Mercurial > repos > iuc > jbrowse

annotate jbrowse.xml @ 46:f90c22c8fa7e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
author iuc
date Thu, 16 Nov 2017 09:44:18 -0500
parents 665c4f3e48ae
children 6b91a500c96d
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f90c22c8fa7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
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1 <tool id="jbrowse" name="JBrowse" version="@WRAPPER_VERSION@.3">
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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 <expand macro="stdio"/>
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8 <version_command>python '${__tool_directory__}/jbrowse.py' --version</version_command>
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9 <command><![CDATA[
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11 #if $action.action_select == "create":
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12 mkdir -p $output.files_path &&
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13 #else:
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14 cp -R $action.update_jbrowse.extra_files_path $output.files_path &&
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15 #end if
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16
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17 ## Copy the XML file into the directory, mostly for debugging
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18 ## but nice if users want to reproduce locally
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19 cp $trackxml $output.files_path/galaxy.xml &&
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20
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21 ## Once that's done, we run the python script to handle the real work
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22 python '$__tool_directory__/jbrowse.py'
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23
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24 --jbrowse \${JBROWSE_SOURCE_DIR}
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25 #if str($standalone) == "Complete":
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26 --standalone
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27 #end if
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29 --outdir $output.files_path
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30 $trackxml &&
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31
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32 #if str($standalone) == "Complete":
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33 mv $output.files_path/index.html $output;
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34 #else:
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35 mv $dummyIndex $output;
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36 #end if
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37
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38
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39 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph.
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40 #if str($uglyTestingHack) == "enabled":
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41 mv $trackxml $output
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42 #end if
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43 ]]></command>
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44 <configfiles>
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45 <configfile name="dummyIndex">
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46 <![CDATA[
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47 <html>
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48 <head>
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49 </head>
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50 <body>
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51 <h1>JBrowse Data Directory</h1>
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52 <p>
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53 Hi! This is not a full JBrowse instance. JBrowse v0.4(+?)
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54 started shipping with the ability to produce just the
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55 "data" directory from a JBrowse instance, rather than a
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56 complete, standalone instance. This was intended to be used
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57 with the in-development Apollo integration, but may have other
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58 uses as well.
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59 </p>
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60 <p>
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61 <u>This is not usable on its own</u>. The output dataset may be
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62 used with Apollo, or may be passed through the "JBrowse -
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63 Convert to Standalone" tool in Galaxy to "upgrade" to a full
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64 JBrowse instance.
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65 </p>
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66 </body>
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67 </html>
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68 ]]>
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69 </configfile>
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70 <configfile name="trackxml"><![CDATA[<?xml version="1.0"?>
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71 <root>
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72 <metadata>
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73 <gencode>$gencode</gencode>
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74 <genomes>
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75 #if str($reference_genome.genome_type_select) == "indexed":
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76 <genome path="${reference_genome.genomes.fields.path}">
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77 <metadata />
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78 </genome>s
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79 #else
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80 #for $genome in $reference_genome.genomes:
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81 <genome path="$genome">
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82 <metadata>
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83 <dataset id="${__app__.security.encode_id($genome.id)}" hid="${genome.hid}"
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84 size="${genome.get_size(nice_size=True)}"
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85 edam_format="${genome.datatype.edam_format}"
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86 file_ext="${genome.ext}" />
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87 <history id="${__app__.security.encode_id($genome.history_id)}"
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88 user_email="${genome.history.user.email}"
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89 user_id="${genome.history.user_id}"
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90 display_name="${genome.history.get_display_name()}"/>
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91 <metadata
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92 #for (key, value) in $genome.get_metadata().items():
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93 #if "_types" not in $key:
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94 ${key}="${value}"
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95 #end if
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96 #end for
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97 />
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98 <tool
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99 tool_id="${genome.creating_job.tool_id}"
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100 tool_version="${genome.creating_job.tool_version}"
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101 />
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102 </metadata>
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103 </genome>
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104 #end for
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105 #end if
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106 </genomes>
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107 <general>
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108 <defaultLocation>${jbgen.defaultLocation}</defaultLocation>
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109 <trackPadding>${jbgen.trackPadding}</trackPadding>
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110
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111 <shareLink>${jbgen.shareLink}</shareLink>
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112 <aboutDescription>${jbgen.aboutDescription}</aboutDescription>
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113 <show_tracklist>${jbgen.show_tracklist}</show_tracklist>
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114 <show_nav>${jbgen.show_nav}</show_nav>
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115 <show_overview>${jbgen.show_overview}</show_overview>
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116 <show_menu>${jbgen.show_menu}</show_menu>
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117 <hideGenomeOptions>${jbgen.hideGenomeOptions}</hideGenomeOptions>
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118 </general>
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119 <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl>
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120 </metadata>
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121 <tracks>
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122 #for $tg in $track_groups:
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123 #for $track in $tg.data_tracks:
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124 #if $track.data_format.data_format_select == "rest":
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125 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
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126 <url>${track.data_format.url}</url>
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127 </track>
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128 #else:
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129 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
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130 <files>
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131 #for $dataset in $track.data_format.annotation:
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132 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}">
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133 <metadata>
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134 <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}"
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135 size="${dataset.get_size(nice_size=True)}"
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136 edam_format="${dataset.datatype.edam_format}"
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137 file_ext="${dataset.ext}" />
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138 <history id="${__app__.security.encode_id($dataset.history_id)}"
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139 user_email="${dataset.history.user.email}"
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140 user_id="${dataset.history.user_id}"
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141 display_name="${dataset.history.get_display_name()}"/>
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142 <metadata
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143 #for (key, value) in $dataset.get_metadata().items():
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144 #if "_types" not in $key:
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145 ${key}="${value}"
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146 #end if
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147 #end for
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148 />
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149 <tool
