Mercurial > repos > yating-l > jbrowsearchivecreator

annotate jbrowseArchiveCreator.xml @ 19:62dee5369e80 draft

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planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit afd782e8741a859506794bea92475f620265c50e
author sargentl
date Thu, 13 Sep 2018 17:43:23 -0400
parents 79b23a8afb15
children 85971ec2a527
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1 <tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.3.2">
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2 <description>
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3 This Galaxy tool is used to prepare your files to be ready for displaying on JBrowse with Apollo plugin
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4 </description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <requirements>
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9 <requirement type="package" version="1.2">samtools</requirement>
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10 <requirement type="package" version="0.2.6">tabix</requirement>
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11 <requirement type="package" version="1.9">numpy</requirement>
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12 <requirement type="package" version="1.68">biopython</requirement>
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13 <requirement type="package" version="340">ucsc_hac</requirement>
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14 <requirement type="package" version="1.13.1">jbrowse_tools</requirement>
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15 <requirement type="package" version="1.0">gff3sort</requirement>
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16 </requirements>
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18 <stdio>
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19 </stdio>
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21 <command detect_errors="exit_code"><![CDATA[
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22 mkdir -p $output.extra_files_path;
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24 ## Dump the tool parameters into a JSON file
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25 python2 $json_file parameters.json;
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27 python2 $__tool_directory__/jbrowseArchiveCreator.py --data_json parameters.json -o $output
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28 ]]></command>
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29 <configfiles>
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30 <configfile name="json_file">
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31 import json
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32 import sys
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34 file_path = sys.argv[1]
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35 #set global data_parameter_dict = {}
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37 ## Ask the user to enter the genome name
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38 #silent $data_parameter_dict.update({"genome_name": str($genome_name)})
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40 ## Function to retrieve the data of the inputs
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41 #def prepare_json($datatype, $input_to_prepare, $order_index, $extra_data_dict={})
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42 #set false_path = str($input_to_prepare)
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43 #set $data_dict = {"false_path": $false_path}
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45 #set name = str($input_to_prepare.name)
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46 #silent $data_dict.update({"name": $name})
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47 #silent $data_dict.update($extra_data_dict)
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48 ## Add the ordering by taking the tool form indexes
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49 #silent $data_dict.update({"order_index": $order_index})
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51 #if $datatype in $data_parameter_dict
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52 #silent $data_parameter_dict[$datatype].append($data_dict)
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53 #else
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54 #set array_inputs = []
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55 #silent $array_inputs.append($data_dict)
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56 #silent $data_parameter_dict.update({$datatype: $array_inputs})
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57 #end if
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58 #end def
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60 ## Get the number of digits from tracks, to have a unique integer from group index and track index
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62 #set temp_max_digit = 0
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64 #for $g in $group
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65 #if len($g.format) > $temp_max_digit
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66 #silent temp_max_digit = len($g.format)
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67 #end if
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68 #end for
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70 #set nb_digits_max_track = len(str($temp_max_digit))
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72 ## END Get the number of digits
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74 #for $i_g, $g in enumerate( $group )
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75 #for $i, $f in enumerate( $g.format )
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76 ## Create the order index using index_group+1 concatenated with index_track
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77 #set index_group_final = str($i_g + 1)
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78 #set index_track_final = str($index_group_final) + str($i).zfill($nb_digits_max_track)
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80 ## For each format, we have a few mandatory fields we store in a dict
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81 #set track_color = str($f.formatChoice.track_color)
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82 #set group_name = str($g.group_name)
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83 #set longLabel = str($f.formatChoice.longLabel)
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84
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85 #set extra_data_dict = {"track_color": $track_color,
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86 "group_name": $group_name,
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87 "long_label": $longLabel}
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88 #if $f.formatChoice.format_select == "bam"
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89 #set bam_index = $f.formatChoice.BAM.metadata.bam_index
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90
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91 ## Add Bam format specific fields
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92 #silent $extra_data_dict.update({"index": $bam_index, "nameIndex": str($f.formatChoice.nameIndex)})
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93
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94 #silent $prepare_json("Bam", $f.formatChoice.BAM, $index_track_final, $extra_data_dict)
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95 #end if
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96 #if $f.formatChoice.format_select == "bed"
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97 #silent $extra_data_dict.update({"nameIndex": str($f.formatChoice.bedChoice.nameIndex)})
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98 #if $f.formatChoice.bedChoice.bed_select == "bed_generic"
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99 #silent $prepare_json("Bed", $f.formatChoice.bedChoice.BED_generic, $index_track_final,
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100 $extra_data_dict)
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101 #end if
