Mercurial > repos > yating-l > jbrowse_hub

annotate jbrowse_hub.xml @ 56:95b9d8acc235 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit a505d6c97db9d044761b5ce92be4a39cb84eda29-dirty
author yating-l
date Fri, 31 Mar 2017 12:38:58 -0400
parents 3e5b6f6a9abe
children ed17bb465bde
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1 <tool id="jbrowse_hub" name="JBrowse Hub Creator" version="1.0">
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2 <description>
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3 This Galaxy tool is used to prepare your files to be ready for displaying on JBrowse
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4 </description>
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6 <requirements>
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7 <requirement type="package" version="1.2">samtools</requirement>
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8 <requirement type="package" version="1.9">numpy</requirement>
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9 <requirement type="package" version="1.68">biopython</requirement>
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10 <requirement type="package" version="1.0">ucsc_tools_340</requirement>
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11 <requirement type="package" version="1.12.1">jbrowse_tools</requirement>
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12 </requirements>
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14 <stdio>
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15 </stdio>
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17 <command detect_errors="exit_code"><![CDATA[
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18 python $__tool_directory__/jbrowse_hub.py
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19 --fasta '$reference'
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20 --genome_name '$genome_name'
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22 ## json metadata recording from Remi's hub-archive-creator.xml
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23 #import json
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24 #set global data_parameter_dict = {}
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25
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26 ## Function to retrieve the data of the inputs
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27 #def prepare_json($input_to_prepare, $extra_data_dict={})
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28 #set false_path = str($input_to_prepare)
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29 #set name = $input_to_prepare.name
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31 #set data_dict = {"name": $name}
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32 #silent data_dict.update($extra_data_dict)
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34 #silent $data_parameter_dict.update({$false_path: $data_dict})
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36 #end def
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37
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38 #for $g in $group
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39 #for $f in $g.format
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40 #set track_label = str($f.formatChoice.label)
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41 #set group_name = str($g.group_name)
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42 #set extra_data_dict = {"label" : $track_label, "category" : $group_name}
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43 #if $f.formatChoice.format_select == 'bed'
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44 #set track_color = str($f.formatChoice.track_color)
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45 #if $f.formatChoice.bedChoice.bed_select == 'bed_generic_option'
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46 --bed $f.formatChoice.bedChoice.BED_generic
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47 #silent $prepare_json($f.formatChoice.bedChoice.BED_generic, extra_data_dict)
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48 #silent extra_data_dict.update({"color" : $track_color})
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49 #elif $f.formatChoice.bedChoice.bed_select == 'bed_simple_repeats_option'
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50 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats
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51 #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, extra_data_dict)
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52 #elif $f.formatChoice.bedChoice.bed_select == 'bed_splice_junctions_option'
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53 --bedSpliceJunctions $f.formatChoice.bedChoice.BED_splice_junctions
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54 #silent $prepare_json($f.formatChoice.bedChoice.BED_splice_junctions, extra_data_dict)
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55 #end if
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56 #end if
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57 #if $f.formatChoice.format_select == 'bam'
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58 --bam $f.formatChoice.BAM
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59 #silent $prepare_json($f.formatChoice.BAM, extra_data_dict)
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60 #end if
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61 #if $f.formatChoice.format_select == 'gff3'
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62 #set track_color = str($f.formatChoice.track_color)
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63 #silent extra_data_dict.update({"color" : $track_color})
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64 #if $f.formatChoice.gff3Choice.gff3_select == 'gff3_generic'
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65 --gff3 $f.formatChoice.gff3Choice.GFF3_generic
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66 #silent $prepare_json($f.formatChoice.gff3Choice.GFF3_generic, extra_data_dict)
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67 #esif $f.formatChoice.gff3Choice.gff3_select == 'gff3_transcript'
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68 --gff3_transcript $f.formatChoice.gff3Choice.GFF3_transcript
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69 #silent $prepare_json($f.formatChoice.gff3Choice.GFF3_transcript, extra_data_dict)
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70 #elif $f.formatChoice.gff3Choice.gff3_select == 'gff3_mrna'
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71 --gff3_mrna $f.formatChoice.gff3Choice.GFF3_mrna
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72 #silent $prepare_json($f.formatChoice.gff3Choice.GFF3_mrna, extra_data_dict)
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73 #end if
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74 #end if
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75 #if $f.formatChoice.format_select == 'blastxml'
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76 --blastxml $f.formatChoice.BlastXML
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77 #silent $prepare_json($f.formatChoice.BlastXML, extra_data_dict)
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78 #end if
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79 #if $f.formatChoice.format_select == 'gtf'
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80 --gtf $f.formatChoice.GTF
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81 #set track_color = str($f.formatChoice.track_color)
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82 #silent extra_data_dict.update({"color" : $track_color})
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83 #silent $prepare_json($f.formatChoice.GTF, extra_data_dict)
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84 #end if
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85 #if $f.formatChoice.format_select == 'bigwig'
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86 --bigwig $f.formatChoice.BIGWIG
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87 #set pos_color = str($f.formatChoice.pos_color)
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88 #set neg_color = str($f.formatChoice.neg_color)
