Mercurial > repos > iuc > jbrowse

annotate jbrowse.xml @ 35:3235aeb45c22 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 22ed9cb1e65cff5239df7ad4c76eaf0e981cf279"
author iuc
date Wed, 18 Dec 2019 10:46:52 -0500
parents 9de82b4963e6
children 7ed0827da5a8
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1 <tool id="jbrowse" name="JBrowse" version="@TOOL_VERSION@+@WRAPPER_VERSION@">
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2 <description>genome browser</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <version_command>python '${__tool_directory__}/jbrowse.py' --version</version_command>
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8 <command detect_errors="aggressive"><![CDATA[
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9 #if $action.action_select == "create":
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10 mkdir -p $output.files_path &&
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11 #else:
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12 cp -R $action.update_jbrowse.extra_files_path $output.files_path &&
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13 #end if
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14
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15 ## Copy the XML file into the directory, mostly for debugging
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16 ## but nice if users want to reproduce locally
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17 cp $trackxml $output.files_path/galaxy.xml &&
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19 export JBROWSE_SOURCE_DIR=\$(dirname \$(which prepare-refseqs.pl))/../opt/jbrowse &&
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20
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21 ## Once that's done, we run the python script to handle the real work
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22 python '$__tool_directory__/jbrowse.py'
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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 cp $output.files_path/index.html $output;
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34 #else:
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35 cp $dummyIndex $output;
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36 #end if
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37
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38 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph.
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39 #if str($uglyTestingHack) == "enabled":
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40 cp $trackxml $output
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41 #end if
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42 ]]></command>
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43 <configfiles>
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44 <configfile name="dummyIndex"><![CDATA[
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45 <html>
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46 <head>
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47 </head>
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48 <body>
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49 <h1>JBrowse Data Directory</h1>
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50 <p>
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51 Hi! This is not a full JBrowse instance. JBrowse v0.4(+?)
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52 started shipping with the ability to produce just the
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53 "data" directory from a JBrowse instance, rather than a
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54 complete, standalone instance. This was intended to be used
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55 with the in-development Apollo integration, but may have other
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56 uses as well.
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57 </p>
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58 <p>
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59 <u>This is not usable on its own</u>. The output dataset may be
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60 used with Apollo, or may be passed through the "JBrowse -
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61 Convert to Standalone" tool in Galaxy to "upgrade" to a full
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62 JBrowse instance.
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63 </p>
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64 </body>
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65 </html>
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66 ]]></configfile>
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67 <configfile name="trackxml"><![CDATA[<?xml version="1.0"?>
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68 <root>
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69 <metadata>
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70 <gencode>$gencode</gencode>
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71 <genomes>
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72 #if str($reference_genome.genome_type_select) == "indexed":
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73 <genome path="${reference_genome.genomes.fields.path}">
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74 <metadata />
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75 </genome>s
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76 #else
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77 <genome path="$reference_genome.genome">
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78 <metadata>
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79 <dataset id="${__app__.security.encode_id($reference_genome.genome.id)}" hid="${reference_genome.genome.hid}"
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80 size="${reference_genome.genome.get_size(nice_size=True)}"
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81 edam_format="${reference_genome.genome.datatype.edam_format}"
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82 file_ext="${reference_genome.genome.ext}" />
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83 <history id="${__app__.security.encode_id($reference_genome.genome.history_id)}"
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84 user_email="${reference_genome.genome.history.user.email}"
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85 user_id="${reference_genome.genome.history.user_id}"
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86 display_name="${reference_genome.genome.history.get_display_name()}"/>
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87 <metadata
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88 #for (key, value) in $reference_genome.genome.get_metadata().items():
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89 #if "_types" not in $key:
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90 ${key}="${value}"
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91 #end if
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92 #end for
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93 />
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94 <tool
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95 tool_id="${reference_genome.genome.creating_job.tool_id}"
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96 tool_version="${reference_genome.genome.creating_job.tool_version}"
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97 />
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98 </metadata>
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99 </genome>
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100 #end if
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101 </genomes>
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102 <general>
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103 <defaultLocation>${jbgen.defaultLocation}</defaultLocation>
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104 <trackPadding>${jbgen.trackPadding}</trackPadding>
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105
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106 <shareLink>${jbgen.shareLink}</shareLink>
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107 <aboutDescription>${jbgen.aboutDescription}</aboutDescription>
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108 <show_tracklist>${jbgen.show_tracklist}</show_tracklist>
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109 <show_nav>${jbgen.show_nav}</show_nav>
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110 <show_overview>${jbgen.show_overview}</show_overview>
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111 <show_menu>${jbgen.show_menu}</show_menu>
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112 <hideGenomeOptions>${jbgen.hideGenomeOptions}</hideGenomeOptions>
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113 </general>
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114 <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl>
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115 </metadata>
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116 <tracks>
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117 #for $tg in $track_groups:
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118 #for $track in $tg.data_tracks:
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119 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
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120 #if $track.data_format.data_format_select != "rest" and $track.data_format.data_format_select != "sparql":
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121 <files>
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122 #for $dataset in $track.data_format.annotation:
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123 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}">
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124 <metadata>
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125 <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}"
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126 size="${dataset.get_size(nice_size=True)}"
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127 edam_format="${dataset.datatype.edam_format}"
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128 file_ext="${dataset.ext}" />
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129 <history id="${__app__.security.encode_id($dataset.history_id)}"
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130 user_email="${dataset.history.user.email}"
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131 user_id="${dataset.history.user_id}"
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132 display_name="${dataset.history.get_display_name()}"/>
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133 <metadata
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134 #for (key, value) in $dataset.get_metadata().items():
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135 #if "_types" not in $key and $value is not None and len(str($value)) < 5000:
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136 ${key}="${value}"
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137 #end if
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138 #end for
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139 />
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140 <tool
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141 tool_id="${dataset.creating_job.tool_id}"
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142 tool_version="${dataset.creating_job.tool_version}"
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143 />
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144 </metadata>
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145 </trackFile>
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146 #end for
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147 </files>
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148 #end if
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149
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150 <options>
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151 #if str($track.data_format.data_format_select) == "gene_calls" or str($track.data_format.data_format_select) == "blast" or str($track.data_format.data_format_select) == "rest" or str($track.data_format.data_format_select) == "sparql":
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152 <style>
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153 <overridePlugins>${track.data_format.override_apollo_plugins}</overridePlugins>
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154 <overrideDraggable>${track.data_format.override_apollo_drag}</overrideDraggable>
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155 <className>${track.data_format.jbstyle.style_classname}</className>
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156 <description>${track.data_format.jbstyle.style_description}</description>
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157 <label>${track.data_format.jbstyle.style_label}</label>
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158 <height>${track.data_format.jbstyle.style_height}</height>
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159 <maxHeight>${track.data_format.jbstyle.max_height}</maxHeight>
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160 </style>
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161 <scaling>
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162 #if str($track.data_format.jbcolor_scale.color_score.color_score_select) == "none":
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163 <method>ignore</method>
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164 <scheme>
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165 #if str($track.data_format.jbcolor_scale.color_score.color.color_select) == "automatic":
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166 <color>__auto__</color>
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167 #else
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168 <color>${track.data_format.jbcolor_scale.color_score.color.style_color}</color>
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169 #end if
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170 </scheme>
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171 #else
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172 <method>score</method>
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173 <algo>${track.data_format.jbcolor_scale.color_score.score_scaling}</algo>
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174 <scales>
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175 <type>${track.data_format.jbcolor_scale.color_score.score_scales.scale_select}</type>
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176
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177 #if str($track.data_format.jbcolor_scale.color_score.score_scales.scale_select) == "manual":
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178 <min>${track.data_format.jbcolor_scale.color_score.score_scales.minimum}</min>
