Mercurial > repos > iuc > jbrowse

annotate jbrowse.xml @ 41:8774b28235bb draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 8556ea066463f5e112b6ded2c1527011ab1e3b38"
author iuc
date Thu, 31 Dec 2020 16:00:42 +0000
parents 17359b808b01
children 6cd09d7b5f37
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1 <tool id="jbrowse" name="JBrowse" version="@TOOL_VERSION@+@WRAPPER_VERSION@">
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2 <description>genome browser</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <xrefs>
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7 <xref type="bio.tools">jbrowse</xref>
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8 </xrefs>
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9 <expand macro="requirements"/>
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10 <edam_operations>
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11 <edam_operation>operation_0573</edam_operation>
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12 <edam_operation>operation_0564</edam_operation>
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13 </edam_operations>
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14 <edam_topics>
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15 <edam_topic>topic_3307</edam_topic>
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16 <edam_topic>topic_0092</edam_topic>
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17 </edam_topics>
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18 <version_command>python '${__tool_directory__}/jbrowse.py' --version</version_command>
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19 <command detect_errors="aggressive"><![CDATA[
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20 #if $action.action_select == "create":
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21 mkdir -p $output.files_path &&
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22 #else:
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23 cp -R $action.update_jbrowse.extra_files_path $output.files_path &&
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24 #end if
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25
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26 ## Copy the XML file into the directory, mostly for debugging
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27 ## but nice if users want to reproduce locally
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28 cp $trackxml $output.files_path/galaxy.xml &&
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29
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30 export JBROWSE_SOURCE_DIR=\$(dirname \$(which prepare-refseqs.pl))/../opt/jbrowse &&
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31
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32 ## Once that's done, we run the python script to handle the real work
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33 python '$__tool_directory__/jbrowse.py'
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35 --jbrowse \${JBROWSE_SOURCE_DIR}
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36 --standalone '$standalone'
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38 --outdir $output.files_path
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39 $trackxml &&
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40
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41 #if str($standalone) != "data":
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42 cp $output.files_path/index.html $output;
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43 #else:
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44 cp $dummyIndex $output;
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45 #end if
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46
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47 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph.
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48 #if str($uglyTestingHack) == "enabled":
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49 cp $trackxml $output
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50 #end if
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51 ]]></command>
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52 <configfiles>
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53 <configfile name="dummyIndex"><![CDATA[
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54 <html>
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55 <head>
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56 </head>
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57 <body>
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58 <h1>JBrowse Data Directory</h1>
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59 <p>
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60 Hi! This is not a full JBrowse instance. JBrowse v0.4(+?)
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61 started shipping with the ability to produce just the
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62 "data" directory from a JBrowse instance, rather than a
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63 complete, standalone instance. This was intended to be used
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64 with the in-development Apollo integration, but may have other
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65 uses as well.
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66 </p>
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67 <p>
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68 <u>This is not usable on its own</u>. The output dataset may be
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69 used with Apollo, or may be passed through the "JBrowse -
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70 Convert to Standalone" tool in Galaxy to "upgrade" to a full
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71 JBrowse instance.
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72 </p>
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73 </body>
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74 </html>
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75 ]]></configfile>
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76 <configfile name="trackxml"><![CDATA[<?xml version="1.0"?>
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77 <root>
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78 <metadata>
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79 <gencode>$gencode</gencode>
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80 <genomes>
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81 #if str($reference_genome.genome_type_select) == "indexed":
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82 <genome path="${reference_genome.genomes.fields.path}">
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83 <metadata />
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84 </genome>s
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85 #else
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86 <genome path="$reference_genome.genome">
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87 <metadata>
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88 <dataset id="${__app__.security.encode_id($reference_genome.genome.id)}" hid="${reference_genome.genome.hid}"
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89 size="${reference_genome.genome.get_size(nice_size=True)}"
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90 edam_format="${reference_genome.genome.datatype.edam_format}"
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91 file_ext="${reference_genome.genome.ext}" />
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92 <history id="${__app__.security.encode_id($reference_genome.genome.history_id)}"
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93 #if $reference_genome.genome.history.user:
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94 user_email="${reference_genome.genome.history.user.email}"
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95 user_id="${reference_genome.genome.history.user_id}"
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96 display_name="${reference_genome.genome.history.get_display_name()}"/>
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97 #else
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98 user_email="anonymous"
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99 user_id="-1"
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100 display_name="Unnamed History"/>
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101 #end if
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102 <metadata
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103 #for (key, value) in $reference_genome.genome.get_metadata().items():
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104 #if "_types" not in $key:
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105 ${key}="${value}"
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106 #end if
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107 #end for
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108 />
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109 <tool
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110 tool_id="${reference_genome.genome.creating_job.tool_id}"
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111 tool_version="${reference_genome.genome.creating_job.tool_version}"
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112 />
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113 </metadata>
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114 </genome>
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115 #end if
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116 </genomes>
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117 <general>
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118 <defaultLocation>${jbgen.defaultLocation}</defaultLocation>
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119 <trackPadding>${jbgen.trackPadding}</trackPadding>
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120
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121 <shareLink>${jbgen.shareLink}</shareLink>
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122 <aboutDescription>${jbgen.aboutDescription}</aboutDescription>
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123 <show_tracklist>${jbgen.show_tracklist}</show_tracklist>
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124 <show_nav>${jbgen.show_nav}</show_nav>
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125 <show_overview>${jbgen.show_overview}</show_overview>
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126 <show_menu>${jbgen.show_menu}</show_menu>
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127 <hideGenomeOptions>${jbgen.hideGenomeOptions}</hideGenomeOptions>
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128 </general>
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129 <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl>
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130 </metadata>
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131 <tracks>
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132 #for $tg in $track_groups:
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133 #for $track in $tg.data_tracks:
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134 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
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135 #if $track.data_format.data_format_select != "rest" and $track.data_format.data_format_select != "sparql":
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136 <files>
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137 #for $dataset in $track.data_format.annotation:
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138 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}">
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139 <metadata>
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140 <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}"
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141 size="${dataset.get_size(nice_size=True)}"
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142 edam_format="${dataset.datatype.edam_format}"
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143 file_ext="${dataset.ext}" />
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144 <history id="${__app__.security.encode_id($dataset.history_id)}"
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145 #if $dataset.history.user:
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146 user_email="${dataset.history.user.email}"
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147 user_id="${dataset.history.user_id}"
