Mercurial > repos > yating-l > jbrowsearchivecreator

annotate jbrowse_hub.xml @ 5:e762f4b9e4bd draft

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a3a8cdf5c9b100db56b2534e8718b5fc976435ff
author yating-l
date Fri, 07 Jul 2017 17:21:23 -0400
parents 7e471cdd9e71
children
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e762f4b9e4bd planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a3a8cdf5c9b100db56b2534e8718b5fc976435ff
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1 <tool id="jbrowse_hub" name="JBrowse Archive Creator" version="1.0.1">
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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5
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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 '$genome_name'
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21
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22 #set galaxy_url = str($GALAXY_URL)
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23 #set $jbrowse_url = galaxy_url.replace("8080", "80")
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24 --jbrowse_host '$jbrowse_url'
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26 ## json metadata recording from Remi's hub-archive-creator.xml
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27 #import json
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28 #set global data_parameter_dict = {}
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29
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30 ## Function to retrieve the data of the inputs
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31 #def prepare_json($input_to_prepare, $extra_data_dict={})
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32 #set false_path = str($input_to_prepare)
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33 #set name = $input_to_prepare.name
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34
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35 #set data_dict = {"name": $name}
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36 #silent data_dict.update($extra_data_dict)
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37
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38 #silent $data_parameter_dict.update({$false_path: $data_dict})
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39
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40 #end def
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41
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42 #for $g in $group
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43 #for $f in $g.format
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44 #set track_label = str($f.formatChoice.label)
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45 #set group_name = str($g.group_name)
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46 #set extra_data_dict = {"label" : $track_label, "category" : $group_name}
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47 #if $f.formatChoice.format_select == 'bed'
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48 #set track_color = str($f.formatChoice.track_color)
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49 #silent extra_data_dict.update({"color" : $track_color})
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50 #if $f.formatChoice.bedChoice.bed_select == 'bed_generic_option'
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51 --bed $f.formatChoice.bedChoice.BED_generic
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52 #silent $prepare_json($f.formatChoice.bedChoice.BED_generic, extra_data_dict)
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53 #elif $f.formatChoice.bedChoice.bed_select == 'bed_simple_repeats_option'
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54 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats
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55 #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, extra_data_dict)
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56 #elif $f.formatChoice.bedChoice.bed_select == 'bed_splice_junctions_option'
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57 --bedSpliceJunctions $f.formatChoice.bedChoice.BED_splice_junctions
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58 #silent $prepare_json($f.formatChoice.bedChoice.BED_splice_junctions, extra_data_dict)
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59 #elif $f.formatChoice.bedChoice.bed_select == 'bigpsl'
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60 --bigpsl $f.formatChoice.bedChoice.BigPsl
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61 #silent $prepare_json($f.formatChoice.bedChoice.BigPsl, extra_data_dict)
0
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62 #end if
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63 #end if
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64 #if $f.formatChoice.format_select == 'bam'
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65 --bam $f.formatChoice.BAM
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66 #silent $prepare_json($f.formatChoice.BAM, extra_data_dict)
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67 #end if
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68 #if $f.formatChoice.format_select == 'gff3'
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69 #set track_color = str($f.formatChoice.track_color)
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70 #silent extra_data_dict.update({"color" : $track_color})
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71 #if $f.formatChoice.gff3Choice.gff3_select == 'gff3_generic'
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72 --gff3 $f.formatChoice.gff3Choice.GFF3_generic
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73 #silent $prepare_json($f.formatChoice.gff3Choice.GFF3_generic, extra_data_dict)
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74 #elif $f.formatChoice.gff3Choice.gff3_select == 'gff3_transcript'
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75 --gff3_transcript $f.formatChoice.gff3Choice.GFF3_transcript
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76 #silent $prepare_json($f.formatChoice.gff3Choice.GFF3_transcript, extra_data_dict)
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77 #elif $f.formatChoice.gff3Choice.gff3_select == 'gff3_mrna'
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78 --gff3_mrna $f.formatChoice.gff3Choice.GFF3_mrna
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79 #silent $prepare_json($f.formatChoice.gff3Choice.GFF3_mrna, extra_data_dict)
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80 #end if
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81 #end if
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82 #if $f.formatChoice.format_select == 'blastxml'
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83 --blastxml $f.formatChoice.BlastXML
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84 #silent $prepare_json($f.formatChoice.BlastXML, extra_data_dict)
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85 #end if
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86 #if $f.formatChoice.format_select == 'gtf'
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87 --gtf $f.formatChoice.GTF
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88 #set track_color = str($f.formatChoice.track_color)
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89 #silent extra_data_dict.update({"color" : $track_color})
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90 #silent $prepare_json($f.formatChoice.GTF, extra_data_dict)
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91 #end if
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92 #if $f.formatChoice.format_select == 'bigwig'
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93 --bigwig $f.formatChoice.BIGWIG
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94 #set pos_color = str($f.formatChoice.pos_color)
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95 #set neg_color = str($f.formatChoice.neg_color)
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96 #silent $extra_data_dict.update({"style" : {"pos_color" : $pos_color, "neg_color" : $neg_color}})
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97 #silent $prepare_json($f.formatChoice.BIGWIG, extra_data_dict)
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98 #end if
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99 #end for
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100 #end for
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101
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102 #set all_data_json = json.dumps($data_parameter_dict)
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103 -j '$all_data_json'
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104 -e '$output.extra_files_path'
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105 -o '$output'
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106
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107 ]]></command>