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102 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option"
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103 #silent $prepare_json("BedSimpleRepeats", $f.formatChoice.bedChoice.BED_simple_repeats, $index_track_final,
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104 $extra_data_dict)
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105 #end if
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106 #if $f.formatChoice.bedChoice.bed_select == "bed_splice_junctions_option"
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107 #silent $prepare_json("BedSpliceJunctions", $f.formatChoice.bedChoice.BED_splice_junctions, $index_track_final,
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108 $extra_data_dict)
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109 #end if
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110 #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option"
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111 #set database = str($f.formatChoice.bedChoice.database)
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112 #silent $extra_data_dict.update({"database": $database})
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113 #silent $prepare_json("BedBlastAlignments", $f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final,
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114 $extra_data_dict)
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115 #end if
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116 #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option"
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117 #set database = str($f.formatChoice.bedChoice.database)
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118 #silent $extra_data_dict.update({"database": $database})
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119 #silent $prepare_json("BedBlatAlignments", $f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final,
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120 $extra_data_dict)
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121 #end if
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122 #end if
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123 #if $f.formatChoice.format_select == "blastxml"
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124 #set database = str($f.formatChoice.database)
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125 #silent $extra_data_dict.update({"database": $database, "nameIndex": str($f.formatChoice.nameIndex)})
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126 #silent $prepare_json("BlastXml", $f.formatChoice.BlastXML, $index_track_final,
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127 extra_data_dict)
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128 #end if
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129 #if $f.formatChoice.format_select == "bigwig"
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130 #silent $extra_data_dict.update({"nameIndex": str($f.formatChoice.nameIndex)})
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131 #silent $prepare_json("BigWig", $f.formatChoice.BIGWIG, $index_track_final,
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132 $extra_data_dict)
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133 #end if
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134 #if $f.formatChoice.format_select == 'gff3'
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135 #silent $extra_data_dict.update({"nameIndex": str($f.formatChoice.nameIndex)})
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136 #silent $prepare_json("Gff3", $f.formatChoice.GFF3, $index_track_final,
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137 $extra_data_dict)
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138 #end if
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139 #if $f.formatChoice.format_select == "gtf"
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140 #silent $extra_data_dict.update({"nameIndex": str($f.formatChoice.nameIndex)})
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141 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8
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142 #silent $prepare_json("Gtf", $f.formatChoice.GTF, $index_track_final,
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143 $extra_data_dict)
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144 #end if
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145 #end for
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146 #end for
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147
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148 ## We combine the fasta file dataset name with his false path in a JSON object
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149 #set fasta_json = {"false_path": str($fasta_file), "name": str($fasta_file.name)}
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150 $data_parameter_dict.update({"fasta": $fasta_json})
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151
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152 ## Retrieve the user email
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153 #silent $data_parameter_dict.update({"user_email": str($__user_email__)})
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154
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155 #silent $data_parameter_dict.update({"tool_directory": str($__tool_directory__)})
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156
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157 #silent $data_parameter_dict.update({"extra_files_path": str($output.extra_files_path)})
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158
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159 #silent $data_parameter_dict.update({"debug_mode": str($advanced_options.debug_mode)})
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160
7
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161 #silent $data_parameter_dict.update({"feature_tracks_type": str($advanced_options.feature_tracks_type)})
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162
6
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163 with open(file_path, 'w') as f:
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164 json.dump($data_parameter_dict, f)
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165 </configfile>
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166 </configfiles>
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167
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168 <inputs>
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169 <param
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170 name="genome_name"
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171 type="text"
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172 size="30"
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173 value="unknown"
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174 label="JBrowse Hub Name"
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175 />
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176 <param
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177 format="fasta"
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178 name="fasta_file"
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179 type="data"
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180 label="Reference genome"
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181 />
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182 <repeat name="group" title="New group">
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diff changeset
183 <param type="text" name="group_name" label="Group name" value="Default group"/>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
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184 <repeat name="format" title="New track">
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yating-l
parents:
diff changeset
185 <conditional name="formatChoice">
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186 <param name="format_select" type="select" label="Format">
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187 <option value="bam" selected="true">BAM</option>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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188 <option value="bed">BED</option>
