Mercurial > repos > yating-l > jbrowsearchivecreator

annotate jbrowseArchiveCreator.xml @ 38:d17f629f5486 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit e4c1d387db160a3bf4a1e8abc288bdffbbbe2818-dirty
author yating-l
date Fri, 06 Apr 2018 13:44:56 -0400
parents 43909f065bee
children 4a69515eed63
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1 <tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.0.1">
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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="1.12.4">jbrowse_tools</requirement>
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14 <requirement type="package" version="1.0">gff3sort</requirement>
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15 </requirements>
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17 <stdio>
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18 </stdio>
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20 <command detect_errors="exit_code"><![CDATA[
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21 mkdir -p $output.extra_files_path;
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23 ## Dump the tool parameters into a JSON file
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24 python $json_file parameters.json;
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26 python $__tool_directory__/jbrowseArchiveCreator.py --data_json parameters.json -o $output
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27 ]]></command>
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28 <configfiles>
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29 <configfile name="json_file">
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30 import json
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31 import sys
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33 file_path = sys.argv[1]
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34 #set global data_parameter_dict = {}
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36 ## Ask the user to enter the genome name
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37 #silent $data_parameter_dict.update({"genome_name": str($genome_name)})
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39 ## Function to retrieve the data of the inputs
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40 #def prepare_json($datatype, $input_to_prepare, $order_index, $extra_data_dict={})
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41 #set false_path = str($input_to_prepare)
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42 #set $data_dict = {"false_path": $false_path}
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44 #set name = str($input_to_prepare.name)
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45 #silent $data_dict.update({"name": $name})
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46 #silent $data_dict.update($extra_data_dict)
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47 ## Add the ordering by taking the tool form indexes
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48 #silent $data_dict.update({"order_index": $order_index})
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50 #if $datatype in $data_parameter_dict
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51 #silent $data_parameter_dict[$datatype].append($data_dict)
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52 #else
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53 #set array_inputs = []
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54 #silent $array_inputs.append($data_dict)
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55 #silent $data_parameter_dict.update({$datatype: $array_inputs})
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56 #end if
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57 #end def
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59 ## Get the number of digits from tracks, to have a unique integer from group index and track index
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61 #set temp_max_digit = 0
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63 #for $g in $group
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64 #if len($g.format) > $temp_max_digit
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65 #silent temp_max_digit = len($g.format)
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66 #end if
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67 #end for
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69 #set nb_digits_max_track = len(str($temp_max_digit))
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71 ## END Get the number of digits
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73 #for $i_g, $g in enumerate( $group )
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74 #for $i, $f in enumerate( $g.format )
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75 ## Create the order index using index_group+1 concatenated with index_track
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76 #set index_group_final = str($i_g + 1)
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77 #set index_track_final = str($index_group_final) + str($i).zfill($nb_digits_max_track)
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79 ## For each format, we have a few mandatory fields we store in a dict
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80 #set track_color = str($f.formatChoice.track_color)
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81 #set group_name = str($g.group_name)
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82 #set longLabel = str($f.formatChoice.longLabel)
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83 #set extra_data_dict = {"track_color": $track_color,
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84 "group_name": $group_name,
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85 "long_label": $longLabel}
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86 #if $f.formatChoice.format_select == "bam"
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87 #set bam_index = $f.formatChoice.BAM.metadata.bam_index
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89 ## Add Bam format specific fields
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90 #silent $extra_data_dict.update({"index": $bam_index})
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91
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92 #silent $prepare_json("Bam", $f.formatChoice.BAM, $index_track_final, $extra_data_dict)
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93 #end if
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94 #if $f.formatChoice.format_select == "bed"
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95 #if $f.formatChoice.bedChoice.bed_select == "bed_generic"
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96 #silent $prepare_json("Bed", $f.formatChoice.bedChoice.BED_generic, $index_track_final,
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97 $extra_data_dict)
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98 #end if
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99 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option"
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100 #silent $prepare_json("BedSimpleRepeats", $f.formatChoice.bedChoice.BED_simple_repeats, $index_track_final,
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101 $extra_data_dict)
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102 #end if
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103 #if $f.formatChoice.bedChoice.bed_select == "bed_splice_junctions_option"
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104 #silent $prepare_json("BedSpliceJunctions", $f.formatChoice.bedChoice.BED_splice_junctions, $index_track_final,
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105 $extra_data_dict)
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106 #end if
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107 #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option"
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108 ##set database = str($f.formatChoice.bedChoice.database)
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109 ##silent $extra_data_dict.update({"database": $database})
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110 #silent $prepare_json("BedBlastAlignments", $f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final,
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111 $extra_data_dict)
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112 #end if
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113 #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option"
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114 ##set database = str($f.formatChoice.bedChoice.database)
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115 ##silent $extra_data_dict.update({"database": $database})
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116 #silent $prepare_json("BedBlatAlignments", $f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final,
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117 $extra_data_dict)
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118 #end if
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119 #end if
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120 #if $f.formatChoice.format_select == "blastxml"
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121 #silent $prepare_json("BlastXml", $f.formatChoice.BlastXML, $index_track_final,
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122 extra_data_dict)
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123 #end if
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124 #if $f.formatChoice.format_select == "bigwig"
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125 #silent $prepare_json("BigWig", $f.formatChoice.BIGWIG, $index_track_final,
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126 $extra_data_dict)
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127 #end if
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128 #if $f.formatChoice.format_select == 'gff3'
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129 #silent $prepare_json("Gff3", $f.formatChoice.GFF3, $index_track_final,
