>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1014 </repeat>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1015
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1016 <param name="uglyTestingHack" value="enabled" />
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1017 <output name="output" file="custom_config/test.xml" lines_diff="30"/>
42
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iuc
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diff changeset
1018 </test>
46
f90c22c8fa7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 45
diff changeset
1019 <test>
47
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iuc
parents: 46
diff changeset
1020 <param name="reference_genome|genome_type_select" value="history"/>
53
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iuc
parents: 51
diff changeset
1021 <param name="reference_genome|genome" value="merlin.fa"/>
47
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iuc
parents: 46
diff changeset
1022 <param name="gencode" value="11" />
6b91a500c96d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 46
diff changeset
1023 <param name="standalone" value="Data Directory" />
6b91a500c96d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 46
diff changeset
1024
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iuc
parents: 46
diff changeset
1025 <repeat name="track_groups">
6b91a500c96d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 46
diff changeset
1026 <param name="category" value="Auto Coloured" />
6b91a500c96d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 46
diff changeset
1027 <repeat name="data_tracks">
6b91a500c96d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 46
diff changeset
1028 <conditional name="data_format">
6b91a500c96d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 46
diff changeset
1029 <param name="data_format_select" value="pileup"/>
6b91a500c96d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 46
diff changeset
1030 <param name="annotation" value="bam/merlin-sample.bam"/>
6b91a500c96d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 46
diff changeset
1031 </conditional>
6b91a500c96d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 46
diff changeset
1032 </repeat>
6b91a500c96d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 46
diff changeset
1033 </repeat>
6b91a500c96d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 46
diff changeset
1034
6b91a500c96d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 46
diff changeset
1035 <param name="uglyTestingHack" value="enabled" />
59
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iuc
parents: 58
diff changeset
1036 <output name="output" file="bam/test.xml" lines_diff="42"/>
47
6b91a500c96d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 46
diff changeset
1037 </test>
6b91a500c96d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 46
diff changeset
1038
6b91a500c96d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 46
diff changeset
1039 <test>
46
f90c22c8fa7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 45
diff changeset
1040 <!-- data_table -->
f90c22c8fa7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 45
diff changeset
1041 <param name="reference_genome|genome_type_select" value="indexed"/>
53
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1042 <param name="reference_genome|genome" value="merlin"/>
46
f90c22c8fa7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 45
diff changeset
1043 <param name="gencode" value="1" />
f90c22c8fa7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 45
diff changeset
1044 <param name="standalone" value="Data Directory" />
f90c22c8fa7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 45
diff changeset
1045 <param name="uglyTestingHack" value="enabled" />
59
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1046 <output name="output" file="gencode/test-data_table.xml" lines_diff="4" />
46
f90c22c8fa7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 45
diff changeset
1047 </test>
53
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1048
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1049 <test>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1050 <param name="reference_genome|genome_type_select" value="history"/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1051 <param name="reference_genome|genome" value="merlin.fa"/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1052 <param name="gencode" value="11" />
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1053 <param name="standalone" value="Data Directory" />
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1054
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1055 <repeat name="track_groups">
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1056 <param name="category" value="External endpoints" />
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1057 <repeat name="data_tracks">
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1058 <conditional name="data_format">
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1059 <param name="data_format_select" value="rest"/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1060 <param name="url" value="http://example.org.external/rest_api/"/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1061 <param name="label" value="Rest api"/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1062 </conditional>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1063 </repeat>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1064 <repeat name="data_tracks">
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1065 <conditional name="data_format">
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1066 <param name="data_format_select" value="sparql"/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1067 <param name="url" value="http://example.org.external/sparql/"/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1068 <param name="label" value="Sparql endpoint"/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1069 <param name="query" value=" DEFINE sql:select-option 'order'
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1070 prefix rdf: &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#&gt;
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1071 select ?start,
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1072 ?end,
