Mercurial > repos > yating-l > jbrowsearchivecreator

annotate jbrowseArchiveCreator.xml @ 7:5d5fdcb798da draft

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
author yating-l
date Fri, 20 Apr 2018 13:51:23 -0400
parents 237707a6b74d
children 56d9d10b4990
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1 <tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.1.1">
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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="1.13.1">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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38
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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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49
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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($nb_digits_max_track)
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78
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79 ## For each format, we have a few mandatory fields we store in a dict
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80 #set track_color = str($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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88
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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
7
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153 #silent $data_parameter_dict.update({"feature_tracks_type": str($advanced_options.feature_tracks_type)})
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154
6
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155 with open(file_path, 'w') as f:
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156 json.dump($data_parameter_dict, f)
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157 </configfile>
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158 </configfiles>
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159
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160 <inputs>
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161 <param
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162 name="genome_name"
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163 type="text"
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164 size="30"
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165 value="unknown"
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166 label="JBrowse Hub Name"
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167 />
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168 <param
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169 format="fasta"
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170 name="fasta_file"
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171 type="data"
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172 label="Reference genome"
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173 />
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174 <repeat name="group" title="New group">
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175 <param type="text" name="group_name" label="Group name" value="Default group"/>
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176 <repeat name="format" title="New track">
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177 <conditional name="formatChoice">
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178 <param name="format_select" type="select" label="Format">
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179 <option value="bam" selected="true">BAM</option>
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180 <option value="bed">BED</option>
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181 <option value="blastxml">BlastXML</option>
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182 <option value="bigwig">BigWig</option>
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183 <option value="gff3">GFF3</option>
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184 <option value="gtf">GTF</option>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
185 </param>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
186
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
187 <when value="bam">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
188 <param
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
189 format="bam"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
190 name="BAM"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
191 type="data"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
192 label="BAM File"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
193 />
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
194 <param name="longLabel" type="text" size="30" value = "Sequence Alignment" label="Track label" />
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
195 <param name="track_color" type="color" label="Track color" value="#000000">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
196 <sanitizer>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
197 <valid initial="string.letters,string.digits">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
198 <add value="#"/>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
199 </valid>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
200 </sanitizer>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
201 </param>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
202 </when>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
203 <when value="bed">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
204 <conditional name="bedChoice">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
205 <param name="bed_select" type="select" label="Bed Choice">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
206 <option value="bed_generic">BED format</option>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
207 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
208 <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
209 <option value="bed_blast_alignment_option">Blast alignments (bed12+12 / bigPsl.as)</option>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
210 <option value="bed_blat_alignment_option">BLAT alignments (bigPsl / bigPsl.as)</option>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
211 </param>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
212 <when value="bed_generic">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
213 <param
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
214 format="bed"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
215 name="BED_generic"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
216 type="data"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
217 label="Bed File"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
218 />
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
219 </when>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
220 <when value="bed_simple_repeats_option">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
221 <param
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
222 format="bed"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
223 name="BED_simple_repeats"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
224 type="data"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
225 label="Bed Simple Repeats (Bed4+12) File"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
226 />
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
227 </when>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
228 <when value="bed_splice_junctions_option">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
229 <param
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
230 format="bed"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
231 name="BED_splice_junctions"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
232 type="data"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
233 label="Bed Splice Junctions (Bed12+1) File"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
234 />
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
235 </when>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
236 <when value="bed_blast_alignment_option">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
237 <param
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
238 format="bed"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
239 name="BED_blast_alignment"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
240 type="data"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
241 label="Bed Blast Alignments (Bed12+12) File"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
242 />
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
243 </when>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
244 <when value="bed_blat_alignment_option">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
245 <param
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
246 format="bed"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
247 name="BED_blat_alignment"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
248 type="data"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
249 label="Bed BLAT Alignments (bigPsl) File"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
250 />
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
251 </when>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
252 </conditional>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
253 <param name="longLabel" type="text" size="30" label="Track label" />
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
254 <param name="track_color" type="color" label="Track color" value="#000000">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
255 <sanitizer>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
256 <valid initial="string.letters,string.digits">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
257 <add value="#"/>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
258 </valid>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
259 </sanitizer>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
260 </param>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
261 </when>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
262 <when value="blastxml">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