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150 tool_id="${dataset.creating_job.tool_id}"
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151 tool_version="${dataset.creating_job.tool_version}"
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152 />
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153 </metadata>
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154 </trackFile>
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155 #end for
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156 </files>
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157
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158 <options>
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159 #if str($track.data_format.data_format_select) == "gene_calls" or str($track.data_format.data_format_select) == "blast":
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160 <style>
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161 <overridePlugins>${track.data_format.override_apollo_plugins}</overridePlugins>
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162 <overrideDraggable>${track.data_format.override_apollo_drag}</overrideDraggable>
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163 <className>${track.data_format.jbstyle.style_classname}</className>
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164 <description>${track.data_format.jbstyle.style_description}</description>
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165 <label>${track.data_format.jbstyle.style_label}</label>
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166 <height>${track.data_format.jbstyle.style_height}</height>
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167 <maxHeight>${track.data_format.jbstyle.max_height}</maxHeight>
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168 </style>
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169 <scaling>
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170 #if str($track.data_format.jbcolor_scale.color_score.color_score_select) == "none":
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171 <method>ignore</method>
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172 <scheme>
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173 #if str($track.data_format.jbcolor_scale.color_score.color.color_select) == "automatic":
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174 <color>__auto__</color>
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175 #else
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176 <color>${track.data_format.jbcolor_scale.color_score.color.style_color}</color>
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177 #end if
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178 </scheme>
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179 #else
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180 <method>score</method>
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181 <algo>${track.data_format.jbcolor_scale.color_score.score_scaling}</algo>
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182 <scales>
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183 <type>${track.data_format.jbcolor_scale.color_score.score_scales.scale_select}</type>
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184
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185 #if str($track.data_format.jbcolor_scale.color_score.score_scales.scale_select) == "manual":
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186 <min>${track.data_format.jbcolor_scale.color_score.score_scales.minimum}</min>
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187 <max>${track.data_format.jbcolor_scale.color_score.score_scales.maximum}</max>
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188 #end if
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189 </scales>
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190 <scheme>
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191 <type>${track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme}</type>
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192 ## auto_color
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193 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme) == "opacity":
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194 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.color.color_select) == "automatic":
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195 <color>__auto__</color>
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196 #else
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197 <color>${track.data_format.jbcolor_scale.color_score.color_scheme.color.style_color}</color>
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198 #end if
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199 #end if
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200 </scheme>
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201 #end if
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202 </scaling>
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203 <menus>
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204 #for $menu_item in $track.data_format.jbmenu.track_menu:
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205 <menu>
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206 <action>${menu_item.menu_action}</action>
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207 #if str($menu_item.menu_label) != "":
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208 <label>${menu_item.menu_label}</label>
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209 #end if
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210 #if str($menu_item.menu_title) != "":
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211 <title>${menu_item.menu_title}</title>
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212 #end if
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213 #if str($menu_item.menu_url) != "":
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214 <url>${menu_item.menu_url.replace("&", "&amp;").replace("\"", "&quot;")}</url>
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215 #end if
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216 #if str($menu_item.menu_icon) != "":
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217 <iconClass>${menu_item.menu_icon}</iconClass>
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218 #end if
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219 </menu>
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220 #end for
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221 </menus>
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222 #end if
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223
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224 #if str($track.data_format.data_format_select) == "wiggle":
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225 <wiggle>
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226 <type>${track.data_format.xyplot}</type>
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227 <variance_band>${track.data_format.var_band}</variance_band>
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228 #if str($track.data_format.scaling.scale_select) == "auto_local":
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229 <autoscale>local</autoscale>
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230 #else if str($track.data_format.scaling.scale_select) == "auto_global":
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231 <autoscale>global</autoscale>
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232 #else:
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233 <min>${track.data_format.scaling.minimum}</min>
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234 <max>${track.data_format.scaling.maximum}</max>
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235 #end if
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236 <scale>${track.data_format.scale_select2}</scale>
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237
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238 ## Wiggle tracks need special color config
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239 #if str($track.data_format.jbcolor.color.color_select) != "automatic":
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240 <color_pos>${track.data_format.jbcolor.color.style_pos_color}</color_pos>
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241 <color_neg>${track.data_format.jbcolor.color.style_neg_color}</color_neg>
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242 #else:
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243 <color_pos>__auto__</color_pos>
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244 <color_neg>__auto__</color_neg>
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245 #end if
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246
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247 ## Bicolor pivot config
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248 #if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "zero":
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249 <bicolor_pivot>zero</bicolor_pivot>
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250 #else if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "mean":
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251 <bicolor_pivot>mean</bicolor_pivot>
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252 #else:
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253 <bicolor_pivot>${track.data_format.jbcolor.bicolor_pivot.pivot_point}</bicolor_pivot>
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254 #end if
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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 </pileup>
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265 #else if str($track.data_format.data_format_select) == "blast":
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266 <blast>
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267 #if str($track.data_format.blast_parent) != "":
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268 <parent>${track.data_format.blast_parent}</parent>
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269 #end if
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270 <protein>${track.data_format.is_protein}</protein>
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271 <min_gap>${track.data_format.min_gap}</min_gap>
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272 <index>${track.data_format.index}</index>
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273 </blast>
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274 #else if str($track.data_format.data_format_select) == "gene_calls":
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275 <gff>
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276 <trackType>${track.data_format.track_config.track_class}</trackType>
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277 #if $track.data_format.track_config.track_class == 'JBrowse/View/Track/CanvasFeatures':
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278 #if str($track.data_format.track_config.canvas_options.transcriptType) != "":
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279 <transcriptType>${track.data_format.track_config.canvas_options.transcriptType}</transcriptType>
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280 #end if
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281 #if str($track.data_format.track_config.canvas_options.subParts) != "":
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282 <subParts>${track.data_format.track_config.canvas_options.subParts}</subParts>
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283 #end if
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284 #if str($track.data_format.track_config.canvas_options.impliedUTRs) != "false":
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285 <impliedUTRs>${track.data_format.track_config.canvas_options.impliedUTRs}</impliedUTRs>
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286 #end if
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287 #else if $track.data_format.track_config.track_class == 'JBrowse/View/Track/HTMLFeatures':
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288 #if str($track.data_format.track_config.html_options.transcriptType) != "":
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289 <transcriptType>${track.data_format.track_config.html_options.transcriptType}</transcriptType>