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1073 IF( ?faldo_type = faldo:ForwardStrandPosition,
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1074 1,
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1075 IF( ?faldo_type = faldo:ReverseStrandPosition,
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1076 -1,
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1077 0
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1078 )
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1079 ) as ?strand,
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1080 str(?obj_type_name) as ?type,
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1081 str(?label) as ?name,
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1082 str(?obj_name) as ?description,
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1083 ?obj as ?uniqueID,
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1084 ?parent as ?parentUniqueID
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1085 where {
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1086 values ?faldo_type { faldo:ForwardStrandPosition faldo:ReverseStrandPosition faldo:BothStrandsPosition }
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1087 }"/>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1088 </conditional>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1089 </repeat>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1090 </repeat>
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1091
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1092 <param name="uglyTestingHack" value="enabled" />
59
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 58
diff changeset
1093 <output name="output" file="endpoints/test.xml" lines_diff="16"/>
53
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1094 </test>
30
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
1095 </tests>
0
c77c1d5baadb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
iuc
parents:
diff changeset
1096 <help><![CDATA[
29
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1097 JBrowse-in-Galaxy
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1098 =================
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1099
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1100 JBrowse-in-Galaxy offers a highly configurable, workflow-compatible
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1101 alternative to Trackster.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1102
45
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iuc
parents: 44
diff changeset
1103 Overview
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
1104 --------
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
1105
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
1106 JBrowse is a fast, embeddable genome browser built completely with
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
1107 JavaScript and HTML5.
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
1108
29
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iuc
parents: 17
diff changeset
1109 The JBrowse-in-Galaxy (JiG) tool was written to help build complex
5614cf75bb24 Uploaded
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1110 JBrowse installations straight from Galaxy, taking advantage of the
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iuc
parents: 17
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1111 latest Galaxy features such as dataset collections, sections, and colour
5614cf75bb24 Uploaded
iuc
parents: 17
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1112 pickers. It allows you to build up a JBrowse instance without worrying
5614cf75bb24 Uploaded
iuc
parents: 17
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1113 about how to run the command line tools to format your data, and which
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iuc
parents: 17
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1114 options need to be supplied and where. Additionally it comes with many
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1115 javascript functions to handle colouring of features which would be
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1116 nearly impossible to write without the assistance of this tool.
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diff changeset
1117
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iuc
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diff changeset
1118 The JBrowse-in-Galaxy tool is maintained by `the Galaxy IUC
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1119 <https://github.com/galaxyproject/tools-iuc/issues>`__, who you can help you
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1120 with missing features or bugs in the tool.
29
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iuc
parents: 17
diff changeset
1121
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iuc
parents: 17
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1122 Options
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iuc
parents: 17
diff changeset
1123 -------
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iuc
parents: 17
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1124
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iuc
parents: 17
diff changeset
1125 The first option you encounter is the **Fasta Sequence(s)**. This option
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iuc
parents: 17
diff changeset
1126 now accepts multiple fasta files, allowing you to build JBrowse
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1127 instances that contain data for multiple genomes or chrosomomes
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1128 (generally known as "landmark features" in gff3 terminology.) Up to 30
5614cf75bb24 Uploaded
iuc
parents: 17
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1129 will be shown from the dropdown selector within JBrowse, this is a known
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iuc
parents: 17
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1130 issue.
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1131
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iuc
parents: 51
diff changeset
1132 **Standalone Instances** enable you to have either a complete JBrowse instance
c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1133 in a dataset, or just the data directory without JBrowse (e.g. for Apollo).