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179 <max>${track.data_format.jbcolor_scale.color_score.score_scales.maximum}</max>
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180 #end if
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181 </scales>
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182 <scheme>
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183 <type>${track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme}</type>
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184 ## auto_color
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185 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme) == "opacity":
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186 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.color.color_select) == "automatic":
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187 <color>__auto__</color>
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188 #else
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189 <color>${track.data_format.jbcolor_scale.color_score.color_scheme.color.style_color}</color>
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190 #end if
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191 #end if
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192 </scheme>
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193 #end if
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194 </scaling>
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195 <menus>
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196 #for $menu_item in $track.data_format.jbmenu.track_menu:
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197 <menu>
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198 <action>${menu_item.menu_action}</action>
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199 #if str($menu_item.menu_label) != "":
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200 <label>${menu_item.menu_label}</label>
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201 #end if
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202 #if str($menu_item.menu_title) != "":
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203 <title>${menu_item.menu_title}</title>
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204 #end if
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205 #if str($menu_item.menu_url) != "":
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206 <url>${menu_item.menu_url.replace("&", "&amp;").replace("\"", "&quot;")}</url>
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207 #end if
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208 #if str($menu_item.menu_icon) != "":
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209 <iconClass>${menu_item.menu_icon}</iconClass>
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210 #end if
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211 </menu>
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212 #end for
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213 </menus>
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214 #end if
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215 #if str($track.data_format.data_format_select) in ["gene_calls", "pileup", "blast", "wiggle", "vcf"]:
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216 <custom_config>
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217 #for $custom_option in $track.data_format.jb_custom_config.option:
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218 <${custom_option.opt_key}>
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219 <${custom_option.opt_value.val_type}>${$custom_option.opt_value.val}</${custom_option.opt_value.val_type}>
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220 </${custom_option.opt_key}>
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221 #end for
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222 </custom_config>
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223 #end if
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224
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225 #if str($track.data_format.data_format_select) == "wiggle":
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226 <wiggle>
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227 <type>${track.data_format.xyplot}</type>
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228 <variance_band>${track.data_format.var_band}</variance_band>
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229 #if str($track.data_format.scaling.scale_select) == "auto_local":
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230 <autoscale>local</autoscale>
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231 #else if str($track.data_format.scaling.scale_select) == "auto_global":
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232 <autoscale>global</autoscale>
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233 #else:
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234 <min>${track.data_format.scaling.minimum}</min>
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235 <max>${track.data_format.scaling.maximum}</max>
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236 #end if
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237 <scale>${track.data_format.scale_select2}</scale>
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238
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239 ## Wiggle tracks need special color config
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240 #if str($track.data_format.jbcolor.color.color_select) != "automatic":
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241 <color_pos>${track.data_format.jbcolor.color.style_pos_color}</color_pos>
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242 <color_neg>${track.data_format.jbcolor.color.style_neg_color}</color_neg>
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243 #else:
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244 <color_pos>__auto__</color_pos>
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245 <color_neg>__auto__</color_neg>
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246 #end if
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247
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248 ## Bicolor pivot config
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249 #if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "zero":
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250 <bicolor_pivot>zero</bicolor_pivot>
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251 #else if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "mean":
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252 <bicolor_pivot>mean</bicolor_pivot>
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253 #else:
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254 <bicolor_pivot>${track.data_format.jbcolor.bicolor_pivot.pivot_point}</bicolor_pivot>
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255 #end if
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256 <multibigwig>${track.data_format.MultiBigWig}</multibigwig>
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257 </wiggle>
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258 #else if str($track.data_format.data_format_select) == "pileup":
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259 <pileup>
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260 <auto_snp>${track.data_format.auto_snp}</auto_snp>
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261 <bam_indices>
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262 #for $dataset in $track.data_format.annotation:
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263 <bam_index>${dataset.metadata.bam_index}</bam_index>
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264 #end for
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265 </bam_indices>
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266 <chunkSizeLimit>${track.data_format.chunkSizeLimit}</chunkSizeLimit>
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267 </pileup>
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268 #else if str($track.data_format.data_format_select) == "blast":
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269 <blast>
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270 #if str($track.data_format.blast_parent) != "":
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271 <parent>${track.data_format.blast_parent}</parent>
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272 #end if
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273 <protein>${track.data_format.is_protein}</protein>
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274 <min_gap>${track.data_format.min_gap}</min_gap>
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275 <index>${track.data_format.index}</index>
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276 </blast>
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277 #else if str($track.data_format.data_format_select) == "gene_calls":
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278 <gff>
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279 <trackType>${track.data_format.track_config.track_class}</trackType>
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280 #if $track.data_format.track_config.track_class in ['JBrowse/View/Track/CanvasFeatures', 'NeatCanvasFeatures/View/Track/NeatFeatures']:
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281 #if str($track.data_format.track_config.canvas_options.transcriptType) != "":
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282 <transcriptType>${track.data_format.track_config.canvas_options.transcriptType}</transcriptType>
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283 #end if
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284 #if str($track.data_format.track_config.canvas_options.subParts) != "":
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285 <subParts>${track.data_format.track_config.canvas_options.subParts}</subParts>
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286 #end if
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287 #if str($track.data_format.track_config.canvas_options.impliedUTRs) != "false":
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288 <impliedUTRs>${track.data_format.track_config.canvas_options.impliedUTRs}</impliedUTRs>
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289 #end if
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290 #else if $track.data_format.track_config.track_class in ['JBrowse/View/Track/HTMLFeatures', 'NeatHTMLFeatures/View/Track/NeatFeatures']:
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291 #if str($track.data_format.track_config.html_options.topLevelFeatures) != "":
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292 <topLevelFeatures>${track.data_format.track_config.html_options.topLevelFeatures}</topLevelFeatures>
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293 #end if
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294 #end if
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295 #if $track.data_format.match_part.match_part_select:
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296 <match>${track.data_format.match_part.name}</match>
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297 #end if
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298 <index>${track.data_format.index}</index>
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299 </gff>
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300 #else if str($track.data_format.data_format_select) == "rest":
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301 <label>${track.data_format.label}</label>
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302 <rest>
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303 <url>${track.data_format.url}</url>
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304 </rest>
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305 #else if str($track.data_format.data_format_select) == "sparql":
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306 <label>${track.data_format.label}</label>
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307 <sparql>
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308 <url>${track.data_format.url}</url>
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309 <query>${track.data_format.query}</query>
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310 </sparql>
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311 #end if
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312 </options>
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313 </track>
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314 #end for
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315 #end for
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316 </tracks>
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317 ## Disable plugins until https://github.com/GMOD/jbrowse/issues/1288 is fixed
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318 ## <plugins
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319 ## ComboTrackSelector="${plugins.ComboTrackSelector}"
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320 ## Bookmarks="${plugins.Bookmarks}"
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321 ## GCContent="${plugins.GCContent}"
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322 ## BlastView="${plugins.BlastView}"
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323 ## theme="${plugins.theme}"
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324 ## />
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325 <plugins
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326 ComboTrackSelector="${plugins.ComboTrackSelector}"
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327 Bookmarks=""
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328 GCContent="${plugins.GCContent}"
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329 BlastView="${plugins.BlastView}"
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330 theme=""
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331 />
31
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332 </root>
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333 ]]></configfile>
1
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334 </configfiles>
0
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335 <inputs>
8
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336 <conditional name="reference_genome">
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337 <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select">
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338 <option selected="True" value="indexed">Use a built-in genome</option>
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339 <option value="history">Use a genome from history</option>
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340 </param>
8
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341 <when value="indexed">
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342 <param
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343 help="If your genome of interest is not listed, contact the Galaxy team"
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344 label="Select a reference genome"