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89 #silent $extra_data_dict.update({"style" : {"pos_color" : $pos_color, "neg_color" : $neg_color}})
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90 #silent $prepare_json($f.formatChoice.BIGWIG, extra_data_dict)
0
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91 #end if
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92 #end for
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93 #end for
31
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94
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95 #set all_data_json = json.dumps($data_parameter_dict)
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96 -j '$all_data_json'
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97 -e '$output.extra_files_path'
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98 -o '$output'
31
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99
0
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100 ]]></command>
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101
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102 <inputs>
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103 <param name="reference" type="data" format="fasta" label="Reference Genome" />
5
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104 <param name="genome_name" type="text" size="30" value="unknown" label="Genome name" />
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105 <repeat name="group" title="New group">
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106 <param type="text" name="group_name" label="Group name" value="Default group"/>
0
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107 <repeat name="format" title="New track">
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108 <conditional name="formatChoice">
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109 <param name="format_select" type="select" label="Format">
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110 <option value="bam" selected="true">BAM</option>
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111 <option value="bed">BED</option>
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112 <option value="blastxml">BLASTXML</option>
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113 <option value="bigwig">BIGWIG</option>
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114 <option value="gff3">GFF3</option>
0
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115 <option value="gtf">GTF</option>
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116 </param>
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117
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118 <when value="bam">
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119 <param
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120 format="bam"
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121 name="BAM"
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122 type="data"
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123 label="BAM File"
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124 />
37
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125 <param name="label" type="text" size="30" value = "Sequence Alignment" label="Track name" />
0
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126 </when>
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127 <when value="bed">
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128 <conditional name="bedChoice">
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129 <param name="bed_select" type="select" label="Bed Choice">
50
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130 <option value="bed_generic_option">BED format</option>
0
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131 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
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132 <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option>
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133 </param>
50
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134 <when value="bed_generic_option">
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135 <param
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136 format="bed"
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137 name="BED_generic"
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138 type="data"
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139 label="Bed File"
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140 />
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141 </when>
0
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142 <when value="bed_simple_repeats_option">
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143 <param
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144 format="bed"
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145 name="BED_simple_repeats"
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146 type="data"
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147 label="Bed Simple Repeats (Bed4+12) File"
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148 />
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149 </when>
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150 <when value="bed_splice_junctions_option">
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151 <param
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152 format="bed"
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153 name="BED_splice_junctions"
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154 type="data"
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155 label="Bed Splice Junctions (Bed12+1) File"
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156 />
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157 </when>
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158 </conditional>
37
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159 <param name="label" type="text" size="30" value="BED file" label="Track name" />
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160 <param name="track_color" type="color" label="Track color" value="#daa520">
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161 <sanitizer>
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162 <valid initial="string.letters,string.digits">
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163 <add value="#"/>
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164 </valid>
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165 </sanitizer>
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166 </param>
0
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167 </when>
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168 <when value="blastxml">
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169 <param
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170 format="blastxml"
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171 name="BlastXML"
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172 type="data"
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173 label="Blast Alignments File"
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174 />
37
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175 <param name="label" type="text" size="30" value="Blast Alignment" label="Track name" />
0
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176 </when>
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177 <when value="bigwig">
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178 <param
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179 format="bigwig"
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180 name="BIGWIG"
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181 type="data"
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182 label="BIGWIG File"
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183 />
37
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184 <param name="label" type="text" size="30" value="Sequence Coverage" label="Track name" />
39
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185 <param name="pos_color" type="color" label="Positive Coverage Color" value="#FFA600">
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186 <sanitizer>