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290 #end if
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291 #end if
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292 #if $track.data_format.match_part.match_part_select:
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293 <match>${track.data_format.match_part.name}</match>
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294 #end if
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295 <index>${track.data_format.index}</index>
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296 </gff>
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297 ## #else if str($track.data_format.data_format_select) == "sparql":
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298 ## <sparql>
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299 ## <url>${track.data_format.url}</url>
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300 ## <label>${track.data_format.label}</label>
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301 ## <!-- This is going to be an absolutey nightmare -->
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302 ## <query>${track.data_format.query}</query>
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303 ## </sparql>
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304 #end if
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305 </options>
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306 </track>
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307 #end if
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308 #end for
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309 #end for
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310 </tracks>
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311 <plugins
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312 ComboTrackSelector="${plugins.ComboTrackSelector}"
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313 Bookmarks="${plugins.Bookmarks}"
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314 GCContent="${plugins.GCContent}"
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315 theme="${plugins.theme}"
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316 />
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317 </root>]]></configfile>
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318 </configfiles>
0
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319 <inputs>
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320 <conditional name="reference_genome">
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321 <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select">
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322 <option selected="True" value="indexed">Use a built-in genome</option>
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323 <option value="history">Use a genome from history</option>
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324 </param>
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325 <when value="indexed">
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326 <param
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327 help="If your genome of interest is not listed, contact the Galaxy team"
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328 label="Select a reference genome"
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329 name="genomes"
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330 type="select"
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331 >
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332 <options from_data_table="all_fasta">
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333 <filter column="2" type="sort_by" />
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334 <validator message="No genomes are available for the selected input dataset" type="no_options" />
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335 </options>
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336 </param>
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337 </when>
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338 <when value="history">
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339 <param
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340 format="fasta"
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341 label="Select the reference genome"
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342 name="genomes"
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343 type="data"
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344 multiple="True" />
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345 </when>
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346 </conditional>
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347
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348 <param name="standalone" label="Produce Standalone Instance" type="boolean" truevalue="Complete" falsevalue="Data Directory" help="Produce a full, working JBrowse instance or just the data directory. Data dir mode is experimental and intended to be used with Apollo" checked="True"/>
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349
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350 <param label="Genetic Code" name="gencode" type="select">
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351 <option value="1">1. The Standard Code</option>
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352 <option value="2">2. The Vertebrate Mitochondrial Code</option>
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353 <option value="3">3. The Yeast Mitochondrial Code</option>
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354 <option value="4">4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
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355 <option value="5">5. The Invertebrate Mitochondrial Code</option>
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356 <option value="6">6. The Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
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357 <option value="9">9. The Echinoderm and Flatworm Mitochondrial Code</option>
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358 <option value="10">10. The Euplotid Nuclear Code</option>
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359 <option value="11">11. The Bacterial, Archaeal and Plant Plastid Code</option>
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360 <option value="12">12. The Alternative Yeast Nuclear Code</option>
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361 <option value="13">13. The Ascidian Mitochondrial Code</option>
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362 <option value="14">14. The Alternative Flatworm Mitochondrial Code</option>
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363 <option value="16">16. Chlorophycean Mitochondrial Code</option>
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364 <option value="21">21. Trematode Mitochondrial Code</option>
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365 <option value="22">22. Scenedesmus obliquus Mitochondrial Code</option>
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366 <option value="23">23. Thraustochytrium Mitochondrial Code</option>
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367 <option value="24">24. Pterobranchia Mitochondrial Code</option>
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368 <option value="25">25. Candidate Division SR1 and Gracilibacteria Code</option>
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369 </param>
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370
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371 <conditional name="action">
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372 <param type="select" label="JBrowse-in-Galaxy Action" name="action_select">
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373 <option value="create">New JBrowse Instance</option>
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374 <option value="update">Update exising JBrowse Instance</option>
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375 </param>
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376 <when value="create" />
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377 <when value="update">
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378 <param label="Previous JBrowse Instance"
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379 name="update_jbrowse"
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380 type="data"
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381 format="html" />
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382 </when>
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383 </conditional>
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384
16
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385 <repeat name="track_groups" title="Track Group">
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386 <param label="Track Category"
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387 name="category"
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388 type="text"
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389 value="Default"
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390 help="Organise your tracks into Categories for a nicer end-user experience. You can use #date# and it will be replaced with the current date in 'yyyy-mm-dd' format, which is very useful for repeatedly updating a JBrowse instance when member databases / underlying tool versions are updated." optional="False"/>
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391 <repeat name="data_tracks" title="Annotation Track">
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392 <conditional name="data_format" label="Track Options">
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393 <param type="select" label="Track Type" name="data_format_select">
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394 <option value="gene_calls">GFF/GFF3/BED/GBK Features</option>
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395 <option value="pileup">BAM Pileups</option>
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396 <option value="blast">Blast XML</option>
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397 <option value="wiggle">BigWig XY</option>
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398 <option value="vcf">VCF SNPs</option>
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399 <option value="rest">REST Endpoint</option>
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400 <!--<option value="sparql">SPARQL</option>-->
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401 </param>
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402 <when value="blast">
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403 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" />
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404
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405 <param label="Features used in Blast Search"
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406 help="in GFF3. This is used so we know where to map features. E.g. where results of which CDS Protein32 match up to. The query IDs in your blast results should MATCH some feature IDs in your GFF3 file. This is an optional field and is most useful if using JBrowse to display protein blast results on a DNA genome. blastn results don't need this, blastp results on a protein sequence don't need this."
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407 format="gff3"
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408 name="blast_parent"
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409 optional="true"
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410 type="data"/>
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411
16
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412 <param label="Minimum Gap Size"
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413 help="before a new match_part feature is created"
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414 name="min_gap"
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415 type="integer"
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416 value="10"
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417 min="2" />
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418 <param label="Is this a protein blast search?"