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345 name="genomes"
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346 type="select"
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347 >
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348 <options from_data_table="all_fasta">
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349 <filter column="2" type="sort_by" />
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350 <validator message="No genomes are available for the selected input dataset" type="no_options" />
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351 </options>
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352 </param>
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353 </when>
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354 <when value="history">
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355 <param
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356 format="fasta"
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357 label="Select the reference genome"
25
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358 name="genome"
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359 type="data" />
5
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360 </when>
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361 </conditional>
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362
22
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parents: 21
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363 <param name="standalone" type="boolean" truevalue="Complete" falsevalue="Data Directory" checked="true" label="Produce Standalone Instance" help="Produce a full, working JBrowse instance or just the data directory. Data dir mode is experimental and intended to be used with Apollo"/>
3
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parents: 1
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364
22
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365 <param name="gencode" type="select" label="Genetic Code">
3
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parents: 1
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366 <option value="1">1. The Standard Code</option>
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parents: 1
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367 <option value="2">2. The Vertebrate Mitochondrial Code</option>
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368 <option value="3">3. The Yeast Mitochondrial Code</option>
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parents: 1
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369 <option value="4">4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
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370 <option value="5">5. The Invertebrate Mitochondrial Code</option>
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parents: 1
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371 <option value="6">6. The Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
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372 <option value="9">9. The Echinoderm and Flatworm Mitochondrial Code</option>
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parents: 1
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373 <option value="10">10. The Euplotid Nuclear Code</option>
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parents: 1
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374 <option value="11">11. The Bacterial, Archaeal and Plant Plastid Code</option>
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parents: 1
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375 <option value="12">12. The Alternative Yeast Nuclear Code</option>
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parents: 1
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376 <option value="13">13. The Ascidian Mitochondrial Code</option>
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parents: 1
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377 <option value="14">14. The Alternative Flatworm Mitochondrial Code</option>
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parents: 1
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378 <option value="16">16. Chlorophycean Mitochondrial Code</option>
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parents: 1
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379 <option value="21">21. Trematode Mitochondrial Code</option>
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parents: 1
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380 <option value="22">22. Scenedesmus obliquus Mitochondrial Code</option>
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parents: 1
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381 <option value="23">23. Thraustochytrium Mitochondrial Code</option>
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parents: 1
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382 <option value="24">24. Pterobranchia Mitochondrial Code</option>
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parents: 1
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383 <option value="25">25. Candidate Division SR1 and Gracilibacteria Code</option>
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parents: 1
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384 </param>
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385
8
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diff changeset
386 <conditional name="action">
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387 <param type="select" label="JBrowse-in-Galaxy Action" name="action_select">
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388 <option value="create">New JBrowse Instance</option>
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389 <option value="update">Update exising JBrowse Instance</option>
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390 </param>
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391 <when value="create" />
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392 <when value="update">
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393 <param name="update_jbrowse" type="data" format="html" label="Previous JBrowse Instance" />
8
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394 </when>
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395 </conditional>
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396
3
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parents: 1
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397 <repeat name="track_groups" title="Track Group">
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parents: 1
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398 <param label="Track Category"
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parents: 1
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399 name="category"
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parents: 1
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400 type="text"
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parents: 1
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401 value="Default"
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402 help="Organise your tracks into Categories for a nicer end-user experience. You can use #date# and it will be replaced with the current date in 'yyyy-mm-dd' format, which is very useful for repeatedly updating a JBrowse instance when member databases / underlying tool versions are updated." optional="False"/>
0
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403 <repeat name="data_tracks" title="Annotation Track">
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parents: 16
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404 <conditional name="data_format" label="Track Options">
1
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parents: 0
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405 <param type="select" label="Track Type" name="data_format_select">
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0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
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parents: 31
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406 <option value="gene_calls">GFF/GFF3/BED Features</option>
1
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parents: 0
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407 <option value="pileup">BAM Pileups</option>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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parents: 0
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408 <option value="blast">Blast XML</option>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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parents: 0
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409 <option value="wiggle">BigWig XY</option>
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parents: 0
diff changeset
410 <option value="vcf">VCF SNPs</option>
17
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parents: 16
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411 <option value="rest">REST Endpoint</option>
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412 <option value="sparql">SPARQL</option>
1
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parents: 0
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413 </param>
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parents: 0
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414 <when value="blast">
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parents: 1
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415 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" />
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parents: 0
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416
3
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parents: 1
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417 <param label="Features used in Blast Search"
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parents: 1
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418 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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419 format="gff3"
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parents: 1
diff changeset
420 name="blast_parent"
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parents: 1
diff changeset
421 optional="true"
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parents: 1
diff changeset
422 type="data"/>
1
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parents: 0
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423
3
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parents: 1
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424 <param label="Minimum Gap Size"
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parents: 1
diff changeset
425 help="before a new match_part feature is created"
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parents: 1
diff changeset
426 name="min_gap"
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parents: 1
diff changeset
427 type="integer"
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parents: 1
diff changeset
428 value="10"
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parents: 1
diff changeset
429 min="2" />
1
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parents: 0
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430 <param label="Is this a protein blast search?"
3
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parents: 1
diff changeset
431 type="boolean"
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parents: 1
diff changeset
432 name="is_protein"
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parents: 1
diff changeset
433 truevalue="true"
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parents: 1
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434 falsevalue="false" />
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parents: 1
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435
8
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parents: 6
diff changeset
436 <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" />
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437
3
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diff changeset
438 <expand macro="track_styling"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
439 classname="feature"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
440 label="description"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
441 description="Hit_titles"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
442 height="600px"/>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
443 <expand macro="color_selection"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
444 token_scaling_lin_select="false"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
445 token_scaling_log_select="true" />
31
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iuc
parents: 30
diff changeset
446 <expand macro="track_custom_config" />
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
447 <expand macro="track_menu" />
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
448 <expand macro="track_display" />
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
449 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
450 <when value="vcf">
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
451 <expand macro="input_conditional" label="SNP Track Data" format="vcf" />
31
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
452 <expand macro="track_custom_config" />
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
453 <expand macro="track_display" />
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
454 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
455 <when value="gene_calls">
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
456 <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" />
17
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iuc
parents: 16
diff changeset
457 <conditional name="match_part" label="match/match_part data">
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
458 <param label="This is match/match_part data"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
459 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
460 name="match_part_select"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
461 truevalue="true"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
462 falsevalue="false" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
463 <when value="true">
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
464 <param label="Match Part Feature Type"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
465 name="name"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
466 type="text"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
467 value="match"
21
1c718d8b3532 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9cac72c004cc7ef57be997e2fdafb3b1839a300f
iuc
parents: 19
diff changeset
468 help="Match_parts have several options for the parent feature type, such as cDNA_match, match, translated_nucleotide_match, etc. Please select the appropriate one here. You can leave empty to try autodetection (only works with CanvasFeatures track type)."