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130 $extra_data_dict)
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131 #end if
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132 #if $f.formatChoice.format_select == "gtf"
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133 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8
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134 #silent $prepare_json("Gtf", $f.formatChoice.GTF, $index_track_final,
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135 $extra_data_dict)
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136 #end if
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137 #end for
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138 #end for
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139
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140 ## We combine the fasta file dataset name with his false path in a JSON object
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141 #set fasta_json = {"false_path": str($fasta_file), "name": str($fasta_file.name)}
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142 $data_parameter_dict.update({"fasta": $fasta_json})
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143
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144 ## Retrieve the user email
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145 #silent $data_parameter_dict.update({"user_email": str($__user_email__)})
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146
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147 #silent $data_parameter_dict.update({"tool_directory": str($__tool_directory__)})
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148
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149 #silent $data_parameter_dict.update({"extra_files_path": str($output.extra_files_path)})
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150
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151 #silent $data_parameter_dict.update({"debug_mode": str($advanced_options.debug_mode)})
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152
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153 with open(file_path, 'w') as f:
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154 json.dump($data_parameter_dict, f)
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155 </configfile>
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156 </configfiles>
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157
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158 <inputs>
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159 <param
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160 name="genome_name"
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161 type="text"
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162 size="30"
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163 value="unknown"
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164 label="JBrowse Hub Name"
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165 />
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166 <param
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167 format="fasta"
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168 name="fasta_file"
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169 type="data"
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170 label="Reference genome"
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171 />
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172 <repeat name="group" title="New group">
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173 <param type="text" name="group_name" label="Group name" value="Default group"/>
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174 <repeat name="format" title="New track">
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175 <conditional name="formatChoice">
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176 <param name="format_select" type="select" label="Format">
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177 <option value="bam" selected="true">BAM</option>
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178 <option value="bed">BED</option>
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179 <option value="blastxml">BlastXML</option>
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180 <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
181 <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
182 <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
183 </param>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
184
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
185 <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
186 <param
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
187 format="bam"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
188 name="BAM"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
189 type="data"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
190 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
191 />
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
192 <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
193 <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
194 <sanitizer>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
195 <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
196 <add value="#"/>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
197 </valid>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
198 </sanitizer>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
199 </param>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
200 </when>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
201 <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
202 <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
203 <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
204 <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
205 <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
206 <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
207 <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
208 <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
209 </param>
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_generic">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
211 <param
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
212 format="bed"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
213 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
214 type="data"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
215 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
216 />
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
217 </when>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
218 <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
219 <param
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
220 format="bed"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
221 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
222 type="data"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
223 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
224 />
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
225 </when>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
226 <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
227 <param
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
228 format="bed"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
229 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
230 type="data"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
231 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
232 />
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
233 </when>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
234 <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
235 <param
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
236 format="bed"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
237 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
238 type="data"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
239 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
240 />
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
241 </when>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
242 <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
243 <param
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
244 format="bed"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
245 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
246 type="data"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
247 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
248 />
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
249 </when>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
250 </conditional>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
251 <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
252 <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
253 <sanitizer>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
254 <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
255 <add value="#"/>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
256 </valid>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
257 </sanitizer>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
258 </param>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
259 </when>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
260 <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
261 <param
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
262 format="blastxml"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
263 name="BlastXML"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
264 type="data"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
265 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
266 />
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
267 <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
268 <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
269 <sanitizer>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
270 <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
271 <add value="#"/>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
272 </valid>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