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yating-l
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189 <option value="blastxml">BlastXML</option>
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yating-l
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190 <option value="bigwig">BigWig</option>
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yating-l
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191 <option value="gff3">GFF3</option>
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yating-l
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192 <option value="gtf">GTF</option>
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yating-l
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193 </param>
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yating-l
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diff changeset
194
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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195 <when value="bam">
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yating-l
parents:
diff changeset
196 <param
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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197 format="bam"
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198 name="BAM"
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yating-l
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199 type="data"
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200 label="BAM File"
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yating-l
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201 />
15
6464399df918 planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit c69fafd096990eadcc380250703aefd919f80107
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diff changeset
202 <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
6
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203 <param name="longLabel" type="text" size="30" value = "Sequence Alignment" label="Track label" />
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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204 <param name="track_color" type="color" label="Track color" value="#000000">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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205 <sanitizer>
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yating-l
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206 <valid initial="string.letters,string.digits">
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yating-l
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207 <add value="#"/>
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yating-l
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208 </valid>
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yating-l
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209 </sanitizer>
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210 </param>
19
62dee5369e80 planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit afd782e8741a859506794bea92475f620265c50e
sargentl
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diff changeset
211 </when>
6
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212 <when value="bed">
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213 <conditional name="bedChoice">
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214 <param name="bed_select" type="select" label="Bed Choice">
13
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diff changeset
215 <option value="bed_generic">BED Generic</option>
6
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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216 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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217 <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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218 <option value="bed_blast_alignment_option">Blast alignments (bed12+12 / bigPsl.as)</option>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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diff changeset
219 <option value="bed_blat_alignment_option">BLAT alignments (bigPsl / bigPsl.as)</option>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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diff changeset
220 </param>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
221 <when value="bed_generic">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
222 <param
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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223 format="bed"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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diff changeset
224 name="BED_generic"
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yating-l
parents:
diff changeset
225 type="data"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
226 label="Bed File"
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yating-l
parents:
diff changeset
227 />
13
43a700afd457 planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit bcb239c4045d2c47a8acad5fbd29eea03663e187
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diff changeset
228 <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
6
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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diff changeset
229 </when>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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diff changeset
230 <when value="bed_simple_repeats_option">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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diff changeset
231 <param
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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diff changeset
232 format="bed"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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233 name="BED_simple_repeats"
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yating-l
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diff changeset
234 type="data"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
235 label="Bed Simple Repeats (Bed4+12) File"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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diff changeset
236 />
13
43a700afd457 planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit bcb239c4045d2c47a8acad5fbd29eea03663e187
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diff changeset
237 <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
6
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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diff changeset
238 </when>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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diff changeset
239 <when value="bed_splice_junctions_option">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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diff changeset
240 <param
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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diff changeset
241 format="bed"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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diff changeset
242 name="BED_splice_junctions"
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diff changeset
243 type="data"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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diff changeset
244 label="Bed Splice Junctions (Bed12+1) File"
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yating-l
parents:
diff changeset
245 />
13
43a700afd457 planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit bcb239c4045d2c47a8acad5fbd29eea03663e187
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diff changeset
246 <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
6
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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diff changeset
247 </when>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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diff changeset
248 <when value="bed_blast_alignment_option">
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diff changeset
249 <param
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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250 format="bed"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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251 name="BED_blast_alignment"