1c718d8b3532 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9cac72c004cc7ef57be997e2fdafb3b1839a300f
iuc
parents: 19
diff changeset
469 optional="True"/>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
470 </when>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
471 <when value="false" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
472 </conditional>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
473
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
474 <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
475
10
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
476 <conditional name="track_config">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
477 <param type="select" label="JBrowse Track Type [Advanced]" name="track_class">
26
08776ba76cf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 75f6e483debb4c0d388bf4a54df81ee89af598d5
iuc
parents: 25
diff changeset
478 <option value="NeatHTMLFeatures/View/Track/NeatFeatures" selected="true">Neat HTML Features</option>
08776ba76cf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 75f6e483debb4c0d388bf4a54df81ee89af598d5
iuc
parents: 25
diff changeset
479 <option value="NeatCanvasFeatures/View/Track/NeatFeatures">Neat Canvas Features</option>
10
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
480 <option value="JBrowse/View/Track/HTMLFeatures">HTML Features</option>
26
08776ba76cf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 75f6e483debb4c0d388bf4a54df81ee89af598d5
iuc
parents: 25
diff changeset
481 <option value="JBrowse/View/Track/CanvasFeatures">Canvas Features</option>
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
482 <option value="BlastView/View/Track/CanvasFeatures">Blast Features</option><!-- Disable plugins until https://github.com/GMOD/jbrowse/issues/1288 is fixed -->
10
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
483 </param>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
484 <when value="JBrowse/View/Track/CanvasFeatures">
27
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 26
diff changeset
485 <expand macro="canvas_options" />
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 26
diff changeset
486 </when>
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 26
diff changeset
487 <when value="JBrowse/View/Track/HTMLFeatures">
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 26
diff changeset
488 <expand macro="html_options" />
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 26
diff changeset
489 </when>
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 26
diff changeset
490 <when value="BlastView/View/Track/CanvasFeatures" />
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 26
diff changeset
491 <when value="NeatHTMLFeatures/View/Track/NeatFeatures">
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 26
diff changeset
492 <expand macro="html_options" />
26
08776ba76cf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 75f6e483debb4c0d388bf4a54df81ee89af598d5
iuc
parents: 25
diff changeset
493 </when>
27
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 26
diff changeset
494 <when value="NeatCanvasFeatures/View/Track/NeatFeatures">
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 26
diff changeset
495 <expand macro="canvas_options" />
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 26
diff changeset
496 </when>
10
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
497 </conditional>
27
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 26
diff changeset
498 <expand macro="track_styling"
30
ca2def38369c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 74554507efb46fb40ce6e12f0b73425e52ec0977
iuc
parents: 29
diff changeset
499 classname="feature"
27
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 26
diff changeset
500 label="product,name,id"
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 26
diff changeset
501 description="note,description"
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 26
diff changeset
502 height="10px"/>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
503 <expand macro="color_selection" />
31
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
504 <expand macro="track_custom_config" />
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
505 <expand macro="track_menu" />
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
506 <expand macro="track_display" />
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
507 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
508 <when value="pileup">
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
509 <expand macro="input_conditional" label="BAM Track Data" format="bam" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
510 <param label="Autogenerate SNP Track"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
511 help="Not recommended for deep coverage BAM files"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
512 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
513 name="auto_snp"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
514 truevalue="true"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
515 falsevalue="false" />
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
516 <param label="Maximum size of BAM chunks"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
517 name="chunkSizeLimit"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
518 type="integer"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
519 help="Maximum size in bytes of BAM chunks that the browser will try to deal with. When this is exceeded, most tracks will display 'Too much data' message."
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
520 value="5000000" />
31
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
521 <expand macro="track_custom_config" />
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
522 <expand macro="track_display" />
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
523 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
524 <when value="wiggle">
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
525 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
526
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
527 <param label="Use XYPlot"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
528 help="instead of continuous colored band"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
529 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
530 name="xyplot"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
531 truevalue="JBrowse/View/Track/Wiggle/XYPlot"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
532 falsevalue="JBrowse/View/Track/Wiggle/Density" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
533 <param label="Show variance band"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
534 help="Only for XYPlots"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
535 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
536 name="var_band"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
537 truevalue="true"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
538 falsevalue="false" />
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
539
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
540 <conditional name="scaling" label="Scaling">
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
541 <param type="select" label="Track Scaling" name="scale_select">
23
dba3c47e1798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit cf2c8f3039021b645ac45980a02ffe1f69a3f958
iuc
parents: 22
diff changeset
542 <option value="auto_local" selected="true">Autoscale (local)</option>
dba3c47e1798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit cf2c8f3039021b645ac45980a02ffe1f69a3f958
iuc
parents: 22
diff changeset
543 <option value="auto_global">Autoscale (global)</option>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
544 <option value="fixed">Specify Min/Max</option>
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
545 </param>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
546 <when value="auto_local"></when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
547 <when value="auto_global"></when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
548 <when value="fixed">
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
549 <param label="Track minimum" name="minimum"
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
550 type="integer" value="0" />
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
551 <param label="Track maximum" name="maximum"
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
552 type="integer" value="100" />
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
553 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
554 </conditional>
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
555 <param type="select" label="Visual Scaling" name="scale_select2">
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
556 <option value="linear" selected="true">Linear</option>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
557 <option value="log">Logarithmic (Dynamically Calculated)</option>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
558 </param>
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
559
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
560 <param label="Use MultiBigWig Plugin" name="MultiBigWig" truevalue="True" falsevalue="" type="boolean"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
561 help="MultiBigWig is a plugin to group multiple big-wig tracks in a more aesthetically pleasing format and to show data in a higher density display." />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
562
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
563 <expand macro="color_selection_minmax" />
31
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
564 <expand macro="track_custom_config" />
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
565 <expand macro="track_display" />
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
566 </when>
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
567 <when value="rest">
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
568 <param type="text" label="REST Endpoint" name="url" />
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
569 <param type="text" label="Track Label" name="label" value="REST Genes" />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
570 <expand macro="track_styling"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
571 classname="feature"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
572 label="description"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
573 description="Hit_titles"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
574 height="600px"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
575 <expand macro="color_selection"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
576 token_scaling_lin_select="false"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
577 token_scaling_log_select="true" />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
578 <expand macro="track_menu" />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
579 <expand macro="track_display" />
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
580 </when>
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
581
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
582 <when value="sparql">
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
583 <param type="text" label="SPARQL Server URL" name="url" />
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
584 <param type="text" label="Track Label" name="label" value="SPARQL Genes" />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
585 <param type="text" label="SPARQL Query" name="query" area="true">
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
586 <sanitizer>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
587 <mapping initial="galaxy.util.mapped_chars">
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
588 <add source="&#10;" target=" " />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
589 <add source="&gt;" target="__gt__" />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
590 <add source="&lt;" target="__lt__" />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
591 </mapping>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
592 <valid initial="default">
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
593 <add value="|" />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
594 <add value="#" />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
595 <add value="{"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
596 <add value="}"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
597 <add value="!"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
598 <add value="?"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
599 <add value="&amp;"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
600 <add value="+"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
601 <add value="="/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
602 <add value="'"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
603 <add value='"'/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
604 </valid>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
605 </sanitizer>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
606 </param>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
607 <expand macro="track_styling"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
608 classname="feature"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
609 label="description"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
610 description="Hit_titles"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
611 height="600px"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
612 <expand macro="color_selection"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
613 token_scaling_lin_select="false"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
614 token_scaling_log_select="true" />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
615 <expand macro="track_menu" />
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
616 <expand macro="track_display" />
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
617 </when>
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
618 </conditional>
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
619 </repeat>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
620 </repeat>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
621
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
622 <expand macro="general_options" />
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
623 <!-- Disable plugins until https://github.com/GMOD/jbrowse/issues/1288 is fixed -->
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
624 <section name="plugins" title="Plugins" expanded="false">
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
625
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
626 <param
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
627 label="BlastView" name="BlastView" truevalue="True" falsevalue="" type="boolean" checked="true"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
628 help="A JBrowse plugin for viewing blast alignments. This plugin makes MANY assumptions about the format of your data, and may not work without those assumptions: 1) you use protein_match / match_part 2) your features have a Blast_qseq, Blast_mseq, and Blast_sseq attribute in their GFF3 representation." />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
629
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
630 <param
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
631 label="Combo Track Selector" name="ComboTrackSelector" truevalue="True" falsevalue="" type="boolean"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
632 help="ComboTrackSelector is a plugin to allow the co-existence of the Hierarchical and Faceted Track selectors in JBrowse, built for/by the Arabidopsis Information Portal (Araport) project" />
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
633 <!-- No way to disable now that it's built in jbrowse conda package -->
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
634 <!--param
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
635 label="Bookmarks" name="Bookmarks" truevalue="True" falsevalue="" type="boolean"
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
636 help="JBrowse plugin allowing users to manage a persistent list of bookmarks kept in localstorage" /-->
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
637
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
638 <param
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
639 label="GC Content" name="GCContent" truevalue="True" falsevalue="" type="boolean"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
640 help="A JBrowse plugin for plotting GC Content and GC Skew. The plugin consists of a storeClass that automatically calculates the percentage of G/C bases in a region, a track type that derives from the Wiggle XY or density types, and a dialog box to adjust the sliding window size, window step size, and the calculation mode (content or skew)." />