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148 display_name="${dataset.history.get_display_name()}"/>
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149 #else
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150 user_email="anonymous"
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151 user_id="-1"
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152 display_name="Unnamed History"/>
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153 #end if
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154 <metadata
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155 #for (key, value) in $dataset.get_metadata().items():
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156 #if "_types" not in $key and $value is not None and len(str($value)) < 5000:
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157 ${key}="${value}"
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158 #end if
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159 #end for
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160 />
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161 <tool
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162 tool_id="${dataset.creating_job.tool_id}"
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163 tool_version="${dataset.creating_job.tool_version}"
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164 />
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165 </metadata>
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166 </trackFile>
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167 #end for
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168 </files>
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169 #end if
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170
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171 <options>
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172 #if str($track.data_format.data_format_select) == "gene_calls" or str($track.data_format.data_format_select) == "blast" or str($track.data_format.data_format_select) == "rest" or str($track.data_format.data_format_select) == "sparql":
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173 <style>
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174 <overridePlugins>${track.data_format.override_apollo_plugins}</overridePlugins>
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175 <overrideDraggable>${track.data_format.override_apollo_drag}</overrideDraggable>
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176 <className>${track.data_format.jbstyle.style_classname}</className>
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177 <description>${track.data_format.jbstyle.style_description}</description>
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178 <label>${track.data_format.jbstyle.style_label}</label>
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179 <height>${track.data_format.jbstyle.style_height}</height>
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180 <maxHeight>${track.data_format.jbstyle.max_height}</maxHeight>
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181 </style>
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182 <scaling>
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183 #if str($track.data_format.jbcolor_scale.color_score.color_score_select) == "none":
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184 <method>ignore</method>
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185 <scheme>
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186 #if str($track.data_format.jbcolor_scale.color_score.color.color_select) == "automatic":
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187 <color>__auto__</color>
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188 #else
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189 <color>${track.data_format.jbcolor_scale.color_score.color.style_color}</color>
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190 #end if
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191 </scheme>
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192 #else
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193 <method>score</method>
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194 <algo>${track.data_format.jbcolor_scale.color_score.score_scaling}</algo>
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195 <scales>
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196 <type>${track.data_format.jbcolor_scale.color_score.score_scales.scale_select}</type>
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197
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198 #if str($track.data_format.jbcolor_scale.color_score.score_scales.scale_select) == "manual":
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199 <min>${track.data_format.jbcolor_scale.color_score.score_scales.minimum}</min>
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200 <max>${track.data_format.jbcolor_scale.color_score.score_scales.maximum}</max>
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201 #end if
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202 </scales>
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203 <scheme>
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204 <type>${track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme}</type>
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205 ## auto_color
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206 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme) == "opacity":
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207 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.color.color_select) == "automatic":
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208 <color>__auto__</color>
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209 #else
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210 <color>${track.data_format.jbcolor_scale.color_score.color_scheme.color.style_color}</color>
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211 #end if
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212 #end if
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213 </scheme>
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214 #end if
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215 </scaling>
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216 <menus>
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217 #for $menu_item in $track.data_format.jbmenu.track_menu:
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218 <menu>
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219 <action>${menu_item.menu_action}</action>
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220 #if str($menu_item.menu_label) != "":
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221 <label>${menu_item.menu_label}</label>
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222 #end if
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223 #if str($menu_item.menu_title) != "":
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224 <title>${menu_item.menu_title}</title>
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225 #end if
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226 #if str($menu_item.menu_url) != "":
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227 <url>${menu_item.menu_url.replace("&", "&amp;").replace("\"", "&quot;")}</url>
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228 #end if
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229 #if str($menu_item.menu_icon) != "":
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230 <iconClass>${menu_item.menu_icon}</iconClass>
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231 #end if
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232 </menu>
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233 #end for
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234 </menus>
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235 #end if
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236 #if str($track.data_format.data_format_select) in ["gene_calls", "pileup", "blast", "wiggle", "vcf"]:
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237 <custom_config>
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238 #for $custom_option in $track.data_format.jb_custom_config.option:
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239 <${custom_option.opt_key}>
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240 <${custom_option.opt_value.val_type}>${$custom_option.opt_value.val}</${custom_option.opt_value.val_type}>
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241 </${custom_option.opt_key}>
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242 #end for
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243 </custom_config>
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244 #end if
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245
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246 #if str($track.data_format.data_format_select) == "wiggle":
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247 <wiggle>
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248 <type>${track.data_format.xyplot}</type>
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249 <variance_band>${track.data_format.var_band}</variance_band>
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250 #if str($track.data_format.scaling.scale_select) == "auto_local":
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251 <autoscale>local</autoscale>
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252 #else if str($track.data_format.scaling.scale_select) == "auto_global":
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253 <autoscale>global</autoscale>
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254 #else:
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255 <min>${track.data_format.scaling.minimum}</min>
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256 <max>${track.data_format.scaling.maximum}</max>
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257 #end if
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258 <scale>${track.data_format.scale_select2}</scale>
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259
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260 ## Wiggle tracks need special color config
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261 #if str($track.data_format.jbcolor.color.color_select) != "automatic":
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262 <color_pos>${track.data_format.jbcolor.color.style_pos_color}</color_pos>
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263 <color_neg>${track.data_format.jbcolor.color.style_neg_color}</color_neg>
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264 #else:
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265 <color_pos>__auto__</color_pos>
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266 <color_neg>__auto__</color_neg>
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267 #end if
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268
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269 ## Bicolor pivot config
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270 #if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "zero":
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271 <bicolor_pivot>zero</bicolor_pivot>
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272 #else if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "mean":
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273 <bicolor_pivot>mean</bicolor_pivot>
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274 #else:
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275 <bicolor_pivot>${track.data_format.jbcolor.bicolor_pivot.pivot_point}</bicolor_pivot>
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276 #end if
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277 <multibigwig>${track.data_format.MultiBigWig}</multibigwig>
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278 </wiggle>
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279 #else if str($track.data_format.data_format_select) == "pileup":
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280 <pileup>
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281 <auto_snp>${track.data_format.auto_snp}</auto_snp>
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282 <bam_indices>
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283 #for $dataset in $track.data_format.annotation:
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284 <bam_index>${dataset.metadata.bam_index}</bam_index>
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285 #end for
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286 </bam_indices>
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287 <chunkSizeLimit>${track.data_format.chunkSizeLimit}</chunkSizeLimit>