29
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iuc
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1134 Currently Galaxy copies the entire JBrowse directory in order to have a
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1135 complete, downloadable file that contains a ready-to-go JBrowse
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iuc
parents: 17
diff changeset
1136 instance. This is obviously an anti-feature because users don't want a
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iuc
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diff changeset
1137 complete copy of JBrowse (12Mb) that's duplicated for every JBrowse
29
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iuc
parents: 17
diff changeset
1138 dataset in their history, and admins don't want useless copies of
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iuc
parents: 17
diff changeset
1139 JBrowse on disk. Unfortunately we have not come up with the perfect
5614cf75bb24 Uploaded
iuc
parents: 17
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1140 solution just yet, but we're working on it! In the meantime, users have
5614cf75bb24 Uploaded
iuc
parents: 17
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1141 been given the option to produce just the ``data/`` directory. For those
5614cf75bb24 Uploaded
iuc
parents: 17
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1142 unfamiliar with JBrowse, the ``data/`` directory contains processed data
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iuc
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1143 files, but no way to view them. This feature is additionally implemented
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1144 for upcoming `Apollo <https://github.com/gmod/apollo>`__ integration.
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iuc
parents: 17
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1145
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iuc
parents: 17
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1146 **Genetic Code** is a new feature in v0.4 of JiG / v1.12.0 of JBrowse,
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1147 which allows users to specify a non standard genetic code, and have
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1148 JBrowse highlight the correct start and stop codons.
29
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1149
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iuc
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1150 **Track Groups** represent a set of tracks in a single category. These
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iuc
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1151 can be used to let your users understand relationships between large
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1152 groups of tracks.
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1153
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1154 .. image:: sections.png
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1155
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iuc
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1156 Annotation Tracks
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iuc
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diff changeset
1157 -----------------
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iuc
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1158
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1159 Within Track Groups, you have one or more **Annotation Tracks**. Each
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iuc
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1160 Annotation Track is a groups of datasets which have similar styling.
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iuc
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1161 This allows you to rapidly build up JBrowse instances without having to
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iuc
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1162 configure tracks individually. A massive improvement over previous
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iuc
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1163 versions. For example, if you have five different GFF3 files from
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1164 various gene callers that you wish to display, you can take advantage of
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1165 this feature to style all of them similarly.
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1166
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iuc
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1167 There are a few different types of tracks supported, each with their own
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iuc
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1168 set of options:
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iuc
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1169
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parents: 17
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1170 GFF3/BED/GBK
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iuc
parents: 17
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1171 ~~~~~~~~~~~~
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1172
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1173 These are your standard feature tracks. They usually highlight genes,
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iuc
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1174 mRNAs and other features of interest along a genomic region. The
5614cf75bb24 Uploaded
iuc
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1175 underlying tool and this help documentation focus primarily on GFF3
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iuc
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1176 data, and have not been tested extensively with other formats. Automatic
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iuc
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1177 min/max detection will likely fail under BED and GBK datasets.
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iuc
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1178
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iuc
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1179 The data may be of a subclass we call **match/match part** data. This
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iuc
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1180 consists of top level ``match`` features, with a child ``match_part``
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iuc
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1181 feature, and is often used in displaying alignments. (See "Alignments"
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iuc
parents: 17
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1182 section on the `GFF3
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diff changeset
1183 specification <https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md>`__ for more
29
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1184 information). If the data is match/match part, you will need to specify
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iuc
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1185 the top level match feature name, as it can be one of a few different SO
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iuc
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1186 terms, and JiG does not yet have the ability to understand SO terms.
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1187
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iuc
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1188 Next up is the **Styling Options** section, which lets you control a few
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1189 properties on how the track is styled. Most of these you will not need
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iuc
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1190 to configure and can safely leave on defaults. Occasionally you will
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1191 want to change what information is shown in the end product.
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iuc
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1192
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1193 .. image:: styling.png
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iuc
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1194
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iuc
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1195 In the above image you can see some black text, and some blue text. The
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iuc
parents: 17
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1196 source of the black text is configured with the **style.label** option,
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iuc
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1197 and the source of the blue text is configured with the
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iuc
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1198 **style.description** option.
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1199
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1200 Feature Score Scaling & Colouring Options
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iuc
parents: 17
diff changeset
1201 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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iuc
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1202
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1203 First, you need to choose between ignoring the score attribute of GFF3
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iuc
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1204 files, or using it. If you choose to ignore it, all features will be
5614cf75bb24 Uploaded
iuc
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1205 coloured with a solid colour. If you choose to use it, features will
5614cf75bb24 Uploaded
iuc
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1206 have slightly different colours based on their scores.