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108
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109 <inputs>
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110 <param name="GALAXY_URL" type="baseurl" value="" />
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111 <param name="reference" type="data" format="fasta" label="Reference Genome" />
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112 <param name="genome_name" type="text" size="30" value="unknown" label="Genome name" />
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113 <repeat name="group" title="New group">
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114 <param type="text" name="group_name" label="Group name" value="Default group"/>
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115 <repeat name="format" title="New track">
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116 <conditional name="formatChoice">
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117 <param name="format_select" type="select" label="Format">
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118 <option value="bam" selected="true">BAM</option>
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119 <option value="bed">BED</option>
4
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120 <option value="blastxml">BlastXML</option>
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121 <option value="bigwig">BigWig</option>
0
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122 <option value="gff3">GFF3</option>
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123 <option value="gtf">GTF</option>
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124 </param>
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125
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126 <when value="bam">
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diff changeset
127 <param
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128 format="bam"
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129 name="BAM"
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130 type="data"
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131 label="BAM File"
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132 />
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133 <param name="label" type="text" size="30" value = "Sequence Alignment" label="Track name" />
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134 </when>
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135 <when value="bed">
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136 <conditional name="bedChoice">
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137 <param name="bed_select" type="select" label="Bed Choice">
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
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138 <option value="bed_generic_option">BED format</option>
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139 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
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140 <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option>
5
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141 <option value="bigpsl">Blat Alignment (bed12+12 / bigPsl.as)</option>
0
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142 </param>
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143 <when value="bed_generic_option">
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144 <param
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145 format="bed"
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146 name="BED_generic"
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147 type="data"
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148 label="Bed File"
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149 />
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150 </when>
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151 <when value="bed_simple_repeats_option">
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152 <param
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153 format="bed"
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154 name="BED_simple_repeats"
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155 type="data"
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156 label="Bed Simple Repeats (Bed4+12) File"
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157 />
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
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158 </when>
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159 <when value="bed_splice_junctions_option">
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160 <param
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161 format="bed"
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162 name="BED_splice_junctions"
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163 type="data"
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parents:
diff changeset
164 label="Bed Splice Junctions (Bed12+1) File"
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165 />
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166 </when>
5
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167 <when value="bigpsl">
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diff changeset
168 <param
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169 format="bed"
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170 name="BigPsl"
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diff changeset
171 type="data"
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parents: 4
diff changeset
172 label="Blat Alignments File"
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173 />
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174 </when>
0
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175 </conditional>
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176 <param name="label" type="text" size="30" value="BED file" label="Track name" />
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177 <param name="track_color" type="color" label="Track color" value="#daa520">
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178 <sanitizer>
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179 <valid initial="string.letters,string.digits">
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180 <add value="#"/>
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181 </valid>
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diff changeset
182 </sanitizer>
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yating-l
parents:
diff changeset
183 </param>
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
184 </when>
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
185 <when value="blastxml">
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yating-l
parents:
diff changeset
186 <param
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
187 format="blastxml"
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
188 name="BlastXML"
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yating-l
parents:
diff changeset
189 type="data"
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
190 label="Blast Alignments File"
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
191 />
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
192 <param name="label" type="text" size="30" value="Blast Alignment" label="Track name" />
5
e762f4b9e4bd planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a3a8cdf5c9b100db56b2534e8718b5fc976435ff
yating-l
parents: 4
diff changeset
193 <param name="track_color" type="color" label="Track color" value="#daa520">
e762f4b9e4bd planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a3a8cdf5c9b100db56b2534e8718b5fc976435ff
yating-l
parents: 4
diff changeset
194 <sanitizer>
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yating-l
parents: 4
diff changeset
195 <valid initial="string.letters,string.digits">
e762f4b9e4bd planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a3a8cdf5c9b100db56b2534e8718b5fc976435ff
yating-l
parents: 4
diff changeset
196 <add value="#"/>
e762f4b9e4bd planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a3a8cdf5c9b100db56b2534e8718b5fc976435ff
yating-l
parents: 4
diff changeset
197 </valid>
e762f4b9e4bd planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a3a8cdf5c9b100db56b2534e8718b5fc976435ff
yating-l
parents: 4
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198 </sanitizer>
e762f4b9e4bd planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a3a8cdf5c9b100db56b2534e8718b5fc976435ff
yating-l
parents: 4
diff changeset
199 </param>
4
7e471cdd9e71 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 8d93b27353190eb23490c9480e560d84cb60c973
yating-l
parents: 2
diff changeset
200 </when>
0
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yating-l
parents:
diff changeset
201 <when value="bigwig">
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yating-l
parents:
diff changeset
202 <param
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
