Mercurial > repos > yating-l > jbrowsearchivecreator

annotate jbrowseArchiveCreator.xml @ 32:7b955a58d8f2 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 18da3c5b92673ba5030c24c981c6ca7ebe0bf097-dirty
author yating-l
date Fri, 20 Oct 2017 11:22:21 -0400
parents 2191bd0798a9
children 07cc5384dd61
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1 <tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.0.0">
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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="1.9">numpy</requirement>
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11 <requirement type="package" version="1.68">biopython</requirement>
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12 <requirement type="package" version="340">ucsc_hac</requirement>
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13 <requirement type="package" version="1.12.1">jbrowse_tools</requirement>
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14 </requirements>
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16 <stdio>
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17 </stdio>
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19 <command detect_errors="exit_code"><![CDATA[
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20 mkdir -p $output.extra_files_path;
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22 ## Dump the tool parameters into a JSON file
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23 python $json_file parameters.json;
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25 python $__tool_directory__/jbrowseArchiveCreator.py --data_json parameters.json -o $output
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26 ]]></command>
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27 <configfiles>
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28 <configfile name="json_file">
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29 import json
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30 import sys
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32 file_path = sys.argv[1]
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33 #set global data_parameter_dict = {}
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35 ## Ask the user to enter the genome name
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36 #silent $data_parameter_dict.update({"genome_name": str($genome_name)})
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38 ## Function to retrieve the data of the inputs
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39 #def prepare_json($datatype, $input_to_prepare, $order_index, $extra_data_dict={})
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40 #set false_path = str($input_to_prepare)
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41 #set $data_dict = {"false_path": $false_path}
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43 #set name = str($input_to_prepare.name)
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44 #silent $data_dict.update({"name": $name})
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45 #silent $data_dict.update($extra_data_dict)
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46 ## Add the ordering by taking the tool form indexes
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47 #silent $data_dict.update({"order_index": $order_index})
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49 #if $datatype in $data_parameter_dict
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50 #silent $data_parameter_dict[$datatype].append($data_dict)
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51 #else
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52 #set array_inputs = []
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53 #silent $array_inputs.append($data_dict)
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54 #silent $data_parameter_dict.update({$datatype: $array_inputs})
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55 #end if
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56 #end def
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58 ## Get the number of digits from tracks, to have a unique integer from group index and track index
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60 #set temp_max_digit = 0
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62 #for $g in $group
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63 #if len($g.format) > $temp_max_digit
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64 #silent temp_max_digit = len($g.format)
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65 #end if
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66 #end for
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68 #set nb_digits_max_track = len(str($temp_max_digit))
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70 ## END Get the number of digits
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72 #for $i_g, $g in enumerate( $group )
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73 #for $i, $f in enumerate( $g.format )
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74 ## Create the order index using index_group+1 concatenated with index_track
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75 #set index_group_final = str($i_g + 1)
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76 #set index_track_final = str($index_group_final) + str($i).zfill($nb_digits_max_track)
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78 ## For each format, we have a few mandatory fields we store in a dict
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79 #set track_color = str($f.formatChoice.track_color)
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80 #set group_name = str($g.group_name)
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81 #set longLabel = str($f.formatChoice.longLabel)
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82 #set extra_data_dict = {"track_color": $track_color,
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83 "group_name": $group_name,
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84 "long_label": $longLabel}
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85 #if $f.formatChoice.format_select == "bam"
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86 #set bam_index = $f.formatChoice.BAM.metadata.bam_index
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87
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88 ## Add Bam format specific fields
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89 #silent $extra_data_dict.update({"index": $bam_index})
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90
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91 #silent $prepare_json("Bam", $f.formatChoice.BAM, $index_track_final, $extra_data_dict)
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92 #end if
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93 #if $f.formatChoice.format_select == "bed"
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94 #if $f.formatChoice.bedChoice.bed_select == "bed_generic"
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95 #silent $prepare_json("Bed", $f.formatChoice.bedChoice.BED, $index_track_final,
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96 $extra_data_dict)
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97 #end if
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98 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option"
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99 #silent $prepare_json("BedSimpleRepeats", $f.formatChoice.bedChoice.BED_simple_repeats, $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_splice_junctions_option"
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103 #silent $prepare_json("BedSpliceJunctions", $f.formatChoice.bedChoice.BED_splice_junctions, $index_track_final,
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104 $extra_data_dict)
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105 #end if
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106 #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option"
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107 ##set database = str($f.formatChoice.bedChoice.database)
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108 ##silent $extra_data_dict.update({"database": $database})