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187 <valid initial="string.letters,string.digits">
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188 <add value="#"/>
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189 </valid>
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190 </sanitizer>
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191 </param>
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192 <param name="neg_color" type="color" label="Negative Coverage Color" value="#005EFF">
37
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193 <sanitizer>
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194 <valid initial="string.letters,string.digits">
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195 <add value="#"/>
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196 </valid>
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197 </sanitizer>
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198 </param>
0
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199 </when>
31
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200 <when value="gff3">
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201 <conditional name="gff3Choice">
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202 <param name="gff3_select" type="select" label="gff3 type">
50
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203 <option value="gff3_generic">GFF3 format</option>
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204 <option value="gff3_transcript">GFF3 format output from gene prediction tools (e.g. Augustus), structure: gene->transcription->CDS</option>
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205 <option value="gff3_mrna">GFF3 format output from gene prediction tools (e.g. SNAP), structure: gene->mRNA->CDS</option>
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206 </param>
50
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207 <when value="gff3_generic">
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208 <param
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209 format="gff3"
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210 name="GFF3_generic"
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211 type="data"
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212 label="GFF3 File"
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213 />
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214 </when>
31
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215 <when value="gff3_transcript">
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216 <param
41
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217 format="gff3"
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218 name="GFF3_transcript"
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219 type="data"
50
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220 label="GFF3 File from gene prediction"
31
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221 />
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222 </when>
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223 <when value="gff3_mrna">
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224 <param
41
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225 format="gff3"
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226 name="GFF3_mrna"
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227 type="data"
50
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228 label="GFF3 File from gene prediction"
31
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229 />
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230 </when>
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231 </conditional>
37
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232 <param name="label" type="text" size="30" value="Gene Prediction" label="Track name" />
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233 <param name="track_color" type="color" label="Track color" value="#daa520">
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234 <sanitizer>
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235 <valid initial="string.letters,string.digits">
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236 <add value="#"/>
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237 </valid>
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238 </sanitizer>
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239 </param>
0
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240 </when>
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241 <when value="gtf">
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242 <param
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243 format="gtf"
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244 name="GTF"
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245 type="data"
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246 label="GTF File"
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247 />
37
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248 <param name="label" type="text" size="30" value="Assembled Transcripts" label="Track name" />
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249 <param name="track_color" type="color" label="Track color" value="#daa520">
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250 <sanitizer>
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251 <valid initial="string.letters,string.digits">
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252 <add value="#"/>
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253 </valid>
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254 </sanitizer>
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255 </param>
0
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256 </when>
42
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257 </conditional>
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258 </repeat>
0
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259 </repeat>
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260 </inputs>
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261
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262 <outputs>
5
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263 <data format="html" name="output" label="${tool.name}" />
0
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264 </outputs>
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265 <tests>
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266 <test>
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267 <param name="reference" value="dbia3/raw/dbia3.fa" />
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268 <param name="output" value="hubtest" />
43
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269 <repeat name="group">
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270 <param name="group_name" value="Default group"/>
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271 <repeat name="format">
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272 <conditional name="formatChoice">
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273 <param name="format_select" value="gff3_transcript"/>
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274 <param name="GFF3_transcript" value="dbia3/raw/Augustus_on_data_3__GTF_GFF.gff3" />
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275 </conditional>
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276 </repeat>
0
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277 </repeat>
5
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278 <output name="output" file="hubtest" >
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279 </output>
0
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280 </test>
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281 </tests>
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282 <help>
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283 This Galaxy tool will create a tar file which including raw datasets and json datasets that can be used for
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284 JBrowse visualization.
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285 </help>
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286 <citations>
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287 </citations>
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288 </tool>