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288 </pileup>
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289 #else if str($track.data_format.data_format_select) == "blast":
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290 <blast>
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291 #if str($track.data_format.blast_parent) != "":
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292 <parent>${track.data_format.blast_parent}</parent>
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293 #end if
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294 <protein>${track.data_format.is_protein}</protein>
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295 <min_gap>${track.data_format.min_gap}</min_gap>
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296 <index>${track.data_format.index}</index>
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297 </blast>
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298 #else if str($track.data_format.data_format_select) == "gene_calls":
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299 <gff>
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300 <trackType>${track.data_format.track_config.track_class}</trackType>
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301 #if $track.data_format.track_config.track_class in ['JBrowse/View/Track/CanvasFeatures', 'NeatCanvasFeatures/View/Track/NeatFeatures']:
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302 #if str($track.data_format.track_config.canvas_options.transcriptType) != "":
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303 <transcriptType>${track.data_format.track_config.canvas_options.transcriptType}</transcriptType>
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304 #end if
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305 #if str($track.data_format.track_config.canvas_options.subParts) != "":
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306 <subParts>${track.data_format.track_config.canvas_options.subParts}</subParts>
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307 #end if
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308 #if str($track.data_format.track_config.canvas_options.impliedUTRs) != "false":
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309 <impliedUTRs>${track.data_format.track_config.canvas_options.impliedUTRs}</impliedUTRs>
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310 #end if
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311 #else if $track.data_format.track_config.track_class in ['JBrowse/View/Track/HTMLFeatures', 'NeatHTMLFeatures/View/Track/NeatFeatures']:
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312 #if str($track.data_format.track_config.html_options.topLevelFeatures) != "":
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313 <topLevelFeatures>${track.data_format.track_config.html_options.topLevelFeatures}</topLevelFeatures>
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314 #end if
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315 #end if
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316 #if $track.data_format.match_part.match_part_select:
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317 <match>${track.data_format.match_part.name}</match>
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318 #end if
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319 <index>${track.data_format.index}</index>
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320 </gff>
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321 #else if str($track.data_format.data_format_select) == "rest":
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322 <label>${track.data_format.label}</label>
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323 <rest>
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324 <url>${track.data_format.url}</url>
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325 </rest>
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326 #else if str($track.data_format.data_format_select) == "sparql":
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327 <label>${track.data_format.label}</label>
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328 <sparql>
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329 <url>${track.data_format.url}</url>
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330 <query>${track.data_format.query}</query>
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331 </sparql>
3
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332 #end if
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333 </options>
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334 </track>
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335 #end for
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336 #end for
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337 </tracks>
25
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338 ## Disable plugins until https://github.com/GMOD/jbrowse/issues/1288 is fixed
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339 ## <plugins
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340 ## ComboTrackSelector="${plugins.ComboTrackSelector}"
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341 ## Bookmarks="${plugins.Bookmarks}"
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342 ## GCContent="${plugins.GCContent}"
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343 ## BlastView="${plugins.BlastView}"
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344 ## theme="${plugins.theme}"
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345 ## />
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346 <plugins
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347 ComboTrackSelector="${plugins.ComboTrackSelector}"
25
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348 Bookmarks=""
17
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349 GCContent="${plugins.GCContent}"
25
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350 BlastView="${plugins.BlastView}"
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351 theme=""
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352 />
31
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353 </root>
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354 ]]></configfile>
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355 </configfiles>
0
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356 <inputs>
8
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357 <conditional name="reference_genome">
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358 <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select">
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359 <option selected="True" value="indexed">Use a built-in genome</option>
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360 <option value="history">Use a genome from history</option>
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361 </param>
8
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362 <when value="indexed">
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363 <param
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364 help="If your genome of interest is not listed, contact the Galaxy team"
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365 label="Select a reference genome"
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366 name="genomes"
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367 type="select"
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368 >
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369 <options from_data_table="all_fasta">
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370 <filter column="2" type="sort_by" />
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371 <validator message="No genomes are available for the selected input dataset" type="no_options" />
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372 </options>
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373 </param>
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374 </when>
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diff changeset
375 <when value="history">
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376 <param
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377 format="fasta"
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378 label="Select the reference genome"
25
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379 name="genome"
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380 type="data" />
5
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381 </when>
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382 </conditional>
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383
40
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384 <param name="standalone" label="Output JBrowse" type="select">
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385 <option value="complete">Complete, for viewing and further local development (JBrowse, tools, documentation, etc.)</option>
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386 <option value="minimal" selected="true">Minimal for viewing (Documentation removed)</option>
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387 <option value="data">Data directory only (primarily for use with Apollo, requires extra steps to serve as website)</option>
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388 </param>
3
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389
22
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390 <param name="gencode" type="select" label="Genetic Code">
3
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391 <option value="1">1. The Standard Code</option>
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392 <option value="2">2. The Vertebrate Mitochondrial Code</option>
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393 <option value="3">3. The Yeast Mitochondrial Code</option>
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394 <option value="4">4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
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395 <option value="5">5. The Invertebrate Mitochondrial Code</option>
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396 <option value="6">6. The Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
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397 <option value="9">9. The Echinoderm and Flatworm Mitochondrial Code</option>
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398 <option value="10">10. The Euplotid Nuclear Code</option>
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399 <option value="11">11. The Bacterial, Archaeal and Plant Plastid Code</option>
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parents: 1
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400 <option value="12">12. The Alternative Yeast Nuclear Code</option>
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parents: 1
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401 <option value="13">13. The Ascidian Mitochondrial Code</option>
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parents: 1
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402 <option value="14">14. The Alternative Flatworm Mitochondrial Code</option>
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parents: 1
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403 <option value="16">16. Chlorophycean Mitochondrial Code</option>
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parents: 1
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404 <option value="21">21. Trematode Mitochondrial Code</option>
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parents: 1
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405 <option value="22">22. Scenedesmus obliquus Mitochondrial Code</option>
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parents: 1
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406 <option value="23">23. Thraustochytrium Mitochondrial Code</option>
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parents: 1
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407 <option value="24">24. Pterobranchia Mitochondrial Code</option>
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parents: 1
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408 <option value="25">25. Candidate Division SR1 and Gracilibacteria Code</option>
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409 </param>
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410
8
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diff changeset
411 <conditional name="action">
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412 <param type="select" label="JBrowse-in-Galaxy Action" name="action_select">
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413 <option value="create">New JBrowse Instance</option>