273 </sanitizer>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
274 </param>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
parents:
diff changeset
275 </when>
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276 <when value="bigwig">
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277 <param
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278 format="bigwig"
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279 name="BIGWIG"
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280 type="data"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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diff changeset
281 label="BIGWIG File"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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282 />
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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283 <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
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284 <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
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285 <sanitizer>
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286 <valid initial="string.letters,string.digits">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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287 <add value="#"/>
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288 </valid>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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289 </sanitizer>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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290 </param>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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291 </when>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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292 <when value="gff3">
33
07cc5384dd61 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 74a020b6b0a2fa7ff5670d7f154de838dee51dfd
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293 <param
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294 format="gff3"
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295 name="GFF3"
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296 type="data"
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297 label="GFF3 File"
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298 />
25
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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299 <param name="longLabel" type="text" size="30" value="Gene Prediction" label="Track name" />
33
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300 <param name="track_color" type="color" label="Track color" value="#000000">
25
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301 <sanitizer>
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302 <valid initial="string.letters,string.digits">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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303 <add value="#"/>
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304 </valid>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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305 </sanitizer>
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306 </param>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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307 </when>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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308 <when value="gtf">
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309 <param
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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310 format="gtf"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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311 name="GTF"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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312 type="data"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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diff changeset
313 label="GTF File"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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314 />
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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315 <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
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316 <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
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317 <sanitizer>
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318 <valid initial="string.letters,string.digits">
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diff changeset
319 <add value="#"/>
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320 </valid>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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diff changeset
321 </sanitizer>
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322 </param>
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323 </when>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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324 </conditional>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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325 </repeat>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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326 </repeat>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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327 <conditional name="advanced_options">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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328 <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
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329 <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
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330 <option value="on">Display advanced options</option>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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331 </param>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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diff changeset
332 <!-- TODO: Avoid redundancy here -->
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333 <when value="on">
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334 <param name="debug_mode" type="select" label="Activate debug mode">
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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335 <option value="false" selected="true">No</option>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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336 <option value="true">Yes</option>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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337 <help>
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338 Use this option if you are a G-OnRamp developer
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339 </help>
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340 </param>
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341 </when>
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342 <when value="off">
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343 <param name="debug_mode" type="hidden"
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344 value="false">
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345 </param>
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346 </when>
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347 </conditional>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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348 </inputs>
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349
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350 <outputs>
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351 <data format="jbrowsehub" name="output" label="${tool.name}" />
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352 </outputs>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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353 <tests>
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354 <test>
32
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355 <param name="genome_name" value="Dbia3"/>
7b955a58d8f2 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 18da3c5b92673ba5030c24c981c6ca7ebe0bf097-dirty
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356 <param name="fasta_file" value="common/dbia3.fa"/>
7b955a58d8f2 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 18da3c5b92673ba5030c24c981c6ca7ebe0bf097-dirty
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357 <output name="output" file="only_genome/only_genome.html">
7b955a58d8f2 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 18da3c5b92673ba5030c24c981c6ca7ebe0bf097-dirty
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358 <!-- Use macro to check the whole common structure without repeated code -->
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359 <expand macro="verify_hub_structure_no_track" test="only_genome" />
7b955a58d8f2 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 18da3c5b92673ba5030c24c981c6ca7ebe0bf097-dirty
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360 </output>
25
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361 </test>
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362 </tests>
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363 <help>
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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364 This Galaxy tool will create a jbrowse hub which including binary datasets and json datasets that can be used for
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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365 JBrowse visualization.
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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366 </help>
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367 <citations>
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368 </citations>
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369 </tool>