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109 #silent $prepare_json("BedBlastAlignments", $f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final,
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110 $extra_data_dict)
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111 #end if
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112 #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option"
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113 ##set database = str($f.formatChoice.bedChoice.database)
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114 ##silent $extra_data_dict.update({"database": $database})
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115 #silent $prepare_json("BedBlatAlignments", $f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final,
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116 $extra_data_dict)
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117 #end if
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118 #end if
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119 #if $f.formatChoice.format_select == "blastxml"
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120 #silent $prepare_json($f.formatChoice.BlastXML, extra_data_dict)
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121 #end if
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122 #if $f.formatChoice.format_select == "bigwig"
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123 #set pos_color = str($f.formatChoice.pos_color)
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124 #set neg_color = str($f.formatChoice.neg_color)
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125 #silent $extra_data_dict.update({"style" : {"pos_color" : $pos_color, "neg_color" : $neg_color}})
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126 #silent $prepare_json("BigWig", $f.formatChoice.BIGWIG, $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 == 'gff3'
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130 #if $f.formatChoice.gff3Choice.gff3_select == 'gff3_generic'
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131 #silent $prepare_json("Gff3", $f.formatChoice.GFF3, $index_track_final,
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132 $extra_data_dict)
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133 #elif $f.formatChoice.gff3Choice.gff3_select == 'gff3_transcript'
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134 #silent $prepare_json("Gff3_transcript", $f.formatChoice.GFF3, $index_track_final,
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135 $extra_data_dict)
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136 #elif $f.formatChoice.gff3Choice.gff3_select == 'gff3_mrna'
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137 #silent $prepare_json("Gff3_mrna", $f.formatChoice.GFF3, $index_track_final,
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138 $extra_data_dict)
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139 #end if
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140 #end if
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141 #if $f.formatChoice.format_select == "gtf"
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142 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8
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143 #silent $prepare_json("Gtf", $f.formatChoice.GTF, $index_track_final,
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144 $extra_data_dict)
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145 #end if
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146 #end for
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147 #end for
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148
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149 ## We combine the fasta file dataset name with his false path in a JSON object
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150 #set fasta_json = {"false_path": str($fasta_file), "name": str($fasta_file.name)}
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151 $data_parameter_dict.update({"fasta": $fasta_json})
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152
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153 ## Retrieve the user email
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154 #silent $data_parameter_dict.update({"user_email": str($__user_email__)})
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155
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156 #silent $data_parameter_dict.update({"tool_directory": str($__tool_directory__)})
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157
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158 #silent $data_parameter_dict.update({"extra_files_path": str($output.extra_files_path)})
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159
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160 #silent $data_parameter_dict.update({"debug_mode": str($advanced_options.debug_mode)})
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161
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162 with open(file_path, 'w') as f:
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163 json.dump($data_parameter_dict, f)
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164 </configfile>
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165 </configfiles>
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166
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167 <inputs>
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168 <param
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169 name="genome_name"
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170 type="text"
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171 size="30"
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172 value="unknown"
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173 label="JBrowse Hub Name"
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174 />
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175 <param
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176 format="fasta"
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177 name="fasta_file"
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178 type="data"
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179 label="Reference genome"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
180 />
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
181 <repeat name="group" title="New group">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
182 <param type="text" name="group_name" label="Group name" value="Default group"/>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
183 <repeat name="format" title="New track">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
184 <conditional name="formatChoice">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
185 <param name="format_select" type="select" label="Format">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
186 <option value="bam" selected="true">BAM</option>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
187 <option value="bed">BED</option>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
188 <option value="blastxml">BlastXML</option>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
189 <option value="bigwig">BigWig</option>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
190 <option value="gff3">GFF3</option>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
191 <option value="gtf">GTF</option>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
192 </param>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
193
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
194 <when value="bam">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
195 <param
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
196 format="bam"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
197 name="BAM"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
198 type="data"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
199 label="BAM File"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
200 />
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
201 <param name="longLabel" type="text" size="30" value = "Sequence Alignment" label="Track label" />