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419 type="boolean"
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420 name="is_protein"
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421 truevalue="true"
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422 falsevalue="false" />
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423
42
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424 <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" />
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425
16
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426 <expand macro="track_styling"
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427 classname="feature"
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428 label="description"
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429 description="Hit_titles"
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430 height="600px"/>
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431 <expand macro="color_selection"
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432 token_scaling_lin_select="false"
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433 token_scaling_log_select="true" />
42
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434 <expand macro="track_menu" />
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435 <expand macro="track_display" />
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436 </when>
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437 <when value="vcf">
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438 <expand macro="input_conditional" label="SNP Track Data" format="vcf" />
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439 <expand macro="track_display" />
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440 </when>
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441 <when value="gene_calls">
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442 <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" />
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443 <conditional name="match_part" label="match/match_part data">
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444 <param label="This is match/match_part data"
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445 type="boolean"
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446 name="match_part_select"
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447 truevalue="true"
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448 falsevalue="false" />
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449 <when value="true">
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450 <param label="Match Part Feature Type"
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451 name="name"
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452 type="text"
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453 value="match"
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454 help="Match_parts have several options for the parent feature type, such as cDNA_match, match, translated_nucleotide_match, etc. Please select the appropriate one here"
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455 optional="False"/>
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456 </when>
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457 <when value="false" />
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458 </conditional>
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459
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460 <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" />
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461
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462 <conditional name="track_config">
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463 <param type="select" label="JBrowse Track Type [Advanced]" name="track_class">
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464 <option value="JBrowse/View/Track/HTMLFeatures">HTML Features</option>
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465 <option value="JBrowse/View/Track/CanvasFeatures" selected="true">Canvas Features</option>
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466 <option value="BlastView/View/Track/CanvasFeatures">Blast Features</option>
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467 </param>
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468 <when value="JBrowse/View/Track/CanvasFeatures">
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469 <section name="canvas_options" title="CanvasFeatures Options [Advanced]" expanded="false">
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470 <param label="Transcript type"
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471 name="transcriptType"
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472 type="text"
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473 value=""
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474 help="If your input files represents transcripts with features not named 'mRNA', give the alternate name here (e.g. 'transcript')"
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475 optional="True"/>
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476 <param label="Subfeatures type"
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477 name="subParts"
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478 type="text"
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parents: 40
diff changeset
479 value=""
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480 help="If you have 'exons' but no corresponding 'CDS' features, specify here the subfeatures that should be displayed (e.g. 'exon')"
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diff changeset
481 optional="True"/>
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482 <param label="Implied UTRs"
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483 name="impliedUTRs"
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iuc
parents: 40
diff changeset
484 type="boolean"
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
485 checked="false"
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iuc
parents: 40
diff changeset
486 truevalue="true"
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iuc
parents: 40
diff changeset
487 falsevalue="false"
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iuc
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diff changeset
488 help="Check this your input files does not contain UTR features, but the UTR can be 'implied' from the difference between the exon and CDS boundaries"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
489 </section>
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iuc
parents: 40
diff changeset
490 </when>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
491 <when value="JBrowse/View/Track/HTMLFeatures">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
492 <section name="html_options" title="HTMLFeatures Options [Advanced]" expanded="false">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
493 <param label="Transcript type"
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
494 name="transcriptType"
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iuc
parents: 40
diff changeset
495 type="text"
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iuc
parents: 40
diff changeset
496 value=""
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
497 help="If your input files represents transcripts, give the name of the corresponding features here (e.g. 'mRNA' or 'transcript')"
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
498 optional="True"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
499 </section>
46
f90c22c8fa7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 45
diff changeset
500 </when>
f90c22c8fa7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 45
diff changeset
501 <when value="BlastView/View/Track/CanvasFeatures" />
42
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iuc
parents: 40
diff changeset
502 </conditional>
16
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iuc
parents: 15
diff changeset
503 <expand macro="track_styling" />
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iuc
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504 <expand macro="color_selection" />
42
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
505 <expand macro="track_menu" />
30
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iuc
parents: 29
diff changeset
506 <expand macro="track_display" />
13
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parents: 12
diff changeset
507 </when>
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iuc
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diff changeset
508 <when value="pileup">
16
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parents: 15
diff changeset
509 <expand macro="input_conditional" label="BAM Track Data" format="bam" />
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iuc
parents: 15
diff changeset
510 <param label="Autogenerate SNP Track"
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iuc
parents: 15
diff changeset
511 help="Not recommended for deep coverage BAM files"
318a0aa5075a Uploaded manually
iuc
parents: 15
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512 type="boolean"
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iuc
parents: 15
diff changeset
513 name="auto_snp"
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parents: 15
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514 truevalue="true"
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iuc
parents: 15
diff changeset
515 falsevalue="false" />
30
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parents: 29
diff changeset
516 <expand macro="track_display" />
13
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iuc
parents: 12
diff changeset
517 </when>
67fb31daef0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 399061eca3a2956704522974446601755503c96d-dirty
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diff changeset
518 <when value="wiggle">
16
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parents: 15
diff changeset
519 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" />
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
520
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parents: 15
diff changeset
521 <param label="Use XYPlot"
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iuc
parents: 15
diff changeset
522 help="instead of continuous colored band"
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iuc
parents: 15
diff changeset
523 type="boolean"
318a0aa5075a Uploaded manually
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parents: 15
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524 name="xyplot"
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iuc
parents: 15
diff changeset
525 truevalue="JBrowse/View/Track/Wiggle/XYPlot"
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
526 falsevalue="JBrowse/View/Track/Wiggle/Density" />
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iuc
parents: 15
diff changeset
527 <param label="Show variance band"
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
528 help="Only for XYPlots"
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
529 type="boolean"
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iuc
parents: 15
diff changeset
530 name="var_band"
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iuc
parents: 15
diff changeset
531 truevalue="true"
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parents: 15
diff changeset
532 falsevalue="false" />
13
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iuc
parents: 12
diff changeset
533
45
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parents: 44
diff changeset
534 <conditional name="scaling" label="Scaling">
13
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iuc
parents: 12
diff changeset
535 <param type="select" label="Track Scaling" name="scale_select">
15
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parents: 14
diff changeset
536 <option value="auto_local">Autoscale (local)</option>
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parents: 15
diff changeset
537 <option value="auto_global" selected="true">Autoscale (global)</option>
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parents: 15
diff changeset
538 <option value="fixed">Specify Min/Max</option>
13
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parents: 12
diff changeset
539 </param>
67fb31daef0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 399061eca3a2956704522974446601755503c96d-dirty
iuc
parents: 12
diff changeset
540 <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
541 <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
542 <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
543 <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
544 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
545 <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
546 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
547 </when>
67fb31daef0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 399061eca3a2956704522974446601755503c96d-dirty
iuc
parents: 12
diff changeset
548 </conditional>
45
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parents: 44
diff changeset
549 <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
550 <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
551 <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
552 </param>
16
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parents: 15
diff changeset
553 <expand macro="color_selection_minmax" />
30
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iuc
parents: 29
diff changeset
554 <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
555 </when>
45
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
556 <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
557 <param type="text" label="REST Endpoint" name="url" />
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
558 </when>
30
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
559 <!--
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
560 <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
561 <param type="text" label="SPARQL Server URL" name="url" />
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
562 <param type="text" label="Track Label" name="key" value="SPARQL Genes" />
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
563 <param type="text" label="SPARQL Query" name="query" area="true" />
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
564 <expand macro="track_display" />
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
565 </when>
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
566 -->
13
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iuc
parents: 12
diff changeset
567 </conditional>
0