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1207
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iuc
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1208 .. image:: opacity.png
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1209
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1210 If you choose **Ignore score**, you may choose between automatically
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iuc
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diff changeset
1211 choosing a colour, or manually specifying one. The automatically chosen
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iuc
parents: 17
diff changeset
1212 colours vary along a brewer palette and generally look quite nice with
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1213 no human intervention required. The manual colour choice is somewhat
5614cf75bb24 Uploaded
iuc
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diff changeset
1214 self explanatory. Clicking on the small coloured square will bring up a
5614cf75bb24 Uploaded
iuc
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diff changeset
1215 colour palette.
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iuc
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1216
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iuc
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1217 If you choose **Base on score**, you're faced with a dizzying array of
5614cf75bb24 Uploaded
iuc
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diff changeset
1218 options. First is the function to map the colour choices to colour
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1219 values. JiG comes with a few functions built in such as linear scaling,
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1220 logarithmic scaling, and blast scaling.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1221
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iuc
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diff changeset
1222 The **linear scaling** method says "take these values, and they map
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1223 directly to a range of output values". **Logarithmic scaling** says
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1224 "please take the log of the score before mapping", and **Blast scaling**
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1225 is further specialised to handle blast data more nicely. These are
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1226 convenience functions to help transform the wide array of possible
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1227 values in the GFF3 score attribute to more meaningful numbers. If you
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1228 need more comprehensive score scaling, it is recommended that you
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1229 pre-process your GFF3 files somehow.
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iuc
parents: 17
diff changeset
1230
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iuc
parents: 17
diff changeset
1231 Once you've selected a scaling method, you can choose to manually
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1232 specify the minimum and maximum expected values, or you can let JiG
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1233 determine them for you automatically.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1234
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iuc
parents: 17
diff changeset
1235 Finally, opacity is the only mapping we currently provide. Future
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1236 iterations will attempt to improve upon this and provide more colour
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1237 scales. The Opacity option maps the highest scoring features to full
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1238 opacity, and everything else to lower ones.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1239
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1240 BAM Pileups
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1241 ~~~~~~~~~~~
5614cf75bb24 Uploaded
iuc
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diff changeset
1242
5614cf75bb24 Uploaded
iuc
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diff changeset
1243 We support BAM files and can automatically generate SNP tracks based on
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1244 that bam data.
5614cf75bb24 Uploaded
iuc
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diff changeset
1245
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1246 .. image:: bam.png
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iuc
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diff changeset
1247
5614cf75bb24 Uploaded
iuc
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diff changeset
1248 This is *strongly discouraged* for high coverage density datasets.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1249 Unfortunately there are no other configuration options exposed for bam
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c6fd9fbd50e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 51
diff changeset
1250 files.