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yating-l
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diff changeset
252 type="data"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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253 label="Bed Blast Alignments (Bed12+12) File"
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diff changeset
254 />
14
3f9971a91096 planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit e526b4e8bef4677b832e940bacb8969a18efc3e3
yating-l
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255 <param name="database" type="select" label="Protein database">
3f9971a91096 planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit e526b4e8bef4677b832e940bacb8969a18efc3e3
yating-l
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256 <option value="NCBI" selected="true">NCBI</option>
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yating-l
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257 <option value="UniProt">UniProt</option>
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yating-l
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258 <option value="FlyBase">FlyBase</option>
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259 <option value="Others">Others</option>
3f9971a91096 planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit e526b4e8bef4677b832e940bacb8969a18efc3e3
yating-l
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diff changeset
260 </param>
13
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diff changeset
261 <param name="nameIndex" type="boolean" checked="true" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
6
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diff changeset
262 </when>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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diff changeset
263 <when value="bed_blat_alignment_option">
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yating-l
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diff changeset
264 <param
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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265 format="bed"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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266 name="BED_blat_alignment"
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yating-l
parents:
diff changeset
267 type="data"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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diff changeset
268 label="Bed BLAT Alignments (bigPsl) File"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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diff changeset
269 />
14
3f9971a91096 planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit e526b4e8bef4677b832e940bacb8969a18efc3e3
yating-l
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diff changeset
270 <param name="database" type="select" label="mRNA database">
3f9971a91096 planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit e526b4e8bef4677b832e940bacb8969a18efc3e3
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diff changeset
271 <option value="NCBI" selected="true">NCBI</option>
3f9971a91096 planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit e526b4e8bef4677b832e940bacb8969a18efc3e3
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diff changeset
272 <option value="Others">Others</option>
3f9971a91096 planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit e526b4e8bef4677b832e940bacb8969a18efc3e3
yating-l
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diff changeset
273 </param>
13
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diff changeset
274 <param name="nameIndex" type="boolean" checked="true" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
6
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diff changeset
275 </when>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
276 </conditional>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
277 <param name="longLabel" type="text" size="30" label="Track label" />
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
278 <param name="track_color" type="color" label="Track color" value="#000000">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
279 <sanitizer>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
280 <valid initial="string.letters,string.digits">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
281 <add value="#"/>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
282 </valid>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
283 </sanitizer>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
284 </param>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
285 </when>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
286 <when value="blastxml">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
287 <param
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
288 format="blastxml"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
289 name="BlastXML"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
290 type="data"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
291 label="Blast Alignments File"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
292 />
14
3f9971a91096 planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit e526b4e8bef4677b832e940bacb8969a18efc3e3
yating-l
parents: 13
diff changeset
293 <param name="database" type="select" label="Protein database">
3f9971a91096 planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit e526b4e8bef4677b832e940bacb8969a18efc3e3
yating-l
parents: 13
diff changeset
294 <option value="NCBI" selected="true">NCBI</option>
3f9971a91096 planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit e526b4e8bef4677b832e940bacb8969a18efc3e3
yating-l
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diff changeset
295 <option value="UniProt">UniProt</option>
3f9971a91096 planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit e526b4e8bef4677b832e940bacb8969a18efc3e3
yating-l
parents: 13
diff changeset
296 <option value="FlyBase">FlyBase</option>
3f9971a91096 planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit e526b4e8bef4677b832e940bacb8969a18efc3e3
yating-l
parents: 13
diff changeset
297 <option value="Others">Others</option>
3f9971a91096 planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit e526b4e8bef4677b832e940bacb8969a18efc3e3
yating-l
parents: 13
diff changeset
298 </param>
15
6464399df918 planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit c69fafd096990eadcc380250703aefd919f80107
yating-l
parents: 14
diff changeset
299 <param name="nameIndex" type="boolean" checked="true" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
6
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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diff changeset
300 <param name="longLabel" type="text" size="30" value="Blast Alignment" label="Track label" />
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
301 <param name="track_color" type="color" label="Track color" value="#000000">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
302 <sanitizer>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
303 <valid initial="string.letters,string.digits">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
304 <add value="#"/>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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diff changeset
305 </valid>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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diff changeset
306 </sanitizer>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
307 </param>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
308 </when>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
309 <when value="bigwig">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
310 <param
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
311 format="bigwig"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
312 name="BIGWIG"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
313 type="data"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
314 label="BIGWIG File"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
315 />
15
6464399df918 planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit c69fafd096990eadcc380250703aefd919f80107
yating-l
parents: 14
diff changeset