263 <param
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
264 format="blastxml"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
265 name="BlastXML"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
266 type="data"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
267 label="Blast Alignments File"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
268 />
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
269 <param name="longLabel" type="text" size="30" value="Blast Alignment" label="Track label" />
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
270 <param name="track_color" type="color" label="Track color" value="#000000">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
271 <sanitizer>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
272 <valid initial="string.letters,string.digits">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
273 <add value="#"/>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
274 </valid>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
275 </sanitizer>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
276 </param>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
277 </when>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
278 <when value="bigwig">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
279 <param
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
280 format="bigwig"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
281 name="BIGWIG"
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diff changeset
282 type="data"
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diff changeset
283 label="BIGWIG File"
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284 />
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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285 <param name="longLabel" type="text" size="30" value="Sequence Coverage" label="Track label" />
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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286 <param name="track_color" type="color" label="Track color" value="#000000">
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287 <sanitizer>
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288 <valid initial="string.letters,string.digits">
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289 <add value="#"/>
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290 </valid>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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291 </sanitizer>
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292 </param>
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293 </when>
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294 <when value="gff3">
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295 <param
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296 format="gff3"
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297 name="GFF3"
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298 type="data"
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299 label="GFF3 File"
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300 />
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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301 <param name="longLabel" type="text" size="30" value="Gene Prediction" label="Track name" />
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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302 <param name="track_color" type="color" label="Track color" value="#000000">
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303 <sanitizer>
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304 <valid initial="string.letters,string.digits">
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305 <add value="#"/>
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306 </valid>
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307 </sanitizer>
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308 </param>
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309 </when>
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310 <when value="gtf">
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311 <param
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312 format="gtf"
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313 name="GTF"
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314 type="data"
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315 label="GTF File"
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316 />
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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317 <param name="longLabel" type="text" size="30" value="Assembled Transcripts" label="Track name" />
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318 <param name="track_color" type="color" label="Track color" value="#000000">
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319 <sanitizer>
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320 <valid initial="string.letters,string.digits">
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321 <add value="#"/>
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322 </valid>
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323 </sanitizer>
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324 </param>
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325 </when>
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326 </conditional>
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327 </repeat>
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328 </repeat>
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329 <conditional name="advanced_options">
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330 <param name="advanced_options_selector" type="select" label="Advanced options">
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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331 <option value="off" selected="true">Hide advanced options</option>
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332 <option value="on">Display advanced options</option>
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333 </param>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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334 <when value="on">
7
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335 <param name="feature_tracks_type" type="select" label="Choose JBrowse feature tracks type">
5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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336 <option value="CanvasFeatures" selected="true">CanvasFeatures</option>
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337 <option value="HTMLFeatures">HTMLFeatures (Create a large number of range-indexed static JSON files. Don't choose this option if you want to upload/transfer output JBrowse hub to CyVerse Data Store!)
5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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338 </option>
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339 </param>
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340 <param name="debug_mode" type="select" label="Activate debug mode">
6
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341 <option value="false" selected="true">No</option>
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342 <option value="true">Yes</option>
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343 <help>
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344 Use this option if you are a G-OnRamp developer
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345 </help>
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346 </param>
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347 </when>
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348 <when value="off">
7
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349 <param name="debug_mode" type="hidden" value="false" />
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350 <param name="feature_tracks_type" type="hidden" value="CanvasFeatures" />
6
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351 </when>
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352 </conditional>
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353 </inputs>
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354
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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355 <outputs>
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356 <data format="jbrowsehub" name="output" label="${tool.name}" />
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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357 </outputs>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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358 <tests>
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359 <test>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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360 <param name="genome_name" value="Dbia3"/>
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361 <param name="fasta_file" value="common/dbia3.fa"/>
7
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362 <output name="output" file="only_genome/${tool.name}.html">
6
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363 <!-- Use macro to check the whole common structure without repeated code -->
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364 <expand macro="verify_hub_structure_no_track" test="only_genome" />
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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diff changeset
365 </output>
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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366 </test>
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367 </tests>
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368 <help>
7
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369 This Galaxy tool will prepare your files to be ready for visualization on JBrowse/Apollo.
6
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370 </help>
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371 <citations>
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372 </citations>
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373 </tool>