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414 <option value="update">Update exising JBrowse Instance</option>
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diff changeset
415 </param>
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diff changeset
416 <when value="create" />
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417 <when value="update">
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418 <param name="update_jbrowse" type="data" format="html" label="Previous JBrowse Instance" />
8
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419 </when>
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420 </conditional>
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421
3
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parents: 1
diff changeset
422 <repeat name="track_groups" title="Track Group">
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parents: 1
diff changeset
423 <param label="Track Category"
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parents: 1
diff changeset
424 name="category"
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parents: 1
diff changeset
425 type="text"
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parents: 1
diff changeset
426 value="Default"
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427 help="Organise your tracks into Categories for a nicer end-user experience. You can use #date# and it will be replaced with the current date in 'yyyy-mm-dd' format, which is very useful for repeatedly updating a JBrowse instance when member databases / underlying tool versions are updated." optional="False"/>
0
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iuc
parents:
diff changeset
428 <repeat name="data_tracks" title="Annotation Track">
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
429 <conditional name="data_format" label="Track Options">
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
430 <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"
iuc
parents: 31
diff changeset
431 <option value="gene_calls">GFF/GFF3/BED Features</option>
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
432 <option value="pileup">BAM Pileups</option>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
433 <option value="blast">Blast XML</option>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
434 <option value="wiggle">BigWig XY</option>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
435 <option value="vcf">VCF SNPs</option>
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
436 <option value="rest">REST Endpoint</option>
25
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iuc
parents: 23
diff changeset
437 <option value="sparql">SPARQL</option>
1
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iuc
parents: 0
diff changeset
438 </param>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
439 <when value="blast">
3
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iuc
parents: 1
diff changeset
440 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" />
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
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441
3
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iuc
parents: 1
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442 <param label="Features used in Blast Search"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
443 help="in GFF3. This is used so we know where to map features. E.g. where results of which CDS Protein32 match up to. The query IDs in your blast results should MATCH some feature IDs in your GFF3 file. This is an optional field and is most useful if using JBrowse to display protein blast results on a DNA genome. blastn results don't need this, blastp results on a protein sequence don't need this."
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
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444 format="gff3"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
445 name="blast_parent"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
446 optional="true"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
447 type="data"/>
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
448
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
449 <param label="Minimum Gap Size"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
450 help="before a new match_part feature is created"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
451 name="min_gap"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
452 type="integer"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
453 value="10"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
454 min="2" />
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
455 <param label="Is this a protein blast search?"
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
456 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
457 name="is_protein"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
458 truevalue="true"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
459 falsevalue="false" />
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
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460
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
461 <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
462
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
463 <expand macro="track_styling"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
464 classname="feature"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
465 label="description"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
466 description="Hit_titles"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
467 height="600px"/>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
468 <expand macro="color_selection"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
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469 token_scaling_lin_select="false"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
470 token_scaling_log_select="true" />
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iuc
parents: 30
diff changeset
471 <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
472 <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
473 <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
474 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
475 <when value="vcf">
3
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
476 <expand macro="input_conditional" label="SNP Track Data" format="vcf" />
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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
477 <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
478 <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
479 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
480 <when value="gene_calls">
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
481 <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" />
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iuc
parents: 16
diff changeset
482 <conditional name="match_part" label="match/match_part data">
3
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iuc
parents: 1
diff changeset
483 <param label="This is match/match_part data"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
484 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
485 name="match_part_select"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
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486 truevalue="true"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
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487 falsevalue="false" />
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
488 <when value="true">
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
489 <param label="Match Part Feature Type"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
490 name="name"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
491 type="text"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
492 value="match"
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1c718d8b3532 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9cac72c004cc7ef57be997e2fdafb3b1839a300f
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parents: 19
diff changeset
493 help="Match_parts have several options for the parent feature type, such as cDNA_match, match, translated_nucleotide_match, etc. Please select the appropriate one here. You can leave empty to try autodetection (only works with CanvasFeatures track type)."
1c718d8b3532 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9cac72c004cc7ef57be997e2fdafb3b1839a300f
iuc
parents: 19
diff changeset
494 optional="True"/>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
495 </when>
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
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496 <when value="false" />
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
497 </conditional>
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
498
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
499 <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
500
10
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
501 <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
502 <param type="select" label="JBrowse Track Type [Advanced]" name="track_class">
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08776ba76cf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 75f6e483debb4c0d388bf4a54df81ee89af598d5
iuc
parents: 25
diff changeset
503 <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
504 <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
505 <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
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parents: 25
diff changeset
506 <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
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parents: 23
diff changeset
507 <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
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parents: 8
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508 </param>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
509 <when value="JBrowse/View/Track/CanvasFeatures">
27
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iuc
parents: 26
diff changeset
510 <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
511 </when>
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 26
diff changeset
512 <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
513 <expand macro="html_options" />
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
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parents: 26
diff changeset
514 </when>
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 26
diff changeset
515 <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
516 <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
517 <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
518 </when>
27
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 26
diff changeset
519 <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
520 <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
521 </when>
10
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
522 </conditional>
27
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 26
diff changeset
523 <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
524 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
525 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
526 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
527 height="10px"/>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
528 <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
529 <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
530 <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
531 <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
532 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
533 <when value="pileup">
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
534 <expand macro="input_conditional" label="BAM Track Data" format="bam" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
535 <param label="Autogenerate SNP Track"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
536 help="Not recommended for deep coverage BAM files"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
537 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
538 name="auto_snp"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
539 truevalue="true"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
540 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
541 <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
542 name="chunkSizeLimit"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
543 type="integer"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
544 help="Maximum size in bytes of BAM chunks that the browser will try to deal with. When this is exceeded, most tracks will display 'Too much data' message."
