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annotate hubArchiveCreator.py @ 10:acc233161f50 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
author rmarenco
date Thu, 21 Jul 2016 05:58:51 -0400
parents 4f9847539a28
children d05236b15f81
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1 #!/usr/bin/python
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2 # -*- coding: utf8 -*-
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4 """
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5 This Galaxy tool permits to prepare your files to be ready for
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6 Assembly Hub visualization.
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7 Program test arguments:
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8 hubArchiveCreator.py -g test-data/augustusDbia3.gff3 -f test-data/dbia3.fa -d . -u ./tools -o output.html
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9 """
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11 import argparse
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12 import collections
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13 import json
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14 import sys
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16 # Internal dependencies
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17 from Bam import Bam
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18 from BedSimpleRepeats import BedSimpleRepeats
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19 from Bed import Bed
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20 from BigWig import BigWig
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21 from util.Fasta import Fasta
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22 from Gff3 import Gff3
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23 from Gtf import Gtf
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24 from TrackHub import TrackHub
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27 # TODO: Verify each subprocessed dependency is accessible [gff3ToGenePred, genePredToBed, twoBitInfo, faToTwoBit, bedToBigBed, sort
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30 def main(argv):
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31 # Command Line parsing init
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32 parser = argparse.ArgumentParser(description='Create a foo.txt inside the given folder.')
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34 # Reference genome mandatory
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35 parser.add_argument('-f', '--fasta', help='Fasta file of the reference genome')
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37 # GFF3 Management
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38 parser.add_argument('--gff3', action='append', help='GFF3 format')
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40 # GTF Management
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41 parser.add_argument('--gtf', action='append', help='GTF format')
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43 # Bed4+12 (TrfBig)
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44 parser.add_argument('--bedSimpleRepeats', action='append', help='Bed4+12 format, using simpleRepeats.as')
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46 # Generic Bed (Blastx transformed to bed)
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47 parser.add_argument('--bed', action='append', help='Bed generic format')
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49 # BigWig Management
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50 parser.add_argument('--bigwig', action='append', help='BigWig format')
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52 # Bam Management
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53 parser.add_argument('--bam', action='append', help='Bam format')
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55 # TODO: Check if the running directory can have issues if we run the tool outside
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56 parser.add_argument('-d', '--directory',
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57 help='Running tool directory, where to find the templates. Default is running directory')
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58 parser.add_argument('-u', '--ucsc_tools_path',
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59 help='Directory where to find the executables needed to run this tool')
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60 parser.add_argument('-e', '--extra_files_path',
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61 help='Name, in galaxy, of the output folder. Where you would want to build the Track Hub Archive')
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62 parser.add_argument('-o', '--output', help='Name of the HTML summarizing the content of the Track Hub Archive')
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64 parser.add_argument('-j', '--data_json', help='Json containing the metadata of the inputs')
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65
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66 parser.add_argument('--user_email', help='Email of the user who launched the Hub Archive Creation')
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68 parser.add_argument('--genome_name', help='UCSC Genome Browser assembly ID')
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69
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70 ucsc_tools_path = ''
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72 toolDirectory = '.'
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73 extra_files_path = '.'