316 <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
6
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
317 <param name="longLabel" type="text" size="30" value="Sequence Coverage" label="Track label" />
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
318 <param name="track_color" type="color" label="Track color" value="#000000">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
319 <sanitizer>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
320 <valid initial="string.letters,string.digits">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
321 <add value="#"/>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
322 </valid>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
323 </sanitizer>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
324 </param>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
325 </when>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
326 <when value="gff3">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
327 <param
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
328 format="gff3"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
329 name="GFF3"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
330 type="data"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
331 label="GFF3 File"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
332 />
15
6464399df918 planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit c69fafd096990eadcc380250703aefd919f80107
yating-l
parents: 14
diff changeset
333 <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
6
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
334 <param name="longLabel" type="text" size="30" value="Gene Prediction" label="Track name" />
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
335 <param name="track_color" type="color" label="Track color" value="#000000">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
336 <sanitizer>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
337 <valid initial="string.letters,string.digits">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
338 <add value="#"/>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
339 </valid>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
340 </sanitizer>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
341 </param>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
342 </when>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
343 <when value="gtf">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
344 <param
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
345 format="gtf"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
346 name="GTF"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
347 type="data"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
348 label="GTF File"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
349 />
15
6464399df918 planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit c69fafd096990eadcc380250703aefd919f80107
yating-l
parents: 14
diff changeset
350 <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
6
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
351 <param name="longLabel" type="text" size="30" value="Assembled Transcripts" label="Track name" />
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
352 <param name="track_color" type="color" label="Track color" value="#000000">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
353 <sanitizer>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
354 <valid initial="string.letters,string.digits">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
355 <add value="#"/>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
356 </valid>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
357 </sanitizer>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
358 </param>
13
43a700afd457 planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit bcb239c4045d2c47a8acad5fbd29eea03663e187
yating-l
parents: 12
diff changeset
359 </when>
6
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
360 </conditional>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
361 </repeat>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
362 </repeat>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
363 <conditional name="advanced_options">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
364 <param name="advanced_options_selector" type="select" label="Advanced options">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
365 <option value="off" selected="true">Hide advanced options</option>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
366 <option value="on">Display advanced options</option>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
367 </param>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
368 <when value="on">
7
5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
yating-l
parents: 6
diff changeset
369 <param name="feature_tracks_type" type="select" label="Choose JBrowse feature tracks type">
5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
yating-l
parents: 6
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370 <option value="CanvasFeatures" selected="true">CanvasFeatures</option>
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371 <option value="HTMLFeatures">HTMLFeatures (Create a large number of range-indexed static JSON files. Don't choose this option if you want to upload/transfer output JBrowse hub to CyVerse Data Store!)
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372 </option>
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373 </param>
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374 <param name="debug_mode" type="select" label="Activate debug mode">
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375 <option value="false" selected="true">No</option>
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376 <option value="true">Yes</option>
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377 <help>
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378 Use this option if you are a G-OnRamp developer
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379 </help>
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380 </param>
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381 </when>
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382 <when value="off">
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383 <param name="debug_mode" type="hidden" value="false" />
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384 <param name="feature_tracks_type" type="hidden" value="CanvasFeatures" />
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385 </when>
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386 </conditional>
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387 </inputs>
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388
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389 <outputs>
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390 <data format="jbrowsehub" name="output" label="${tool.name}" />
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391 </outputs>
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392 <tests>
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393 <test>
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394 <param name="genome_name" value="Dbia3"/>
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395 <param name="fasta_file" value="common/dbia3.fa"/>
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396 <output name="output" file="only_genome/${tool.name}.html">
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397 <!-- Use macro to check the whole common structure without repeated code -->
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398 <expand macro="verify_hub_structure_no_track" test="only_genome" />
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399 </output>
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400 </test>
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401 </tests>
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402 <help>
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403 This Galaxy tool will prepare your files to be ready for visualization on JBrowse/Apollo.
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404 </help>
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405 <citations>
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406 </citations>
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407 </tool>