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
545 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
546 <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
547 <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
548 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
549 <when value="wiggle">
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
550 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
551
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
552 <param label="Use XYPlot"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
553 help="instead of continuous colored band"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
554 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
555 name="xyplot"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
556 truevalue="JBrowse/View/Track/Wiggle/XYPlot"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
557 falsevalue="JBrowse/View/Track/Wiggle/Density" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
558 <param label="Show variance band"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
559 help="Only for XYPlots"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
560 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
561 name="var_band"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
562 truevalue="true"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
563 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
564
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
565 <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
566 <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
567 <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
568 <option value="auto_global">Autoscale (global)</option>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
569 <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
570 </param>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
571 <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
572 <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
573 <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
574 <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
575 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
576 <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
577 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
578 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
579 </conditional>
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
580 <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
581 <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
582 <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
583 </param>
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
584
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
585 <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
586 help="MultiBigWig is a plugin to group multiple big-wig tracks in a more aesthetically pleasing format and to show data in a higher density display." />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
587
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
588 <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
589 <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
590 <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
591 </when>
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
592 <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
593 <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
594 <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
595 <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
596 classname="feature"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
597 label="description"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
598 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
599 height="600px"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
600 <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
601 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
602 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
603 <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
604 <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
605 </when>
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
606
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
607 <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
608 <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
609 <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
610 <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
611 <sanitizer>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
612 <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
613 <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
614 <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
615 <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
616 </mapping>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
617 <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
618 <add value="|" />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
619 <add value="#" />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
620 <add value="{"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
621 <add value="}"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
622 <add value="!"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
623 <add value="?"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
624 <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
625 <add value="+"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
626 <add value="="/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
627 <add value="'"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
628 <add value='"'/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
629 </valid>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
630 </sanitizer>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
631 </param>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
632 <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
633 classname="feature"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
634 label="description"
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635 description="Hit_titles"
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parents: 23
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636 height="600px"/>
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637 <expand macro="color_selection"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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638 token_scaling_lin_select="false"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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639 token_scaling_log_select="true" />
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parents: 23
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640 <expand macro="track_menu" />
5
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parents: 3
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641 <expand macro="track_display" />
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642 </when>
1
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parents: 0
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643 </conditional>
0
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644 </repeat>
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parents: 1
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645 </repeat>
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646
5
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647 <expand macro="general_options" />
25
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parents: 23
diff changeset
648 <!-- Disable plugins until https://github.com/GMOD/jbrowse/issues/1288 is fixed -->
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diff changeset
649 <section name="plugins" title="Plugins" expanded="false">
25
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diff changeset
650
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
651 <param
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents: 23
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652 label="BlastView" name="BlastView" truevalue="True" falsevalue="" type="boolean" checked="true"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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653 help="A JBrowse plugin for viewing blast alignments. This plugin makes MANY assumptions about the format of your data, and may not work without those assumptions: 1) you use protein_match / match_part 2) your features have a Blast_qseq, Blast_mseq, and Blast_sseq attribute in their GFF3 representation." />
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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654
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655 <param
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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parents: 16
diff changeset
656 label="Combo Track Selector" name="ComboTrackSelector" truevalue="True" falsevalue="" type="boolean"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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657 help="ComboTrackSelector is a plugin to allow the co-existence of the Hierarchical and Faceted Track selectors in JBrowse, built for/by the Arabidopsis Information Portal (Araport) project" />
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
658 <!-- No way to disable now that it's built in jbrowse conda package -->
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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659 <!--param
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parents: 16
diff changeset
660 label="Bookmarks" name="Bookmarks" truevalue="True" falsevalue="" type="boolean"
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents: 23
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661 help="JBrowse plugin allowing users to manage a persistent list of bookmarks kept in localstorage" /-->
17
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parents: 16
diff changeset
662
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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parents: 16
diff changeset
663 <param
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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parents: 16
diff changeset
664 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
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665 help="A JBrowse plugin for plotting GC Content and GC Skew. The plugin consists of a storeClass that automatically calculates the percentage of G/C bases in a region, a track type that derives from the Wiggle XY or density types, and a dialog box to adjust the sliding window size, window step size, and the calculation mode (content or skew)." />
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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parents: 16
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666
25
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667 <!--param type="select" label="JBrowse Theme" name="theme">
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parents: 16
diff changeset
668 <option value="" selected="True">Default</option>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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parents: 16
diff changeset
669 <option value="Minimalist">Minimalist</option>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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670 <option value="Dark">Dark</option>
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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671 </param-->
17
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diff changeset
672 </section>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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diff changeset
673
3
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parents: 1
diff changeset
674 <param type="hidden" name="uglyTestingHack" value="" />
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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parents:
diff changeset
675 </inputs>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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diff changeset
676 <outputs>
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parents: 1
diff changeset
677 <data format="html" name="output" label="JBrowse on $on_string - $standalone"/>
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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diff changeset
678 </outputs>
3
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parents: 1
diff changeset
679 <tests>
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parents: 1
diff changeset
680 <test>
8
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parents: 6
diff changeset
681 <param name="reference_genome|genome_type_select" value="history"/>
25
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parents: 23
diff changeset
682 <param name="reference_genome|genome" value="merlin.fa"/>
3
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parents: 1
diff changeset
683 <param name="gencode" value="1" />
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diff changeset
684 <param name="standalone" value="data" />
3
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parents: 1
diff changeset
685 <param name="uglyTestingHack" value="enabled" />
31
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diff changeset
686 <output name="output" file="gencode/test-1.xml" lines_diff="16"/>
3
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
687 </test>
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
688 <test>
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
689 <param name="reference_genome|genome_type_select" value="history"/>
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents: 23
diff changeset
690 <param name="reference_genome|genome" value="merlin.fa"/>
3
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
691 <param name="gencode" value="11" />
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parents: 39
diff changeset
692 <param name="standalone" value="data" />
3
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
693 <param name="uglyTestingHack" value="enabled" />
31
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diff changeset
694 <output name="output" file="gencode/test.xml" lines_diff="16"/>
3
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
695 </test>
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parents: 1
diff changeset
696 <test>
8
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parents: 6
diff changeset
697 <param name="reference_genome|genome_type_select" value="history"/>
25
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diff changeset
698 <param name="reference_genome|genome" value="merlin.fa"/>
3
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parents: 1
diff changeset
699 <param name="gencode" value="11" />
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parents: 39
diff changeset
700 <param name="standalone" value="data" />
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
701 <repeat name="track_groups">
34
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parents: 33
diff changeset
702 <param name="category" value="Default" />
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
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parents: 33
diff changeset
703 <repeat name="data_tracks">
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
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parents: 33
diff changeset
704 <conditional name="data_format">
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
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diff changeset
705 <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"
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diff changeset
706 <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"
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diff changeset
707 </conditional>
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
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parents: 33
diff changeset
708 </repeat>
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
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parents: 33
diff changeset
709 </repeat>
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
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parents: 33
diff changeset
710 <param name="uglyTestingHack" value="enabled" />
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
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parents: 33
diff changeset
711 <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"
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parents: 33
diff changeset
712 </test>
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
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parents: 33
diff changeset
713 <test>
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
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parents: 33
diff changeset
714 <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"
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parents: 33
diff changeset