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
641
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
642 <!--param type="select" label="JBrowse Theme" name="theme">
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
643 <option value="" selected="True">Default</option>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
644 <option value="Minimalist">Minimalist</option>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
645 <option value="Dark">Dark</option>
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
646 </param-->
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
647 </section>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
648
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
649 <param type="hidden" name="uglyTestingHack" value="" />
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
650 </inputs>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
651 <outputs>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
652 <data format="html" name="output" label="JBrowse on $on_string - $standalone"/>
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
653 </outputs>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
654 <tests>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
655 <test>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
656 <!-- gencode -->
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
657 <param name="reference_genome|genome_type_select" value="history"/>
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
658 <param name="reference_genome|genome" value="merlin.fa"/>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
659 <param name="gencode" value="1" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
660 <param name="standalone" value="Data Directory" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
661 <param name="uglyTestingHack" value="enabled" />
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2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
662 <output name="output" file="gencode/test-1.xml" lines_diff="16"/>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
663 </test>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
664 <test>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
665 <param name="reference_genome|genome_type_select" value="history"/>
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
666 <param name="reference_genome|genome" value="merlin.fa"/>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
667 <param name="gencode" value="11" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
668 <param name="standalone" value="Data Directory" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
669 <param name="uglyTestingHack" value="enabled" />
31
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
670 <output name="output" file="gencode/test.xml" lines_diff="16"/>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
671 </test>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
672 <test>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
673 <param name="reference_genome|genome_type_select" value="history"/>
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
674 <param name="reference_genome|genome" value="merlin.fa"/>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
675 <param name="gencode" value="11" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
676 <param name="standalone" value="Data Directory" />
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
677 <repeat name="track_groups">
34
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents: 33
diff changeset
678 <param name="category" value="Default" />
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents: 33
diff changeset
679 <repeat name="data_tracks">
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents: 33
diff changeset
680 <conditional name="data_format">
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents: 33
diff changeset
681 <param name="data_format_select" value="gene_calls"/>
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents: 33
diff changeset
682 <param name="annotation" value="bed/test-3.bed,bed/test-6.bed"/>
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents: 33
diff changeset
683 </conditional>
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents: 33
diff changeset
684 </repeat>
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents: 33
diff changeset
685 </repeat>
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents: 33
diff changeset
686 <param name="uglyTestingHack" value="enabled" />
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents: 33
diff changeset
687 <output name="output" file="bed/test.xml" lines_diff="32"/>
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents: 33
diff changeset
688 </test>
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents: 33
diff changeset
689 <test>
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents: 33
diff changeset
690 <param name="reference_genome|genome_type_select" value="history"/>
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents: 33
diff changeset
691 <param name="reference_genome|genome" value="merlin.fa"/>
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents: 33
diff changeset
692 <param name="gencode" value="11" />
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents: 33
diff changeset
693 <param name="standalone" value="Data Directory" />
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents: 33
diff changeset
694 <repeat name="track_groups">
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
695 <param name="category" value="Auto Coloured" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
696 <repeat name="data_tracks">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
697 <conditional name="data_format">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
698 <param name="data_format_select" value="gene_calls"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
699 <param name="annotation" value="gff3/A.gff,gff3/B.gff,gff3/C.gff,gff3/D.gff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
700 <conditional name="match_part">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
701 <param name="match_part_select" value="false"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
702 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
703 <section name="jbcolor_scale">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
704 <conditional name="color_score">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
705 <param name="color_score_select" value="none"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
706 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
707 <conditional name="color">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
708 <param name="color_select" value="automatic"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
709 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
710 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
711 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
712 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
713 </repeat>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
714
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
715 <repeat name="track_groups">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
716 <param name="category" value="Ignore Scale" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
717 <repeat name="data_tracks">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
718 <conditional name="data_format">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
719 <param name="data_format_select" value="gene_calls"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
720 <param name="annotation" value="gff3/1.gff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
721 <conditional name="match_part">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
722 <param name="match_part_select" value="false"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
723 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
724 <section name="jbcolor_scale">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
725 <conditional name="color_score">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
726 <param name="color_score_select" value="none"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
727 <conditional name="color">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
728 <param name="color_select" value="manual"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
729 <param name="style_color" value="#ff00ff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
730 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
731 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
732 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
733 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
734 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
735 </repeat>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
736
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
737 <repeat name="track_groups">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
738 <param name="category" value="Scaled Colour" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
739 <repeat name="data_tracks">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
740 <conditional name="data_format">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
741 <param name="data_format_select" value="gene_calls"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
742 <param name="annotation" value="gff3/1.gff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
743 <conditional name="match_part">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
744 <param name="match_part_select" value="false"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
745 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
746 <section name="jbcolor_scale">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
747 <conditional name="color_score">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
748 <param name="color_score_select" value="score"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
749 <param name="score_scaling" value="linear"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
750 <conditional name="score_scales">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
751 <param name="scale_select" value="automatic"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
752 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
753 <conditional name="color_scheme">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
754 <param name="score_scheme" value="opacity"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
755 <conditional name="color">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
756 <param name="color_select" value="automatic"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
757 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
758 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
759 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
760 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
761 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
762 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
763 <repeat name="data_tracks">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
764 <conditional name="data_format">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
765 <param name="data_format_select" value="gene_calls"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
766 <param name="annotation" value="gff3/1.gff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
767 <conditional name="match_part">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
768 <param name="match_part_select" value="false"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
769 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
770 <section name="jbcolor_scale">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
771 <conditional name="color_score">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
772 <param name="color_score_select" value="score"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
773 <param name="score_scaling" value="linear"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
774 <conditional name="score_scales">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
775 <param name="scale_select" value="automatic"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
776 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
777 <conditional name="color_scheme">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
778 <param name="score_scheme" value="opacity"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
779 <conditional name="color">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
780 <param name="color_select" value="manual"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
781 <param name="style_color" value="#0000ff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
782 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
783 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
784 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
785 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
786 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
787 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
788 <repeat name="data_tracks">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
789 <conditional name="data_format">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
790 <param name="data_format_select" value="gene_calls"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
791 <param name="annotation" value="gff3/1.gff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
792 <conditional name="match_part">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
793 <param name="match_part_select" value="false"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
794 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
795 <section name="jbcolor_scale">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
796 <conditional name="color_score">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
797 <param name="color_score_select" value="score"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
798 <param name="score_scaling" value="linear"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
799 <conditional name="score_scales">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
800 <param name="scale_select" value="manual"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
801 <param name="minimum" value="0"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
802 <param name="maximum" value="1000"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
803 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
804 <conditional name="color_scheme">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
805 <param name="score_scheme" value="opacity"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
806 <conditional name="color">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
807 <param name="color_select" value="automatic"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
808 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
809 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
810 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
811 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
812 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
813 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
814 <repeat name="data_tracks">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
815 <conditional name="data_format">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
816 <param name="data_format_select" value="gene_calls"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
817 <param name="annotation" value="gff3/1.gff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
818 <conditional name="match_part">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
819 <param name="match_part_select" value="false"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
820 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
821 <section name="jbcolor_scale">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
822 <conditional name="color_score">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
823 <param name="color_score_select" value="score"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
824 <param name="score_scaling" value="linear"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
825 <conditional name="score_scales">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
826 <param name="scale_select" value="manual"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
827 <param name="minimum" value="0"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
828 <param name="maximum" value="1000"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
829 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