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75 # Get the args passed in parameter
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76 args = parser.parse_args()
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77
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78 array_inputs_reference_genome = json.loads(args.fasta)
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80 # TODO: Replace these with the object Fasta
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81 input_fasta_file = array_inputs_reference_genome["false_path"]
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82 input_fasta_file_name = sanitize_name_input(array_inputs_reference_genome["name"])
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83 genome_name = sanitize_name_input(args.genome_name)
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85 reference_genome = Fasta(array_inputs_reference_genome["false_path"],
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86 input_fasta_file_name, genome_name)
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88 user_email = args.user_email
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90 # TODO: Add array for each input because we can add multiple -b for example + filter the data associated
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92 array_inputs_gff3 = args.gff3
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93 array_inputs_bed_simple_repeats = args.bedSimpleRepeats
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94 array_inputs_bed_generic = args.bed
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95 array_inputs_gtf = args.gtf
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96 array_inputs_bam = args.bam
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97 array_inputs_bigwig = args.bigwig
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98
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99 outputFile = args.output
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100 json_inputs_data = args.data_json
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101
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102 json_inputs_data = args.data_json
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103
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104 inputs_data = json.loads(json_inputs_data)
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105 # We remove the spaces in ["name"] of inputs_data
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106 sanitize_name_inputs(inputs_data)
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107
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108 if args.directory:
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109 toolDirectory = args.directory
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110 if args.extra_files_path:
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111 extra_files_path = args.extra_files_path
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112
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113 # TODO: Check here all the binaries / tools we need. Exception if missing
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114
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115 # Create the Track Hub folder
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116 trackHub = TrackHub(reference_genome, user_email, outputFile, extra_files_path, toolDirectory)
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117
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118 all_datatype_dictionary = {}
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119
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120 datatype_parameters = (inputs_data, all_datatype_dictionary)
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121
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122 # Process Augustus
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123 if array_inputs_gff3:
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124 create_ordered_datatype_objects(Gff3, array_inputs_gff3, *datatype_parameters)
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125
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126 # Process Bed simple repeats
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127 if array_inputs_bed_simple_repeats:
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128 create_ordered_datatype_objects(BedSimpleRepeats, array_inputs_bed_simple_repeats, *datatype_parameters)
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129
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130 # Process Bed
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131 if array_inputs_bed_generic:
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132 create_ordered_datatype_objects(Bed, array_inputs_bed_generic, *datatype_parameters)
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133
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134 # Process GTF
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135 if array_inputs_gtf:
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136 create_ordered_datatype_objects(Gtf, array_inputs_gtf, *datatype_parameters)
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137
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138 # Process Bam
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139 if array_inputs_bam:
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140 create_ordered_datatype_objects(Bam, array_inputs_bam, *datatype_parameters)
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141
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142 # Process BigWig
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143 if array_inputs_bigwig:
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144 create_ordered_datatype_objects(BigWig, array_inputs_bigwig, *datatype_parameters)
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145
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146 # Create Ordered Dictionary to add the tracks in the tool form order
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147 all_datatype_ordered_dictionary = collections.OrderedDict(all_datatype_dictionary)
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148
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149 for index, datatypeObject in all_datatype_ordered_dictionary.iteritems():
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150 trackHub.addTrack(datatypeObject.track.trackDb)
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151
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152 # We process all the modifications to create the zip file
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153 #trackHub.createZip()
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154
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155 # We terminate le process and so create a HTML file summarizing all the files
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156 trackHub.terminate()
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157
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158 sys.exit(0)
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159
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160 def sanitize_name_input(string_to_sanitize):
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161 return string_to_sanitize \
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162 .replace("/", "_") \
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163 .replace(" ", "_")
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164
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165 def sanitize_name_inputs(inputs_data):
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166 """
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167 Sometimes output from Galaxy, or even just file name from user have spaces
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168 Also, it can contain '/' character and could break the use of os.path function
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169 :param inputs_data: dict[string, dict[string, string]]
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170 :return:
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171 """
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172 for key in inputs_data:
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173 inputs_data[key]["name"] = sanitize_name_input(inputs_data[key]["name"])
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174
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175
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176 def create_ordered_datatype_objects(ExtensionClass, array_inputs, inputs_data, all_datatype_dictionary):
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177 """
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178 Function which executes the creation all the necessary files / folders for a special Datatype, for TrackHub
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179 and update the dictionary of datatype
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180 :param ExtensionClass: T <= Datatype
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181 :param array_inputs: list[string]
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182 :param inputs_data:
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183 """
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184
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185 datatype_dictionary = {}
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186
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
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187 # TODO: Optimize this double loop
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
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188 for input_false_path in array_inputs:
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
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189 for key, data_value in inputs_data.items():
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
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190 if key == input_false_path:
10
acc233161f50 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
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191 extensionObject = ExtensionClass(input_false_path, data_value)
acc233161f50 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
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192
1
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
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193 datatype_dictionary.update({data_value["order_index"]: extensionObject})
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
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194 all_datatype_dictionary.update(datatype_dictionary)
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
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195
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
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196 if __name__ == "__main__":
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
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197 main(sys.argv)