715 <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"
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parents: 33
diff changeset
716 <param name="gencode" value="11" />
40
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parents: 39
diff changeset
717 <param name="standalone" value="data" />
34
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parents: 33
diff changeset
718 <repeat name="track_groups">
8
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parents: 6
diff changeset
719 <param name="category" value="Auto Coloured" />
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
720 <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
721 <conditional name="data_format">
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
722 <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
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parents: 6
diff changeset
723 <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
724 <conditional name="match_part">
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
725 <param name="match_part_select" value="false"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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diff changeset
726 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
727 <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
728 <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
729 <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
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 name="color">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
732 <param name="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
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 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
735 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
736 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
737 </repeat>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
738
8
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="track_groups">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
740 <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
741 <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
742 <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
743 <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
744 <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
745 <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
746 <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
747 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
748 <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
749 <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
750 <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
751 <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
752 <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
753 <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
754 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
755 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
756 </section>
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 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
759 </repeat>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
760
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
761 <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
762 <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
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="automatic"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
781 </conditional>
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 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
785 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
786 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
787 <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
788 <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
789 <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
790 <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
791 <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
792 <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
793 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
794 <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
795 <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
796 <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
797 <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
798 <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
799 <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
800 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
801 <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
802 <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
803 <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
804 <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
805 <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
806 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
807 </conditional>
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 </section>
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 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
812 <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
813 <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
814 <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
815 <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
816 <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
817 <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
818 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
819 <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
820 <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
821 <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
822 <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
823 <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
824 <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
825 <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
826 <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
827 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
828 <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
829 <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
830 <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
831 <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
832 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
833 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
834 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
835 </section>
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 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
838 <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
839 <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
840 <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
841 <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
842 <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
843 <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
844 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
845 <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
846 <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
847 <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
848 <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
849 <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
850 <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
851 <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
852 <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
853 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
854 <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
855 <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
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="manual"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
858 <param name="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
859 </conditional>
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 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
862 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
863 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
864 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
865 </repeat>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
866
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
867 <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
868 <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
869 <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
870 <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
871 <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
872 <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
873 <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
874 <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
875 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
876 <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
877 <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
878 <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
879 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
880 <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
881 <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
882 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
883 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
884 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
885 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
886 <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
887 <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
888 <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
889 <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
890 <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
891 <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
892 <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
893 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
894 <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
895 <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
896 <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
897 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
898 <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
899 <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
900 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
901 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
902 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
903 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
904 </repeat>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
905
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
906 <param name="uglyTestingHack" value="enabled" />
36
7ed0827da5a8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit e846227dfeed6e58ab8e2ee528e8fbc7c3938f86"
iuc
parents: 35
diff changeset
907 <output name="output" file="gff3/test.xml" lines_diff="260" />
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
908 </test>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
909 <test>
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="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
911 <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
912 <param name="gencode" value="11" />
40
17359b808b01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
parents: 39
diff changeset
913 <param name="standalone" value="data" />
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
914
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
915 <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
916 <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
917 <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
918 <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
919 <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
920 <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
921 <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
922 <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
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 <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
925 <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
926 <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
927 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
928 <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
929 <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
930 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
931 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
932 <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
933 <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
934 <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
935 <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
936 <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
937 <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
938 <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
939 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
940 <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
941 <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
942 <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
943 <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
944 <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
945 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
946 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
947 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
948 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
949 <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
950 <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
951 <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
952 <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
953 <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
954 <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
955 <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
956 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
957 <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
958 <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
959 <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
960 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
961 <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
962 <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
963 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
964 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
965 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
966 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
967 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
968
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
969 <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
970 <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
971 </test>
10
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
972 <test>
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="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
974 <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
975 <param name="gencode" value="11" />
40
17359b808b01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
parents: 39
diff changeset
976 <param name="standalone" value="data" />
10
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
977
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
978 <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
979 <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
980 <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
981 <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
982 <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
983 <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
984 <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
985 <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
986 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
987 <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
988 <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
989 <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
990 <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
991 <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
992 <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
993 </section>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
994 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
995 <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
996 <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
997 <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
998 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
999 <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
1000 <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
1001 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
1002 </section>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
1003 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
1004 </repeat>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
1005 </repeat>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
1006
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
1007 <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
1008 <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
1009 </test>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1010 <test>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1011 <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