c77c1d5baadb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
iuc
parents:
diff changeset
568 </repeat>
16
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parents: 15
diff changeset
569 </repeat>
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
570
30
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
571 <expand macro="general_options" />
45
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iuc
parents: 44
diff changeset
572 <section name="plugins" title="Plugins" expanded="false">
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
573 <param
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
574 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
iuc
parents: 44
diff changeset
575 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" />
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
576 <param
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
577 label="Bookmarks" name="Bookmarks" truevalue="True" falsevalue="" type="boolean"
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
578 help="JBrowse plugin allowing users to manage a persistent list of bookmarks kept in localstorage" />
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
579
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
580 <param
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
581 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
parents: 44
diff changeset
582 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
iuc
parents: 44
diff changeset
583
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
584 <param type="select" label="JBrowse Theme" name="theme">
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
585 <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
586 <option value="Minimalist">Minimalist</option>
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
587 <option value="Dark">Dark</option>
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
588 </param>
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iuc
parents: 44
diff changeset
589 </section>
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
590
16
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iuc
parents: 15
diff changeset
591 <param type="hidden" name="uglyTestingHack" value="" />
0
c77c1d5baadb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
iuc
parents:
diff changeset
592 </inputs>
c77c1d5baadb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
iuc
parents:
diff changeset
593 <outputs>
16
318a0aa5075a Uploaded manually
iuc
parents: 15
diff changeset
594 <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
iuc
parents:
diff changeset
595 </outputs>
30
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iuc
parents: 29
diff changeset
596 <tests>
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iuc
parents: 29
diff changeset
597 <test>
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iuc
parents: 29
diff changeset
598 <!-- gencode -->
42
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iuc
parents: 40
diff changeset
599 <param name="reference_genome|genome_type_select" value="history"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
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600 <param name="reference_genome|genomes" value="merlin.fa"/>
30
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iuc
parents: 29
diff changeset
601 <param name="gencode" value="1" />
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
602 <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
603 <param name="uglyTestingHack" value="enabled" />
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
604 <output name="output" file="gencode/test-1.xml" lines_diff="4" />
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
605 </test>
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
606 <test>
42
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iuc
parents: 40
diff changeset
607 <param name="reference_genome|genome_type_select" value="history"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
608 <param name="reference_genome|genomes" 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
609 <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
610 <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
611 <param name="uglyTestingHack" value="enabled" />
45
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
612 <output name="output" file="gencode/test.xml" lines_diff="14"/>
30
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
613 </test>
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
614 <test>
42
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iuc
parents: 40
diff changeset
615 <param name="reference_genome|genome_type_select" value="history"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
616 <param name="reference_genome|genomes" 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
617 <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
618 <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
619 <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
620 <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
621 <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
622 <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
623 <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
624 <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
625 <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
626 <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
627 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
628 <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
629 <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
630 <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
631 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
632 <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
633 <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
634 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
635 </section>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
636 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
637 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
638 </repeat>
30
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iuc
parents: 29
diff changeset
639
42
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
640 <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
641 <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
642 <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
643 <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
644 <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
645 <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
646 <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
647 <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
648 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
649 <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
650 <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
651 <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
652 <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
653 <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
654 <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
655 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
656 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
657 </section>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
658 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
659 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
660 </repeat>
30
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iuc
parents: 29
diff changeset
661
42
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
662 <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
663 <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
664 <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
665 <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
666 <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
667 <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
668 <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
669 <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
670 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
671 <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
672 <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
673 <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
674 <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
675 <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
676 <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
677 </conditional>
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="color_scheme">
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="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
680 <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
681 <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
682 </conditional>
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 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
685 </section>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
686 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
687 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
688 <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
689 <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
690 <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
691 <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
692 <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
693 <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
694 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
695 <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
696 <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
697 <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
698 <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
699 <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
700 <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
701 </conditional>
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="color_scheme">
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="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
704 <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
705 <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
706 <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
707 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
708 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
709 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
710 </section>
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 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
713 <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
714 <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
715 <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
716 <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
717 <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
718 <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
719 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
720 <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
721 <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
722 <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
723 <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
724 <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
725 <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
726 <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
727 <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
728 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
729 <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
730 <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
731 <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
732 <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
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>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
735 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
736 </section>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
737 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
738 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
739 <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
740 <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
741 <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
742 <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
743 <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
744 <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
745 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
746 <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
747 <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
748 <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
749 <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
750 <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
751 <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
752 <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
753 <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
754 </conditional>
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="color_scheme">
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="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
757 <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
758 <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
759 <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
760 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
761 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
762 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
763 </section>
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 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
766 </repeat>
30
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
767
42
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
768 <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
769 <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
770 <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
771 <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
772 <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
773 <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
774 <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
775 <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
776 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
777 <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
778 <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
779 <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
780 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
781 <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
782 <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
783 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
784 </section>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
785 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
786 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
787 <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
788 <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