203 format="bigwig"
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
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204 name="BIGWIG"
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
205 type="data"
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
206 label="BIGWIG File"
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
207 />
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
208 <param name="label" type="text" size="30" value="Sequence Coverage" label="Track name" />
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
209 <param name="pos_color" type="color" label="Positive Coverage Color" value="#FFA600">
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
210 <sanitizer>
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yating-l
parents:
diff changeset
211 <valid initial="string.letters,string.digits">
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
212 <add value="#"/>
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
213 </valid>
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
214 </sanitizer>
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
215 </param>
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
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216 <param name="neg_color" type="color" label="Negative Coverage Color" value="#005EFF">
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
217 <sanitizer>
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yating-l
parents:
diff changeset
218 <valid initial="string.letters,string.digits">
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
219 <add value="#"/>
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yating-l
parents:
diff changeset
220 </valid>
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
221 </sanitizer>
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
222 </param>
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
223 </when>
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
224 <when value="gff3">
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
225 <conditional name="gff3Choice">
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
226 <param name="gff3_select" type="select" label="gff3 type">
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
227 <option value="gff3_generic">GFF3 format</option>
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
228 <option value="gff3_transcript">GFF3 format output from gene prediction tools (e.g. Augustus), structure: gene->transcription->CDS</option>
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
229 <option value="gff3_mrna">GFF3 format output from gene prediction tools (e.g. SNAP), structure: gene->mRNA->CDS</option>
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
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diff changeset
230 </param>
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
231 <when value="gff3_generic">
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
232 <param
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
233 format="gff3"
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
234 name="GFF3_generic"
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
235 type="data"
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
236 label="GFF3 File"
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
237 />
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
238 </when>
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
239 <when value="gff3_transcript">
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
240 <param
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
241 format="gff3"
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
242 name="GFF3_transcript"
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
243 type="data"
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
244 label="GFF3 File from gene prediction"
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
245 />
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
246 </when>
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
247 <when value="gff3_mrna">
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
248 <param
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
249 format="gff3"
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
250 name="GFF3_mrna"
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
251 type="data"
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
252 label="GFF3 File from gene prediction"
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
253 />
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
254 </when>
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
255 </conditional>
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
256 <param name="label" type="text" size="30" value="Gene Prediction" label="Track name" />
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
257 <param name="track_color" type="color" label="Track color" value="#daa520">
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
258 <sanitizer>
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yating-l
parents:
diff changeset
259 <valid initial="string.letters,string.digits">
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
260 <add value="#"/>
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yating-l
parents:
diff changeset
261 </valid>
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
262 </sanitizer>
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
263 </param>
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
264 </when>
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
265 <when value="gtf">
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
266 <param
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
267 format="gtf"
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
268 name="GTF"
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
269 type="data"
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
270 label="GTF File"
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
271 />
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
272 <param name="label" type="text" size="30" value="Assembled Transcripts" label="Track name" />
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
273 <param name="track_color" type="color" label="Track color" value="#daa520">
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
274 <sanitizer>
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yating-l
parents:
diff changeset
275 <valid initial="string.letters,string.digits">
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
276 <add value="#"/>
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yating-l
parents:
diff changeset
277 </valid>
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
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278 </sanitizer>
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279 </param>
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280 </when>
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281 </conditional>
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282 </repeat>
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283 </repeat>
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284 </inputs>
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285
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286 <outputs>
4
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287 <data format="jbrowsehub" name="output" label="${tool.name}" />
0
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288 </outputs>
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289 <tests>
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290 <test>
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291 <param name="reference" value="dbia3/raw/dbia3.fa" />
2
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292 <param name="genome_name" value="unknown" />
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293 <param name="group_name" value="Default group"/>
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294 <param name="format_select" value="bam" />
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295 <param name="BAM" value="dbia3/raw/HISAT.bam" />
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296 <param name="label" value="" />
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297 <output name="output" file="JBrowse_Archive_Creator_html.html" />
0
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298 </test>
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299 </tests>
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300 <help>
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301 This Galaxy tool will create a tar file which including raw datasets and json datasets that can be used for
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302 JBrowse visualization.
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303 </help>
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304 <citations>
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305 </citations>
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306 </tool>