1012 <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
1013 <param name="gencode" value="11" />
40
17359b808b01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
parents: 39
diff changeset
1014 <param name="standalone" value="data" />
31
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1015
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="track_groups">
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="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
1018 <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
1019 <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
1020 <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
1021 <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
1022 <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
1023 <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
1024 </conditional>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1025 <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
1026 <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
1027 <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
1028 <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
1029 <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
1030 <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
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 name="option">
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1034 <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
1035 <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
1036 <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
1037 <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
1038 </conditional>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1039 </repeat>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1040 <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
1041 <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
1042 <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
1043 <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
1044 <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
1045 </conditional>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1046 </repeat>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1047 <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
1048 <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
1049 <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
1050 <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
1051 <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
1052 </conditional>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1053 </repeat>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1054 </section>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1055 </conditional>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1056 </repeat>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1057 </repeat>
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1058
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 30
diff changeset
1059 <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
1060 <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
1061 </test>
18
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 17
diff changeset
1062 <test>
19
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
1063 <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
1064 <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
1065 <param name="gencode" value="11" />
40
17359b808b01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
parents: 39
diff changeset
1066 <param name="standalone" value="data" />
19
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
1067
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
1068 <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
1069 <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
1070 <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
1071 <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
1072 <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
1073 <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
1074 </conditional>
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
1075 </repeat>
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
1076 </repeat>
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
1077
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
1078 <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
1079 <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
1080 </test>
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
1081
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
1082 <test>
18
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 17
diff changeset
1083 <!-- data_table -->
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
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parents: 17
diff changeset
1084 <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
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parents: 23
diff changeset
1085 <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
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parents: 17
diff changeset
1086 <param name="gencode" value="1" />
40
17359b808b01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
parents: 39
diff changeset
1087 <param name="standalone" value="data" />
18
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 17
diff changeset
1088 <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
1089 <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
1090 </test>
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1091
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents: 23
diff changeset
1092 <test>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1093 <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
1094 <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
1095 <param name="gencode" value="11" />
40
17359b808b01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
parents: 39
diff changeset
1096 <param name="standalone" value="data" />
25
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 <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
1099 <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
1100 <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
1101 <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
1102 <param name="data_format_select" value="rest"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents: 23
diff changeset
1103 <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
1104 <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
1105 </conditional>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1106 </repeat>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1107 <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
1108 <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
1109 <param name="data_format_select" value="sparql"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1110 <param name="url" value="http://example.org.external/sparql/"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1111 <param name="label" value="Sparql endpoint"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1112 <param name="query" value=" DEFINE sql:select-option 'order'
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1113 prefix rdf: &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#&gt;
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1114 select ?start,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1115 ?end,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1116 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
1117 1,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1118 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
1119 -1,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1120 0
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1121 )
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1122 ) as ?strand,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1123 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
1124 str(?label) as ?name,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1125 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
1126 ?obj as ?uniqueID,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1127 ?parent as ?parentUniqueID
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1128 where {
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1129 values ?faldo_type { faldo:ForwardStrandPosition faldo:ReverseStrandPosition faldo:BothStrandsPosition }
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1130 }"/>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1131 </conditional>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1132 </repeat>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1133 </repeat>
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1134
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1135 <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
1136 <output name="output" file="endpoints/test.xml" lines_diff="16"/>
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1137 </test>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1138 </tests>
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
1139 <help><![CDATA[
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1140 JBrowse-in-Galaxy
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1141 =================
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1142
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1143 JBrowse-in-Galaxy offers a highly configurable, workflow-compatible
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1144 alternative to Trackster.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1145
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1146 Overview
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1147 --------
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1148
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1149 JBrowse is a fast, embeddable genome browser built completely with
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1150 JavaScript and HTML5.
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1151
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1152 The JBrowse-in-Galaxy (JiG) tool was written to help build complex
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1153 JBrowse installations straight from Galaxy, taking advantage of the
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1154 latest Galaxy features such as dataset collections, sections, and colour
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1155 pickers. It allows you to build up a JBrowse instance without worrying
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1156 about how to run the command line tools to format your data, and which
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1157 options need to be supplied and where. Additionally it comes with many
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1158 javascript functions to handle colouring of features which would be
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1159 nearly impossible to write without the assistance of this tool.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1160
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1161 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
iuc
parents: 23
diff changeset
1162 <https://github.com/galaxyproject/tools-iuc/issues>`__, who you can help you
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1163 with missing features or bugs in the tool.
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1164
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1165 Options
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1166 -------
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1167
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1168 The first option you encounter is the **Fasta Sequence(s)**. This option
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1169 now accepts multiple fasta files, allowing you to build JBrowse
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1170 instances that contain data for multiple genomes or chrosomomes
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1171 (generally known as "landmark features" in gff3 terminology.) Up to 30
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1172 will be shown from the dropdown selector within JBrowse, this is a known
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1173 issue.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1174
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1175 **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
iuc
parents: 23
diff changeset
1176 in a dataset, or just the data directory without JBrowse (e.g. for Apollo).
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1177 Currently Galaxy copies the entire JBrowse directory in order to have a
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1178 complete, downloadable file that contains a ready-to-go JBrowse
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1179 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
iuc
parents: 23
diff changeset
1180 complete copy of JBrowse (12Mb) that's duplicated for every JBrowse
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1181 dataset in their history, and admins don't want useless copies of
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1182 JBrowse on disk. Unfortunately we have not come up with the perfect
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1183 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
1184 been given the option to produce just the ``data/`` directory. For those
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1185 unfamiliar with JBrowse, the ``data/`` directory contains processed data
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1186 files, but no way to view them. This feature is additionally implemented
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1187 for upcoming `Apollo <https://github.com/gmod/apollo>`__ integration.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1188
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1189 **Genetic Code** is a new feature in v0.4 of JiG / v1.12.0 of JBrowse,
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1190 which allows users to specify a non standard genetic code, and have
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 23
diff changeset
1191 JBrowse highlight the correct start and stop codons.
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1192
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1193 **Track Groups** represent a set of tracks in a single category. These
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1194 can be used to let your users understand relationships between large
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1195 groups of tracks.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1196
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1197 .. image:: sections.png
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1198
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1199 Annotation Tracks
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1200 -----------------
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1201
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1202 Within Track Groups, you have one or more **Annotation Tracks**. Each
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1203 Annotation Track is a groups of datasets which have similar styling.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1204 This allows you to rapidly build up JBrowse instances without having to
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1205 configure tracks individually. A massive improvement over previous
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1206 versions. For example, if you have five different GFF3 files from
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1207 various gene callers that you wish to display, you can take advantage of
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1208 this feature to style all of them similarly.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1209
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1210 There are a few different types of tracks supported, each with their own
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1211 set of options:
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1212
33
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
1213 GFF3/BED
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
1214 ~~~~~~~~
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1215
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1216 These are your standard feature tracks. They usually highlight genes,
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1217 mRNAs and other features of interest along a genomic region. The
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1218 underlying tool and this help documentation focus primarily on GFF3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1219 data, and have not been tested extensively with other formats. Automatic
33
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
1220 min/max detection will fail under BED datasets.