29
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1251
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1252 BlastXML
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1253 ~~~~~~~~
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1254
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iuc
parents: 17
diff changeset
1255 .. image:: blast.png
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1256
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1257 JiG now supports both blastn and blastp datasets. JiG internally uses a
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1258 blastXML to gapped GFF3 tool to convert your blastxml datasets into a
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iuc
parents: 29
diff changeset
1259 format amenable to visualization in JBrowse. This tool is also
29
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iuc
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diff changeset
1260 available separately from the IUC on the toolshed.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1261
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1262 **Minimum Gap Size** reflects how long a gap must be before it becomes a
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1263 real gap in the processed gff3 file. In the picture above, various sizes
5614cf75bb24 Uploaded
iuc
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diff changeset
1264 of gaps can be seen. If the minimum gap size was set much higher, say
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1265 100nt, many of the smaller gaps would disappear, and the features on
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1266 both sides would be merged into one, longer feature. This setting is
5614cf75bb24 Uploaded
iuc
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diff changeset
1267 inversely proportional to runtime and output file size. *Do not set this
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1268 to a low value for large datasets*. By setting this number lower, you
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1269 will have extremely large outputs and extremely long runtimes. The
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1270 default was configured based off of the author's experience, but the
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1271 author only works on small viruses. It is *strongly* recommended that
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1272 you filter your blast results before display, e.g. picking out the top
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1273 10 hits or so.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1274
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1275 **Protein blast search** option merely informs underlying tools that
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1276 they should adjust feature locations by 3x.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1277
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1278 Styling Options
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1279 ^^^^^^^^^^^^^^^
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1280
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1281 Please see the styling options for GFF3 datasets, they are identical.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1282
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1283 Feature Score Scaling & Coloring Options
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1284 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1285
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1286 Please see the score scaling and colouring options for GFF3 datasets,
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1287 they are identical. Remember to set your score scaling to "blast" method
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1288 if you do use it.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1289
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1290 Bigwig XY
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1291 ~~~~~~~~~
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1292
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1293 .. image:: bigwig.png
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1294
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1295 **XYPlot**
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1296
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1297 BigWig tracks can be displayed as a "density" plot which is continuous
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iuc
parents: 29
diff changeset
1298 line which varies in colour, or as an "XYplot." XYplots are preferable
29
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1299 for users to visually identify specific features in a bigwig track,
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1300 however density tracks are more visually compact.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1301
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1302 **Variance Band** is an option available to XYPlots, and can be seen in
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1303 the third and fourth tracks in the above picture. This overlays a mean
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1304 line, and 1 and 2 standard deviation areas.
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1305
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1306 **Track Scaling** is different from colour scaling, instead it
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1307 configures how the track behaves inside of JBrowse. **Autoscaling
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1308 globally** means that JBrowse will determine the minimum and maximum for
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1309 the track, and fix the bounds of the viewport to that. E.g. if your
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1310 track ranges from 1-1000, and the region you're currently zoomed to only
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1311 goes from 0-50, then the viewport range will still show 1-1000. This is
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1312 good for global genomic context. However you may wish to consider
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1313 **autoscaling locally** instead. In the example of a region which varies
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1314 from 0-50, autoscaling locally would cause the individual track's
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1315 viewport to re-adjust and show just the 0-50 region. If neither of these
30
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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diff changeset
1316 options are palatable, you may manually hardcode the minimum and
29
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1317 maximums for the track to scale to.
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1318
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1319 Colour Options
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1320 ^^^^^^^^^^^^^^
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1321
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1322 BigWig tracks have two colours in JBrowse, a positive and a negative
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1323 colour.
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1324
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1325 As always you may manually choose a colour, or let JiG choose for you.
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1326
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diff changeset
1327 One of the more interesting options is the **Bicolor pivot**. This
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1328 option allows you to control the point at which JBrowse switches from
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1329 the positive colour to the negative. In the above graphic, you can see
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1330 this has been configured to "mean" for the first two (orange and blue)
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diff changeset
1331 tracks.
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diff changeset
1332
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diff changeset
1333 VCFs/SNPs
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diff changeset
1334 ~~~~~~~~~
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diff changeset
1335
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1336 These tracks do not support any special configuration.
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diff changeset
1337
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diff changeset
1338 Known Issues
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1339 ------------
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diff changeset
1340
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diff changeset
1341 - More than 30 landmark features cannot be listed in the manual
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diff changeset
1342 selector.
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diff changeset
1343 - Non GFF3 likely has issue with automatically determined min/max
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diff changeset
1344 scores. Manually specify minimum and maximum score attributes, or do
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diff changeset
1345 not use varied colours based on scores to avoid this issue.
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diff changeset
1346
5
b55fad376d87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 344140b8df53b8b7024618bb04594607a045c03a
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diff changeset
1347 @ATTRIBUTION@
0
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parents:
diff changeset
1348 ]]></help>
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c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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diff changeset
1349 <expand macro="citations"/>
0
c77c1d5baadb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
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diff changeset
1350 </tool>