830 <conditional name="color_scheme">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
831 <param name="score_scheme" value="opacity"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
832 <conditional name="color">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
833 <param name="color_select" value="manual"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
834 <param name="style_color" value="#ff0000"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
835 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
836 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
837 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
838 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
839 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
840 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
841 </repeat>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
842
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
843 <repeat name="track_groups">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
844 <param name="category" value="Realistic" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
845 <repeat name="data_tracks">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
846 <conditional name="data_format">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
847 <param name="data_format_select" value="gene_calls"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
848 <param name="annotation" value="gff3/interpro.gff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
849 <conditional name="match_part">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
850 <param name="match_part_select" value="false"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
851 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
852 <section name="jbcolor_scale">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
853 <conditional name="color_score">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
854 <param name="color_score_select" value="none"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
855 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
856 <conditional name="color">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
857 <param name="color_select" value="automatic"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
858 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
859 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
860 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
861 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
862 <repeat name="data_tracks">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
863 <conditional name="data_format">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
864 <param name="data_format_select" value="gene_calls"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
865 <param name="annotation" value="gff3/2.gff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
866 <conditional name="match_part">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
867 <param name="match_part_select" value="true"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
868 <param name="name" value="cDNA_match"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
869 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
870 <section name="jbcolor_scale">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
871 <conditional name="color_score">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
872 <param name="color_score_select" value="none"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
873 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
874 <conditional name="color">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
875 <param name="color_select" value="automatic"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
876 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
877 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
878 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
879 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
880 </repeat>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
881
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
882 <param name="uglyTestingHack" value="enabled" />
34
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents: 33
diff changeset
883 <output name="output" file="gff3/test.xml" lines_diff="240" />
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
884 </test>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
885 <test>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
886 <param name="reference_genome|genome_type_select" value="history"/>
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
887 <param name="reference_genome|genome" value="merlin.fa"/>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
888 <param name="gencode" value="11" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
889 <param name="standalone" value="Data Directory" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
890
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
891 <repeat name="track_groups">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
892 <param name="category" value="With menu or index" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
893 <repeat name="data_tracks">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
894 <conditional name="data_format">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
895 <param name="data_format_select" value="gene_calls"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
896 <param name="annotation" value="gff3/1.gff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
897 <conditional name="match_part">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
898 <param name="match_part_select" value="false"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
899 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
900 <section name="jbcolor_scale">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
901 <conditional name="color_score">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
902 <param name="color_score_select" value="none"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
903 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
904 <conditional name="color">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
905 <param name="color_select" value="automatic"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
906 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
907 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
908 <section name="jbmenu">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
909 <repeat name="track_menu">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
910 <param name="menu_action" value="iframeDialog"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
911 <param name="menu_label" value="Some menu item"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
912 <param name="menu_title" value="Frame title"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
913 <param name="menu_url" value="https://example.com/#!/?id={name}&amp;q={type}&amp;z=&quot;{end}&quot;"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
914 <param name="menu_icon" value="dijitIconNewTask"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
915 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
916 <repeat name="track_menu">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
917 <param name="menu_action" value="newWindow"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
918 <param name="menu_label" value="Another menu item"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
919 <param name="menu_title" value="Frame title 2"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
920 <param name="menu_url" value="https://example.com/#!/?id={name}&amp;q={type}&amp;z=&quot;{end}&quot;"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
921 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
922 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
923 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
924 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
925 <repeat name="data_tracks">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
926 <conditional name="data_format">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
927 <param name="data_format_select" value="gene_calls"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
928 <param name="annotation" value="gff3/1.gff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
929 <param name="index" value="true"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
930 <conditional name="match_part">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
931 <param name="match_part_select" value="false"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
932 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
933 <section name="jbcolor_scale">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
934 <conditional name="color_score">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
935 <param name="color_score_select" value="none"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
936 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
937 <conditional name="color">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
938 <param name="color_select" value="automatic"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
939 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
940 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
941 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
942 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
943 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
944
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
945 <param name="uglyTestingHack" value="enabled" />
31
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
946 <output name="output" file="menus/test.xml" lines_diff="44"/>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
947 </test>
10
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
948 <test>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
949 <param name="reference_genome|genome_type_select" value="history"/>
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
950 <param name="reference_genome|genome" value="merlin.fa"/>
10
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
951 <param name="gencode" value="11" />
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
952 <param name="standalone" value="Data Directory" />
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
953
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
954 <repeat name="track_groups">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
955 <param name="category" value="With canvas config" />
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
956 <repeat name="data_tracks">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
957 <conditional name="data_format">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
958 <param name="data_format_select" value="gene_calls"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
959 <param name="annotation" value="gff3/1.gff"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
960 <conditional name="match_part">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
961 <param name="match_part_select" value="false"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
962 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
963 <conditional name="track_config">
31
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
964 <param name="track_class" value="JBrowse/View/Track/CanvasFeatures"/>
10
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
965 <section name="canvas_options">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
966 <param name="transcriptType" value="transcript"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
967 <param name="subParts" value="exon"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
968 <param name="impliedUTRs" value="true"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
969 </section>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
970 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
971 <section name="jbcolor_scale">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
972 <conditional name="color_score">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
973 <param name="color_score_select" value="none"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
974 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
975 <conditional name="color">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
976 <param name="color_select" value="automatic"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
977 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
978 </section>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
979 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
980 </repeat>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
981 </repeat>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
982
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
983 <param name="uglyTestingHack" value="enabled" />
31
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
984 <output name="output" file="track_config/test.xml" lines_diff="30"/>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
985 </test>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
986 <test>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
987 <param name="reference_genome|genome_type_select" value="history"/>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
988 <param name="reference_genome|genome" value="merlin.fa"/>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
989 <param name="gencode" value="11" />
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
990 <param name="standalone" value="Data Directory" />
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
991
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
992 <repeat name="track_groups">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
993 <param name="category" value="With custom track config" />
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
994 <repeat name="data_tracks">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
995 <conditional name="data_format">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
996 <param name="data_format_select" value="gene_calls"/>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
997 <param name="annotation" value="gff3/1.gff"/>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
998 <conditional name="match_part">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
999 <param name="match_part_select" value="false"/>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1000 </conditional>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1001 <section name="jb_custom_config">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1002 <repeat name="option">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1003 <param name="opt_key" value="displayMode"/>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1004 <conditional name="opt_value">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1005 <param name="val_type" value="text"/>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1006 <param name="val" value="collapsed"/>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1007 </conditional>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1008 </repeat>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1009 <repeat name="option">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1010 <param name="opt_key" value="histograms.height"/>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1011 <conditional name="opt_value">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1012 <param name="val_type" value="integer"/>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1013 <param name="val" value="150"/>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1014 </conditional>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1015 </repeat>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1016 <repeat name="option">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1017 <param name="opt_key" value="maxFeatureScreenDensity"/>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1018 <conditional name="opt_value">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1019 <param name="val_type" value="float"/>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1020 <param name="val" value="0.1"/>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1021 </conditional>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1022 </repeat>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1023 <repeat name="option">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1024 <param name="opt_key" value="style.strandArrow"/>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1025 <conditional name="opt_value">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1026 <param name="val_type" value="boolean"/>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1027 <param name="val" value="false"/>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1028 </conditional>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1029 </repeat>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1030 </section>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1031 </conditional>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1032 </repeat>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1033 </repeat>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1034