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
202 <param name="track_color" type="color" label="Track color" value="#000000">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
203 <sanitizer>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
204 <valid initial="string.letters,string.digits">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
205 <add value="#"/>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
206 </valid>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
207 </sanitizer>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
208 </param>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
209 </when>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
210 <when value="bed">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
211 <conditional name="bedChoice">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
212 <param name="bed_select" type="select" label="Bed Choice">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
213 <option value="bed_generic">BED format</option>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
214 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
215 <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
216 <option value="bed_blast_alignment_option">Blast alignments (bed12+12 / bigPsl.as)</option>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
217 <option value="bed_blat_alignment_option">BLAT alignments (bigPsl / bigPsl.as)</option>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
218 </param>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
219 <when value="bed_generic">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
220 <param
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
221 format="bed"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
222 name="BED_generic"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
223 type="data"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
224 label="Bed File"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
225 />
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
226 </when>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
227 <when value="bed_simple_repeats_option">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
228 <param
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
229 format="bed"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
230 name="BED_simple_repeats"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
231 type="data"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
232 label="Bed Simple Repeats (Bed4+12) File"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
233 />
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
234 </when>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
235 <when value="bed_splice_junctions_option">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
236 <param
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
237 format="bed"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
238 name="BED_splice_junctions"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
239 type="data"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
240 label="Bed Splice Junctions (Bed12+1) File"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
241 />
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
242 </when>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
243 <when value="bed_blast_alignment_option">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
244 <param
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
245 format="bed"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
246 name="BED_blast_alignment"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
247 type="data"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
248 label="Bed Blast Alignments (Bed12+12) File"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
249 />
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
250 </when>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
251 <when value="bed_blat_alignment_option">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
252 <param
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
253 format="bed"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
254 name="BED_blat_alignment"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
255 type="data"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
256 label="Bed BLAT Alignments (bigPsl) File"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
257 />
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
258 </when>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
259 </conditional>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
260 <param name="longLabel" type="text" size="30" label="Track label" />
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
261 <param name="track_color" type="color" label="Track color" value="#000000">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
262 <sanitizer>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
263 <valid initial="string.letters,string.digits">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
264 <add value="#"/>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
265 </valid>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
266 </sanitizer>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
267 </param>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
268 </when>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
269 <when value="blastxml">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
270 <param
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
271 format="blastxml"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
272 name="BlastXML"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
273 type="data"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
274 label="Blast Alignments File"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
275 />
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
276 <param name="longLabel" type="text" size="30" value="Blast Alignment" label="Track label" />
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
277 <param name="track_color" type="color" label="Track color" value="#000000">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
278 <sanitizer>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
279 <valid initial="string.letters,string.digits">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
280 <add value="#"/>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
281 </valid>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
282 </sanitizer>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
283 </param>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
284 </when>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
285 <when value="bigwig">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
286 <param
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
287 format="bigwig"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
288 name="BIGWIG"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
289 type="data"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
290 label="BIGWIG File"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
291 />
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
292 <param name="longLabel" type="text" size="30" value="Sequence Coverage" label="Track label" />
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
293 <param name="track_color" type="color" label="Track color" value="#000000">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
294 <sanitizer>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
295 <valid initial="string.letters,string.digits">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
296 <add value="#"/>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
297 </valid>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
298 </sanitizer>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
299 </param>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
300 </when>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
301 <when value="gff3">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
302 <conditional name="gff3Choice">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
303 <param name="gff3_select" type="select" label="gff3 type">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