789 <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
790 <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
791 <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
792 <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
793 <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
794 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
795 <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
796 <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
797 <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
798 </conditional>
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="color">
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="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
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>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
803 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
804 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
805 </repeat>
30
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
806
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
807 <param name="uglyTestingHack" value="enabled" />
45
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
808 <output name="output" file="gff3/test.xml" lines_diff="64" />
30
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
809 </test>
42
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
810 <test>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
811 <param name="reference_genome|genome_type_select" value="history"/>
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="reference_genome|genomes" value="merlin.fa"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
813 <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
814 <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
815
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
816 <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
817 <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
818 <repeat name="data_tracks">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
819 <conditional name="data_format">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
820 <param name="data_format_select" value="gene_calls"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
821 <param name="annotation" value="gff3/1.gff"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
822 <conditional name="match_part">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
823 <param name="match_part_select" value="false"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
824 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
825 <section name="jbcolor_scale">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
826 <conditional name="color_score">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
827 <param name="color_score_select" value="none"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
828 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
829 <conditional name="color">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
830 <param name="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
831 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
832 </section>
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="jbmenu">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
834 <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
835 <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
836 <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
837 <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
838 <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
839 <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
840 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
841 <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
842 <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
843 <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
844 <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
845 <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
846 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
847 </section>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
848 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
849 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
850 <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
851 <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
852 <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
853 <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
854 <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
855 <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
856 <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
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 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
859 <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
860 <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
861 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
862 <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
863 <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
864 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
865 </section>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
866 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
867 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
868 </repeat>
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iuc
parents: 40
diff changeset
869
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="uglyTestingHack" value="enabled" />
45
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iuc
parents: 44
diff changeset
871 <output name="output" file="menus/test.xml" lines_diff="24"/>
42
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
872 </test>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
873 <test>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
874 <param name="reference_genome|genome_type_select" value="history"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
875 <param name="reference_genome|genomes" value="merlin.fa"/>
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="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
877 <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
878
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
879 <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
880 <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
881 <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
882 <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
883 <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
884 <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
885 <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
886 <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
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 <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
889 <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
890 <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
891 <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
892 <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
893 </section>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
894 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
895 <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
896 <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
897 <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
898 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
899 <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
900 <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
901 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
902 </section>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
903 </conditional>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
904 </repeat>
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
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
907 <param name="uglyTestingHack" value="enabled" />
45
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
908 <output name="output" file="track_config/test.xml" lines_diff="26"/>
42
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
909 </test>
46
f90c22c8fa7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 45
diff changeset
910 <test>
f90c22c8fa7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 45
diff changeset
911 <!-- data_table -->
f90c22c8fa7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 45
diff changeset
912 <param name="reference_genome|genome_type_select" value="indexed"/>
f90c22c8fa7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 45
diff changeset
913 <param name="reference_genome|genomes" value="merlin"/>
f90c22c8fa7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 45
diff changeset
914 <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
915 <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
916 <param name="uglyTestingHack" value="enabled" />
f90c22c8fa7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 45
diff changeset
917 <output name="output" file="gencode/test-data_table.xml" lines_diff="4" />
f90c22c8fa7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 45
diff changeset
918 </test>
30
12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
919 </tests>
0
c77c1d5baadb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
iuc
parents:
diff changeset
920 <help><![CDATA[
29
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iuc
parents: 17
diff changeset
921 JBrowse-in-Galaxy
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
922 =================
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
923
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
924 JBrowse-in-Galaxy offers a highly configurable, workflow-compatible
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
925 alternative to Trackster.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
926
45
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
927 Overview
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
928 --------
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
929
665c4f3e48ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 44
diff changeset
930 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
931 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
932
29
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
933 The JBrowse-in-Galaxy (JiG) tool was written to help build complex
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
934 JBrowse installations straight from Galaxy, taking advantage of the
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
935 latest Galaxy features such as dataset collections, sections, and colour
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
936 pickers. It allows you to build up a JBrowse instance without worrying
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
937 about how to run the command line tools to format your data, and which
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
938 options need to be supplied and where. Additionally it comes with many
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
939 javascript functions to handle colouring of features which would be
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
940 nearly impossible to write without the assistance of this tool.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
941
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
942 The JBrowse-in-Galaxy tool is maintained by `Eric
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
943 Rasche <mailto:esr+jig@tamu.edu>`__, who you can contact if you
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
944 encounter missing features or bugs.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
945
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
946 Options
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iuc
parents: 17
diff changeset
947 -------
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iuc
parents: 17
diff changeset
948
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
949 The first option you encounter is the **Fasta Sequence(s)**. This option
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
950 now accepts multiple fasta files, allowing you to build JBrowse
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
951 instances that contain data for multiple genomes or chrosomomes
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
952 (generally known as "landmark features" in gff3 terminology.) Up to 30
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
953 will be shown from the dropdown selector within JBrowse, this is a known
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
954 issue.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
955
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
956 **Standalone Instances** are a somewhat in-development feature.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
957 Currently Galaxy copies the entire JBrowse directory in order to have a
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
958 complete, downloadable file that contains a ready-to-go JBrowse
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
959 instance. This is obviously an anti-feature because users don't want a
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
960 complete copy of JBrowse (6-20Mb) that's duplicated for every JBrowse
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
961 dataset in their history, and admins don't want useless copies of
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
962 JBrowse on disk. Unfortunately we have not come up with the perfect
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
963 solution just yet, but we're working on it! In the meantime, users have
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
964 been given the option to produce just the ``data/`` directory. For those
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
965 unfamiliar with JBrowse, the ``data/`` directory contains processed data
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
966 files, but no way to view them. This feature is additionally implemented
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
967 for upcoming `Apollo <https://github.com/gmod/apollo>`__ integration.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
968
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
969 **Genetic Code** is a new feature in v0.4 of JiG / v1.12.0 of JBrowse,
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
970 which allows users to specify a non standard genetic code, and have
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
971 JBrowse highlight the correct start and stop codons. If you would like
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
972 to use a coding table not provided by this list, please let
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
973 `me <mailto:esr+jig@tamu.edu>`__ know so that I may add support for
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
974 this.