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1035 <param name="uglyTestingHack" value="enabled" />
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1036 <output name="output" file="custom_config/test.xml" lines_diff="30"/>
10
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
1037 </test>
18
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 17
diff changeset
1038 <test>
19
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
1039 <param name="reference_genome|genome_type_select" value="history"/>
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1040 <param name="reference_genome|genome" value="merlin.fa"/>
19
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
1041 <param name="gencode" value="11" />
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
1042 <param name="standalone" value="Data Directory" />
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
1043
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
1044 <repeat name="track_groups">
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
1045 <param name="category" value="Auto Coloured" />
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
1046 <repeat name="data_tracks">
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
1047 <conditional name="data_format">
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
1048 <param name="data_format_select" value="pileup"/>
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
1049 <param name="annotation" value="bam/merlin-sample.bam"/>
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
1050 </conditional>
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
1051 </repeat>
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
1052 </repeat>
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
1053
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
1054 <param name="uglyTestingHack" value="enabled" />
31
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1055 <output name="output" file="bam/test.xml" lines_diff="42"/>
19
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
1056 </test>
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
1057
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
1058 <test>
18
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 17
diff changeset
1059 <!-- data_table -->
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 17
diff changeset
1060 <param name="reference_genome|genome_type_select" value="indexed"/>
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1061 <param name="reference_genome|genome" value="merlin"/>
18
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 17
diff changeset
1062 <param name="gencode" value="1" />
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 17
diff changeset
1063 <param name="standalone" value="Data Directory" />
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 17
diff changeset
1064 <param name="uglyTestingHack" value="enabled" />
31
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1065 <output name="output" file="gencode/test-data_table.xml" lines_diff="4" />
18
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 17
diff changeset
1066 </test>
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1067
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1068 <test>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1069 <param name="reference_genome|genome_type_select" value="history"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1070 <param name="reference_genome|genome" value="merlin.fa"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1071 <param name="gencode" value="11" />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1072 <param name="standalone" value="Data Directory" />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1073
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1074 <repeat name="track_groups">
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1075 <param name="category" value="External endpoints" />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1076 <repeat name="data_tracks">
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1077 <conditional name="data_format">
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1078 <param name="data_format_select" value="rest"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1079 <param name="url" value="http://example.org.external/rest_api/"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1080 <param name="label" value="Rest api"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1081 </conditional>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1082 </repeat>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1083 <repeat name="data_tracks">
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1084 <conditional name="data_format">
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1085 <param name="data_format_select" value="sparql"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
1086 <param name="url" value="http://example.org.external/sparql/"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
1087 <param name="label" value="Sparql endpoint"/>
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diff changeset
1088 <param name="query" value=" DEFINE sql:select-option 'order'
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
1089 prefix rdf: &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#&gt;
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
1090 select ?start,
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parents: 23
diff changeset
1091 ?end,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1092 IF( ?faldo_type = faldo:ForwardStrandPosition,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1093 1,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1094 IF( ?faldo_type = faldo:ReverseStrandPosition,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1095 -1,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1096 0
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1097 )
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1098 ) as ?strand,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1099 str(?obj_type_name) as ?type,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1100 str(?label) as ?name,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
1101 str(?obj_name) as ?description,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1102 ?obj as ?uniqueID,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
1103 ?parent as ?parentUniqueID
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
1104 where {
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
1105 values ?faldo_type { faldo:ForwardStrandPosition faldo:ReverseStrandPosition faldo:BothStrandsPosition }
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
1106 }"/>
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diff changeset
1107 </conditional>
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diff changeset
1108 </repeat>
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diff changeset
1109 </repeat>
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diff changeset
1110
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diff changeset
1111 <param name="uglyTestingHack" value="enabled" />
31
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diff changeset
1112 <output name="output" file="endpoints/test.xml" lines_diff="16"/>
25
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diff changeset
1113 </test>
3
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diff changeset
1114 </tests>
0
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parents:
diff changeset
1115 <help><![CDATA[
3
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parents: 1
diff changeset
1116 JBrowse-in-Galaxy
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1117 =================
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parents: 1
diff changeset
1118
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parents: 1
diff changeset
1119 JBrowse-in-Galaxy offers a highly configurable, workflow-compatible
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parents: 1
diff changeset
1120 alternative to Trackster.
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diff changeset
1121
17
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diff changeset
1122 Overview
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diff changeset
1123 --------
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diff changeset
1124
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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diff changeset
1125 JBrowse is a fast, embeddable genome browser built completely with
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diff changeset
1126 JavaScript and HTML5.
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diff changeset
1127
3
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parents: 1
diff changeset
1128 The JBrowse-in-Galaxy (JiG) tool was written to help build complex
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1129 JBrowse installations straight from Galaxy, taking advantage of the
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iuc
parents: 1
diff changeset
1130 latest Galaxy features such as dataset collections, sections, and colour
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1131 pickers. It allows you to build up a JBrowse instance without worrying
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parents: 1
diff changeset
1132 about how to run the command line tools to format your data, and which
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1133 options need to be supplied and where. Additionally it comes with many
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1134 javascript functions to handle colouring of features which would be
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1135 nearly impossible to write without the assistance of this tool.
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1136
25
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diff changeset
1137 The JBrowse-in-Galaxy tool is maintained by `the Galaxy IUC
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
1138 <https://github.com/galaxyproject/tools-iuc/issues>`__, who you can help you
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
1139 with missing features or bugs in the tool.
3
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iuc
parents: 1
diff changeset
1140
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parents: 1
diff changeset
1141 Options
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parents: 1
diff changeset
1142 -------
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1143
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1144 The first option you encounter is the **Fasta Sequence(s)**. This option
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iuc
parents: 1
diff changeset
1145 now accepts multiple fasta files, allowing you to build JBrowse
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1146 instances that contain data for multiple genomes or chrosomomes
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1147 (generally known as "landmark features" in gff3 terminology.) Up to 30
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1148 will be shown from the dropdown selector within JBrowse, this is a known
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1149 issue.
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1150
25
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diff changeset
1151 **Standalone Instances** enable you to have either a complete JBrowse instance
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
1152 in a dataset, or just the data directory without JBrowse (e.g. for Apollo).
3
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parents: 1
diff changeset
1153 Currently Galaxy copies the entire JBrowse directory in order to have a
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1154 complete, downloadable file that contains a ready-to-go JBrowse
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1155 instance. This is obviously an anti-feature because users don't want a
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
1156 complete copy of JBrowse (12Mb) that's duplicated for every JBrowse
3
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parents: 1
diff changeset
1157 dataset in their history, and admins don't want useless copies of
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1158 JBrowse on disk. Unfortunately we have not come up with the perfect
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1159 solution just yet, but we're working on it! In the meantime, users have
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1160 been given the option to produce just the ``data/`` directory. For those
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1161 unfamiliar with JBrowse, the ``data/`` directory contains processed data
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1162 files, but no way to view them. This feature is additionally implemented
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1163 for upcoming `Apollo <https://github.com/gmod/apollo>`__ integration.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1164
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1165 **Genetic Code** is a new feature in v0.4 of JiG / v1.12.0 of JBrowse,
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1166 which allows users to specify a non standard genetic code, and have
25
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diff changeset
1167 JBrowse highlight the correct start and stop codons.
3
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iuc
parents: 1
diff changeset
1168
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1169 **Track Groups** represent a set of tracks in a single category. These
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1170 can be used to let your users understand relationships between large
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iuc
parents: 1
diff changeset
1171 groups of tracks.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1172
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1173 .. image:: sections.png
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1174
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1175 Annotation Tracks
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1176 -----------------
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1177
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1178 Within Track Groups, you have one or more **Annotation Tracks**. Each
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1179 Annotation Track is a groups of datasets which have similar styling.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1180 This allows you to rapidly build up JBrowse instances without having to
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1181 configure tracks individually. A massive improvement over previous
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1182 versions. For example, if you have five different GFF3 files from
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1183 various gene callers that you wish to display, you can take advantage of
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1184 this feature to style all of them similarly.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1185
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1186 There are a few different types of tracks supported, each with their own
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1187 set of options:
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1188
33
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parents: 31
diff changeset
1189 GFF3/BED
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diff changeset
1190 ~~~~~~~~
3
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parents: 1
diff changeset
1191
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iuc
parents: 1
diff changeset
1192 These are your standard feature tracks. They usually highlight genes,
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1193 mRNAs and other features of interest along a genomic region. The
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1194 underlying tool and this help documentation focus primarily on GFF3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1195 data, and have not been tested extensively with other formats. Automatic
33
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diff changeset
1196 min/max detection will fail under BED datasets.