304 <option value="gff3_generic">GFF3 format</option>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
305 <option value="gff3_transcript">GFF3 format output from gene prediction tools (e.g. Augustus), structure: gene->transcription->CDS</option>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
306 <option value="gff3_mrna">GFF3 format output from gene prediction tools (e.g. SNAP), structure: gene->mRNA->CDS</option>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
307 </param>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
308 <when value="gff3_generic">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
309 <param
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
310 format="gff3"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
311 name="GFF3_generic"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
312 type="data"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
313 label="GFF3 File"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
314 />
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
315 </when>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
316 <when value="gff3_transcript">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
317 <param
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
318 format="gff3"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
319 name="GFF3_transcript"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
320 type="data"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
321 label="GFF3 File from gene prediction"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
322 />
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
323 </when>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
324 <when value="gff3_mrna">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
325 <param
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
326 format="gff3"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
327 name="GFF3_mrna"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
328 type="data"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
329 label="GFF3 File from gene prediction"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
330 />
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
331 </when>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
332 </conditional>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
333 <param name="longLabel" type="text" size="30" value="Gene Prediction" label="Track name" />
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
334 <param name="track_color" type="color" label="Track color" value="#daa520">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
335 <sanitizer>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
336 <valid initial="string.letters,string.digits">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
337 <add value="#"/>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
338 </valid>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
339 </sanitizer>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
340 </param>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
341 </when>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
342 <when value="gtf">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
343 <param
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
344 format="gtf"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
345 name="GTF"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
346 type="data"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
347 label="GTF File"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
348 />
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
349 <param name="longLabel" type="text" size="30" value="Assembled Transcripts" label="Track name" />
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
350 <param name="track_color" type="color" label="Track color" value="#000000">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
351 <sanitizer>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
352 <valid initial="string.letters,string.digits">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
353 <add value="#"/>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
354 </valid>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
355 </sanitizer>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
356 </param>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
357 </when>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
358 </conditional>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
359 </repeat>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
360 </repeat>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
361 <conditional name="advanced_options">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
362 <param name="advanced_options_selector" type="select" label="Advanced options">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
363 <option value="off" selected="true">Hide advanced options</option>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
364 <option value="on">Display advanced options</option>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
365 </param>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
366 <!-- TODO: Avoid redundancy here -->
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
367 <when value="on">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
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368 <param name="debug_mode" type="select" label="Activate debug mode">
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369 <option value="false" selected="true">No</option>
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370 <option value="true">Yes</option>
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371 <help>
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372 Use this option if you are a G-OnRamp developer
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373 </help>
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374 </param>
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375 </when>
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376 <when value="off">
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377 <param name="debug_mode" type="hidden"
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378 value="false">
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379 </param>
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380 </when>
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381 </conditional>
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382 </inputs>
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383
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384 <outputs>
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385 <data format="jbrowsehub" name="output" label="${tool.name}" />
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386 </outputs>
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387 <tests>
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388 <test>
32
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389 <param name="genome_name" value="Dbia3"/>
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390 <param name="fasta_file" value="common/dbia3.fa"/>
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391 <output name="output" file="only_genome/only_genome.html">
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392 <!-- Use macro to check the whole common structure without repeated code -->
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393 <expand macro="verify_hub_structure_no_track" test="only_genome" />
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394 </output>
25
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395 </test>
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396 </tests>
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397 <help>
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398 This Galaxy tool will create a jbrowse hub which including binary datasets and json datasets that can be used for
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399 JBrowse visualization.
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400 </help>
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401 <citations>
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402 </citations>
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403 </tool>