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1221
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1222 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
1223 consists of top level ``match`` features, with a child ``match_part``
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1224 feature, and is often used in displaying alignments. (See "Alignments"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1225 section on the `GFF3
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
1226 specification <https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md>`__ for more
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1227 information). If the data is match/match part, you will need to specify
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1228 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
1229 terms, and JiG does not yet have the ability to understand SO terms.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1230
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1231 Next up is the **Styling Options** section, which lets you control a few
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1232 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
1233 to configure and can safely leave on defaults. Occasionally you will
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1234 want to change what information is shown in the end product.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1235
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1236 .. image:: styling.png
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1237
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1238 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
1239 source of the black text is configured with the **style.label** option,
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1240 and the source of the blue text is configured with the
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1241 **style.description** option.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1242
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1243 Feature Score Scaling & Colouring Options
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1244 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1245
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1246 First, you need to choose between ignoring the score attribute of GFF3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1247 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
1248 coloured with a solid colour. If you choose to use it, features will
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1249 have slightly different colours based on their scores.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1250
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1251 .. image:: opacity.png
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1252
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1253 If you choose **Ignore score**, you may choose between automatically
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1254 choosing a colour, or manually specifying one. The automatically chosen
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1255 colours vary along a brewer palette and generally look quite nice with
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1256 no human intervention required. The manual colour choice is somewhat
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1257 self explanatory. Clicking on the small coloured square will bring up a
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1258 colour palette.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1259
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1260 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
1261 options. First is the function to map the colour choices to colour
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1262 values. JiG comes with a few functions built in such as linear scaling,
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1263 logarithmic scaling, and blast scaling.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1264
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1265 The **linear scaling** method says "take these values, and they map
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1266 directly to a range of output values". **Logarithmic scaling** says
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1267 "please take the log of the score before mapping", and **Blast scaling**
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1268 is further specialised to handle blast data more nicely. These are
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1269 convenience functions to help transform the wide array of possible
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1270 values in the GFF3 score attribute to more meaningful numbers. If you
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1271 need more comprehensive score scaling, it is recommended that you
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1272 pre-process your GFF3 files somehow.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1273
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1274 Once you've selected a scaling method, you can choose to manually
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1275 specify the minimum and maximum expected values, or you can let JiG
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1276 determine them for you automatically.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1277
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1278 Finally, opacity is the only mapping we currently provide. Future
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1279 iterations will attempt to improve upon this and provide more colour
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1280 scales. The Opacity option maps the highest scoring features to full
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1281 opacity, and everything else to lower ones.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1282
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1283 BAM Pileups
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1284 ~~~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1285
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1286 We support BAM files and can automatically generate SNP tracks based on
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1287 that bam data.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1288
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1289 .. image:: bam.png
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1290
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1291 This is *strongly discouraged* for high coverage density datasets.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1292 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
1293 files.
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1294
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1295 BlastXML
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1296 ~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1297
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1298 .. image:: blast.png
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1299
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1300 JiG now supports both blastn and blastp datasets. JiG internally uses a
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1301 blastXML to gapped GFF3 tool to convert your blastxml datasets into a
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1302 format amenable to visualization in JBrowse. This tool is also
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1303 available separately from the IUC on the toolshed.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1304
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1305 **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
1306 real gap in the processed gff3 file. In the picture above, various sizes
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1307 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
1308 100nt, many of the smaller gaps would disappear, and the features on
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1309 both sides would be merged into one, longer feature. This setting is
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1310 inversely proportional to runtime and output file size. *Do not set this
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1311 to a low value for large datasets*. By setting this number lower, you
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1312 will have extremely large outputs and extremely long runtimes. The
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1313 default was configured based off of the author's experience, but the
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1314 author only works on small viruses. It is *strongly* recommended that
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1315 you filter your blast results before display, e.g. picking out the top
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1316 10 hits or so.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1317
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1318 **Protein blast search** option merely informs underlying tools that
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1319 they should adjust feature locations by 3x.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1320
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1321 Styling Options
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1322 ^^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1323
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1324 Please see the styling options for GFF3 datasets, they are identical.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1325
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1326 Feature Score Scaling & Coloring Options
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1327 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1328
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1329 Please see the score scaling and colouring options for GFF3 datasets,
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1330 they are identical. Remember to set your score scaling to "blast" method
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1331 if you do use it.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1332
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1333 Bigwig XY
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1334 ~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1335
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1336 .. image:: bigwig.png
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1337
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1338 **XYPlot**
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1339
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1340 BigWig tracks can be displayed as a "density" plot which is continuous
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1341 line which varies in colour, or as an "XYplot." XYplots are preferable
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1342 for users to visually identify specific features in a bigwig track,
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1343 however density tracks are more visually compact.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1344
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1345 **Variance Band** is an option available to XYPlots, and can be seen in
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1346 the third and fourth tracks in the above picture. This overlays a mean
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1347 line, and 1 and 2 standard deviation areas.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1348
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1349 **Track Scaling** is different from colour scaling, instead it
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1350 configures how the track behaves inside of JBrowse. **Autoscaling
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1351 globally** means that JBrowse will determine the minimum and maximum for
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1352 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
1353 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
1354 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
1355 good for global genomic context. However you may wish to consider
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1356 **autoscaling locally** instead. In the example of a region which varies
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1357 from 0-50, autoscaling locally would cause the individual track's
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1358 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
1359 options are palatable, you may manually hardcode the minimum and
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1360 maximums for the track to scale to.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1361
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1362 Colour Options
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1363 ^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1364
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1365 BigWig tracks have two colours in JBrowse, a positive and a negative
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1366 colour.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1367
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1368 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
1369
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1370 One of the more interesting options is the **Bicolor pivot**. This
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1371 option allows you to control the point at which JBrowse switches from
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1372 the positive colour to the negative. In the above graphic, you can see
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1373 this has been configured to "mean" for the first two (orange and blue)
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1374 tracks.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1375
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1376 VCFs/SNPs
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1377 ~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1378
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1379 These tracks do not support any special configuration.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1380
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1381 Known Issues
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1382 ------------
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1383
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1384 - More than 30 landmark features cannot be listed in the manual
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1385 selector.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1386 - Non GFF3 likely has issue with automatically determined min/max
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1387 scores. Manually specify minimum and maximum score attributes, or do
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1388 not use varied colours based on scores to avoid this issue.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1389
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
1390 @ATTRIBUTION@
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
1391 ]]></help>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
1392 <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
1393 </tool>