3
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iuc
parents: 1
diff changeset
1197
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1198 The data may be of a subclass we call **match/match part** data. This
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1199 consists of top level ``match`` features, with a child ``match_part``
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1200 feature, and is often used in displaying alignments. (See "Alignments"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1201 section on the `GFF3
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 6
diff changeset
1202 specification <https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md>`__ for more
3
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1203 information). If the data is match/match part, you will need to specify
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1204 the top level match feature name, as it can be one of a few different SO
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1205 terms, and JiG does not yet have the ability to understand SO terms.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1206
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1207 Next up is the **Styling Options** section, which lets you control a few
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1208 properties on how the track is styled. Most of these you will not need
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1209 to configure and can safely leave on defaults. Occasionally you will
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1210 want to change what information is shown in the end product.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1211
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1212 .. image:: styling.png
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1213
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1214 In the above image you can see some black text, and some blue text. The
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1215 source of the black text is configured with the **style.label** option,
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1216 and the source of the blue text is configured with the
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1217 **style.description** option.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1218
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1219 Feature Score Scaling & Colouring Options
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1220 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1221
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1222 First, you need to choose between ignoring the score attribute of GFF3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1223 files, or using it. If you choose to ignore it, all features will be
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1224 coloured with a solid colour. If you choose to use it, features will
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1225 have slightly different colours based on their scores.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1226
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1227 .. image:: opacity.png
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1228
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1229 If you choose **Ignore score**, you may choose between automatically
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1230 choosing a colour, or manually specifying one. The automatically chosen
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1231 colours vary along a brewer palette and generally look quite nice with
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1232 no human intervention required. The manual colour choice is somewhat
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1233 self explanatory. Clicking on the small coloured square will bring up a
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1234 colour palette.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1235
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1236 If you choose **Base on score**, you're faced with a dizzying array of
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1237 options. First is the function to map the colour choices to colour
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1238 values. JiG comes with a few functions built in such as linear scaling,
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1239 logarithmic scaling, and blast scaling.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1240
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1241 The **linear scaling** method says "take these values, and they map
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1242 directly to a range of output values". **Logarithmic scaling** says
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1243 "please take the log of the score before mapping", and **Blast scaling**
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1244 is further specialised to handle blast data more nicely. These are
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1245 convenience functions to help transform the wide array of possible
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1246 values in the GFF3 score attribute to more meaningful numbers. If you
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1247 need more comprehensive score scaling, it is recommended that you
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1248 pre-process your GFF3 files somehow.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1249
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1250 Once you've selected a scaling method, you can choose to manually
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1251 specify the minimum and maximum expected values, or you can let JiG
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1252 determine them for you automatically.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1253
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1254 Finally, opacity is the only mapping we currently provide. Future
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1255 iterations will attempt to improve upon this and provide more colour
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1256 scales. The Opacity option maps the highest scoring features to full
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1257 opacity, and everything else to lower ones.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1258
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1259 BAM Pileups
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1260 ~~~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1261
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1262 We support BAM files and can automatically generate SNP tracks based on
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1263 that bam data.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1264
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1265 .. image:: bam.png
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1266
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1267 This is *strongly discouraged* for high coverage density datasets.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1268 Unfortunately there are no other configuration options exposed for bam
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1269 files.
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1270
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1271 BlastXML
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1272 ~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1273
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1274 .. image:: blast.png
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1275
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1276 JiG now supports both blastn and blastp datasets. JiG internally uses a
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1277 blastXML to gapped GFF3 tool to convert your blastxml datasets into a
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1278 format amenable to visualization in JBrowse. This tool is also
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1279 available separately from the IUC on the toolshed.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1280
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1281 **Minimum Gap Size** reflects how long a gap must be before it becomes a
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1282 real gap in the processed gff3 file. In the picture above, various sizes
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1283 of gaps can be seen. If the minimum gap size was set much higher, say
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1284 100nt, many of the smaller gaps would disappear, and the features on
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1285 both sides would be merged into one, longer feature. This setting is
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1286 inversely proportional to runtime and output file size. *Do not set this
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1287 to a low value for large datasets*. By setting this number lower, you
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1288 will have extremely large outputs and extremely long runtimes. The
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1289 default was configured based off of the author's experience, but the
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1290 author only works on small viruses. It is *strongly* recommended that
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1291 you filter your blast results before display, e.g. picking out the top
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1292 10 hits or so.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1293
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1294 **Protein blast search** option merely informs underlying tools that
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1295 they should adjust feature locations by 3x.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1296
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1297 Styling Options
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1298 ^^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1299
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1300 Please see the styling options for GFF3 datasets, they are identical.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1301
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1302 Feature Score Scaling & Coloring Options
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1303 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1304
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1305 Please see the score scaling and colouring options for GFF3 datasets,
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1306 they are identical. Remember to set your score scaling to "blast" method
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1307 if you do use it.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1308
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1309 Bigwig XY
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1310 ~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1311
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1312 .. image:: bigwig.png
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1313
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1314 **XYPlot**
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1315
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1316 BigWig tracks can be displayed as a "density" plot which is continuous
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1317 line which varies in colour, or as an "XYplot." XYplots are preferable
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1318 for users to visually identify specific features in a bigwig track,
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1319 however density tracks are more visually compact.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1320
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1321 **Variance Band** is an option available to XYPlots, and can be seen in
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1322 the third and fourth tracks in the above picture. This overlays a mean
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1323 line, and 1 and 2 standard deviation areas.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1324
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1325 **Track Scaling** is different from colour scaling, instead it
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1326 configures how the track behaves inside of JBrowse. **Autoscaling
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1327 globally** means that JBrowse will determine the minimum and maximum for
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1328 the track, and fix the bounds of the viewport to that. E.g. if your
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1329 track ranges from 1-1000, and the region you're currently zoomed to only
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1330 goes from 0-50, then the viewport range will still show 1-1000. This is
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1331 good for global genomic context. However you may wish to consider
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1332 **autoscaling locally** instead. In the example of a region which varies
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1333 from 0-50, autoscaling locally would cause the individual track's
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1334 viewport to re-adjust and show just the 0-50 region. If neither of these
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1335 options are palatable, you may manually hardcode the minimum and
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1336 maximums for the track to scale to.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1337
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1338 Colour Options
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1339 ^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1340
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1341 BigWig tracks have two colours in JBrowse, a positive and a negative
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1342 colour.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1343
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1344 As always you may manually choose a colour, or let JiG choose for you.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1345
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1346 One of the more interesting options is the **Bicolor pivot**. This
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1347 option allows you to control the point at which JBrowse switches from
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1348 the positive colour to the negative. In the above graphic, you can see
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1349 this has been configured to "mean" for the first two (orange and blue)
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1350 tracks.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1351
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1352 VCFs/SNPs
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1353 ~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1354
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1355 These tracks do not support any special configuration.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1356
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1357 Known Issues
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1358 ------------
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1359
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1360 - More than 30 landmark features cannot be listed in the manual
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1361 selector.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1362 - Non GFF3 likely has issue with automatically determined min/max
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1363 scores. Manually specify minimum and maximum score attributes, or do
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1364 not use varied colours based on scores to avoid this issue.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1365
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
1366 @ATTRIBUTION@
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
1367 ]]></help>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
1368 <expand macro="citations"/>
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
1369 </tool>