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iuc
parents: 17
diff changeset
975
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
976 **Track Groups** represent a set of tracks in a single category. These
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
977 can be used to let your users understand relationships between large
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
978 groups of tracks.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
979
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iuc
parents: 17
diff changeset
980 .. image:: sections.png
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iuc
parents: 17
diff changeset
981
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iuc
parents: 17
diff changeset
982 Annotation Tracks
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
983 -----------------
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iuc
parents: 17
diff changeset
984
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iuc
parents: 17
diff changeset
985 Within Track Groups, you have one or more **Annotation Tracks**. Each
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
986 Annotation Track is a groups of datasets which have similar styling.
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iuc
parents: 17
diff changeset
987 This allows you to rapidly build up JBrowse instances without having to
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iuc
parents: 17
diff changeset
988 configure tracks individually. A massive improvement over previous
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
989 versions. For example, if you have five different GFF3 files from
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iuc
parents: 17
diff changeset
990 various gene callers that you wish to display, you can take advantage of
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
991 this feature to style all of them similarly.
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iuc
parents: 17
diff changeset
992
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
993 There are a few different types of tracks supported, each with their own
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
994 set of options:
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
995
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parents: 17
diff changeset
996 GFF3/BED/GBK
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
997 ~~~~~~~~~~~~
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
998
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
999 These are your standard feature tracks. They usually highlight genes,
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1000 mRNAs and other features of interest along a genomic region. The
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iuc
parents: 17
diff changeset
1001 underlying tool and this help documentation focus primarily on GFF3
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1002 data, and have not been tested extensively with other formats. Automatic
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1003 min/max detection will likely fail under BED and GBK datasets.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1004
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1005 The data may be of a subclass we call **match/match part** data. This
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1006 consists of top level ``match`` features, with a child ``match_part``
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1007 feature, and is often used in displaying alignments. (See "Alignments"
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1008 section on the `GFF3
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parents: 40
diff changeset
1009 specification <https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md>`__ for more
29
5614cf75bb24 Uploaded
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parents: 17
diff changeset
1010 information). If the data is match/match part, you will need to specify
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1011 the top level match feature name, as it can be one of a few different SO
5614cf75bb24 Uploaded
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parents: 17
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1012 terms, and JiG does not yet have the ability to understand SO terms.
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parents: 17
diff changeset
1013
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1014 Next up is the **Styling Options** section, which lets you control a few
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parents: 17
diff changeset
1015 properties on how the track is styled. Most of these you will not need
5614cf75bb24 Uploaded
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parents: 17
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1016 to configure and can safely leave on defaults. Occasionally you will
5614cf75bb24 Uploaded
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parents: 17
diff changeset
1017 want to change what information is shown in the end product.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1018
5614cf75bb24 Uploaded
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parents: 17
diff changeset
1019 .. image:: styling.png
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iuc
parents: 17
diff changeset
1020
5614cf75bb24 Uploaded
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parents: 17
diff changeset
1021 In the above image you can see some black text, and some blue text. The
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iuc
parents: 17
diff changeset
1022 source of the black text is configured with the **style.label** option,
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1023 and the source of the blue text is configured with the
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1024 **style.description** option.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1025
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1026 Feature Score Scaling & Colouring Options
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1027 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1028
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1029 First, you need to choose between ignoring the score attribute of GFF3
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1030 files, or using it. If you choose to ignore it, all features will be
5614cf75bb24 Uploaded
iuc
parents: 17
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1031 coloured with a solid colour. If you choose to use it, features will
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1032 have slightly different colours based on their scores.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1033
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1034 .. image:: opacity.png
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parents: 17
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1035
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parents: 17
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1036 If you choose **Ignore score**, you may choose between automatically
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1037 choosing a colour, or manually specifying one. The automatically chosen
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1038 colours vary along a brewer palette and generally look quite nice with
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1039 no human intervention required. The manual colour choice is somewhat
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1040 self explanatory. Clicking on the small coloured square will bring up a
5614cf75bb24 Uploaded
iuc
parents: 17
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1041 colour palette.
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iuc
parents: 17
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1042
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1043 If you choose **Base on score**, you're faced with a dizzying array of
5614cf75bb24 Uploaded
iuc
parents: 17
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1044 options. First is the function to map the colour choices to colour
5614cf75bb24 Uploaded
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parents: 17
diff changeset
1045 values. JiG comes with a few functions built in such as linear scaling,
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1046 logarithmic scaling, and blast scaling.
5614cf75bb24 Uploaded
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parents: 17
diff changeset
1047
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1048 The **linear scaling** method says "take these values, and they map
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1049 directly to a range of output values". **Logarithmic scaling** says
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1050 "please take the log of the score before mapping", and **Blast scaling**
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1051 is further specialised to handle blast data more nicely. These are
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1052 convenience functions to help transform the wide array of possible
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1053 values in the GFF3 score attribute to more meaningful numbers. If you
5614cf75bb24 Uploaded
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parents: 17
diff changeset
1054 need more comprehensive score scaling, it is recommended that you
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1055 pre-process your GFF3 files somehow.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1056
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iuc
parents: 17
diff changeset
1057 Once you've selected a scaling method, you can choose to manually
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1058 specify the minimum and maximum expected values, or you can let JiG
5614cf75bb24 Uploaded
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parents: 17
diff changeset
1059 determine them for you automatically.
5614cf75bb24 Uploaded
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parents: 17
diff changeset
1060
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parents: 17
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1061 Finally, opacity is the only mapping we currently provide. Future
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1062 iterations will attempt to improve upon this and provide more colour
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1063 scales. The Opacity option maps the highest scoring features to full
5614cf75bb24 Uploaded
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parents: 17
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1064 opacity, and everything else to lower ones.
5614cf75bb24 Uploaded
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1065
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parents: 17
diff changeset
1066 BAM Pileups
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1067 ~~~~~~~~~~~
5614cf75bb24 Uploaded
iuc
parents: 17
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1068
5614cf75bb24 Uploaded
iuc
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1069 We support BAM files and can automatically generate SNP tracks based on
5614cf75bb24 Uploaded
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1070 that bam data.
5614cf75bb24 Uploaded
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parents: 17
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1071
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iuc
parents: 17
diff changeset
1072 .. image:: bam.png
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1073
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parents: 17
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1074 This is *strongly discouraged* for high coverage density datasets.
5614cf75bb24 Uploaded
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parents: 17
diff changeset
1075 Unfortunately there are no other configuration options exposed for bam
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1076 files. If you find JBrowse options you wish to see exposed, please let
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1077 `me <mailto:esr+jig@tamu.edu>`__ know.
5614cf75bb24 Uploaded
iuc
parents: 17
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1078
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iuc
parents: 17
diff changeset
1079 BlastXML
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1080 ~~~~~~~~
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1081
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iuc
parents: 17
diff changeset
1082 .. image:: blast.png
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iuc
parents: 17
diff changeset
1083
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iuc
parents: 17
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1084 JiG now supports both blastn and blastp datasets. JiG internally uses a
5614cf75bb24 Uploaded
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parents: 17
diff changeset
1085 blastXML to gapped GFF3 tool to convert your blastxml datasets into a
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parents: 29
diff changeset
1086 format amenable to visualization in JBrowse. This tool is also
29
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parents: 17
diff changeset
1087 available separately from the IUC on the toolshed.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1088
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1089 **Minimum Gap Size** reflects how long a gap must be before it becomes a
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1090 real gap in the processed gff3 file. In the picture above, various sizes
5614cf75bb24 Uploaded
iuc
parents: 17
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1091 of gaps can be seen. If the minimum gap size was set much higher, say
5614cf75bb24 Uploaded
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parents: 17
diff changeset
1092 100nt, many of the smaller gaps would disappear, and the features on
5614cf75bb24 Uploaded
iuc
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diff changeset
1093 both sides would be merged into one, longer feature. This setting is
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1094 inversely proportional to runtime and output file size. *Do not set this
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1095 to a low value for large datasets*. By setting this number lower, you
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1096 will have extremely large outputs and extremely long runtimes. The
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1097 default was configured based off of the author's experience, but the
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1098 author only works on small viruses. It is *strongly* recommended that
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1099 you filter your blast results before display, e.g. picking out the top
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1100 10 hits or so.
5614cf75bb24 Uploaded
iuc
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diff changeset
1101
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1102 **Protein blast search** option merely informs underlying tools that
5614cf75bb24 Uploaded
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parents: 17
diff changeset
1103 they should adjust feature locations by 3x.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1104
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1105 Styling Options
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1106 ^^^^^^^^^^^^^^^
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1107
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1108 Please see the styling options for GFF3 datasets, they are identical.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1109
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1110 Feature Score Scaling & Coloring Options
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1111 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1112
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iuc
parents: 17
diff changeset
1113 Please see the score scaling and colouring options for GFF3 datasets,
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1114 they are identical. Remember to set your score scaling to "blast" method
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1115 if you do use it.
5614cf75bb24 Uploaded
iuc
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diff changeset
1116
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1117 Bigwig XY
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1118 ~~~~~~~~~
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1119
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1120 .. image:: bigwig.png
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1121
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1122 **XYPlot**
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1123
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1124 BigWig tracks can be displayed as a "density" plot which is continuous
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iuc
parents: 29
diff changeset
1125 line which varies in colour, or as an "XYplot." XYplots are preferable
29
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1126 for users to visually identify specific features in a bigwig track,
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1127 however density tracks are more visually compact.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1128
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1129 **Variance Band** is an option available to XYPlots, and can be seen in
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1130 the third and fourth tracks in the above picture. This overlays a mean
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1131 line, and 1 and 2 standard deviation areas.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1132
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1133 **Track Scaling** is different from colour scaling, instead it
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1134 configures how the track behaves inside of JBrowse. **Autoscaling
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1135 globally** means that JBrowse will determine the minimum and maximum for
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1136 the track, and fix the bounds of the viewport to that. E.g. if your
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1137 track ranges from 1-1000, and the region you're currently zoomed to only
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1138 goes from 0-50, then the viewport range will still show 1-1000. This is
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1139 good for global genomic context. However you may wish to consider
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1140 **autoscaling locally** instead. In the example of a region which varies
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1141 from 0-50, autoscaling locally would cause the individual track's
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1142 viewport to re-adjust and show just the 0-50 region. If neither of these
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12d5699f92e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 29
diff changeset
1143 options are palatable, you may manually hardcode the minimum and
29
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1144 maximums for the track to scale to.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1145
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1146 Colour Options
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1147 ^^^^^^^^^^^^^^
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1148
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1149 BigWig tracks have two colours in JBrowse, a positive and a negative
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1150 colour.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1151
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1152 As always you may manually choose a colour, or let JiG choose for you.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1153
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1154 One of the more interesting options is the **Bicolor pivot**. This
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1155 option allows you to control the point at which JBrowse switches from
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1156 the positive colour to the negative. In the above graphic, you can see
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1157 this has been configured to "mean" for the first two (orange and blue)
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1158 tracks.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1159
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1160 VCFs/SNPs
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1161 ~~~~~~~~~
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1162
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1163 These tracks do not support any special configuration.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1164
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1165 Known Issues
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1166 ------------
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1167
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1168 - More than 30 landmark features cannot be listed in the manual
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1169 selector.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1170 - Non GFF3 likely has issue with automatically determined min/max
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1171 scores. Manually specify minimum and maximum score attributes, or do
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1172 not use varied colours based on scores to avoid this issue.
5614cf75bb24 Uploaded
iuc
parents: 17
diff changeset
1173
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iuc
parents: 4
diff changeset
1174
b55fad376d87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents: 4
diff changeset
1175 @ATTRIBUTION@
0
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iuc
parents:
diff changeset
1176 ]]></help>
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iuc
parents: 40
diff changeset
1177 <expand macro="citations"/>
0
c77c1d5baadb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
iuc
parents:
diff changeset
1178 </tool>